From owner-chemistry@ccl.net Wed Sep 14 07:56:00 2011 From: "Sergio Manzetti sergio.manzetti ~ gmail.com" To: CCL Subject: CCL:G: Question on Charge distribution Gaussian Message-Id: <-45443-110914075044-17486-SlKByiMc6leJoLdjapfFEQ__server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=20cf307d00d0dee25604ace55d75 Date: Wed, 14 Sep 2011 13:50:29 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti===gmail.com] --20cf307d00d0dee25604ace55d75 Content-Type: text/plain; charset=ISO-8859-1 Dear CCLrs. I am running calculations on a nitrenium molecule, with the positively charge Ar-NH+ using Gaussian. The charge is assigned on the Nitrogen atom in the input file ( in accord to literature), however in the results it becomes localized on neighbour atoms, at times as distance as a phenyl ring away. Is this the peculiar nature of the charged molecules, or am I running the wrong setting? The input is: #P B3LYP/6-311+G* # Opt # polar # Gfinput IOP(6/7=3) Pop=full Density Test # Units(Ang,Deg) Dinitropyrene 0 1 C 1.18010000 -0.27278000 -0.00014000 C 2.60899000 -0.24741000 -0.00009000 C 1.13615000 2.20214000 0.00041000 C 2.56505000 2.22752000 0.00080000..... Thanks Sergio --20cf307d00d0dee25604ace55d75 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCLrs. I am running calculations on a nitrenium molecule, with the pos= itively charge Ar-NH+ using Gaussian. The charge is assigned on the Nitroge= n atom in the input file ( in accord to literature), however in the results= it becomes localized on neighbour atoms, at times as distance as a phenyl = ring away. Is this the peculiar nature of the charged molecules, or am I ru= nning the wrong=A0 setting?

The input is:

#P B3LYP/6-311+G*
# Opt
#=A0 polar
# Gfi= nput IOP(6/7=3D3)=A0 Pop=3Dfull=A0 Density=A0 Test
# Units(Ang,Deg)
=
Dinitropyrene

0 1
=A0C=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0 1.18010000=A0=A0 -0.27278000=A0=A0 -0.00014000
=A0C=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.60899000=A0=A0 -0= .24741000=A0=A0 -0.00009000
=A0C=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0 1.13615000=A0=A0=A0 2.20214000=A0=A0=A0 0.00041000
=A0C=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.56505000=A0=A0=A0 2.2275= 2000=A0=A0=A0 0.00080000.....


Thanks

Sergio
--20cf307d00d0dee25604ace55d75-- From owner-chemistry@ccl.net Wed Sep 14 08:30:00 2011 From: "Krati joshi kjjulie.joshi|*|gmail.com" To: CCL Subject: CCL:G: Problem in ONIOM calculations Message-Id: <-45444-110914080300-4236-iNIp5ioffPjwO3lCiVzB6Q\a/server.ccl.net> X-Original-From: "Krati joshi" Date: Wed, 14 Sep 2011 08:02:57 -0400 Sent to CCL by: "Krati joshi" [kjjulie.joshi]|[gmail.com] Dear all, I have some problem in ONIOM calculations.i am doing three layer ONIOM calculation. The 3 layers of ONIOM consists of following atoms- 1.High-Si,4O,3H,Na, with 25 H2O around it-QM(DFT) 2.Middle layer-27H2O molecules-SEM(AM1) 3.Low-28H2O molecules-MM(UFF) I have selected all the layers properly by using gauss view.I am using Gaussian 09 for my calculations.After running for a long time say about 6-8 hours my jobs crashes with the following error message- "Error in internal coordinates. error termination via Lnk1e in ../../../l301.exe" I am not able to understand what is the problem with my jobs. If anybody knows anything about it then pls suggest me. it will be of great help to me.Thanks in advance. > From KRATI JOSHI catalysis Division NCL Pune, India email- kjjulie.joshi-at-gmail.com From owner-chemistry@ccl.net Wed Sep 14 09:06:00 2011 From: "psavita psavita*crlindia.com" To: CCL Subject: CCL: Ligand Protein docking Message-Id: <-45445-110913084942-16750-7Z8Unu67elR0eX/wrmpP6w*|*server.ccl.net> X-Original-From: "psavita" Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Tue, 13 Sep 2011 18:25:59 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: "psavita" [psavita**crlindia.com]
Hello Kaamini,

Following is the response from= my colleague Arundhati in the Life Sciences team.
Kindly get in touch w= ith her for more details.

Hi There,

I am not sure if you are = interested in AutoDock4 or =0DAutoDock4.1. I am not able to find AutoDock 4= .1 on official download =0Dpage of the community. 
=0DUsing AutoDo= ck4 the task of protein-ligand docking is little difficult =0Dfor beginners= . There are tutorials available for the same at http://autodock.scripp= s.edu/faqs-help/tutorial/.
=0DIt involves step wise execution of fo= llowing task.
1. Preparation of ligand and protein molecule as per AutoD= ock format.
2. Preparation of grid and docking parameters files.
3. E= xecuting autogrid as par the parameters to build energy maps for atoms with= in grid.
=0D4. Performing docking using the executable autodock.
5. = Analysis of =0Dresults that may involve building docked pose, extracting en= ergy and =0DRMSD information and getting h-bond information.

One has= to take =0Dcare of file format he/she is using before starting the process= . Also it=0D needs to tweek the grid and docking parameters for better resu= lts.

You can try the automated protein-ligand docking workflow provi= ded by CRL (www.cr= lindia.com).=0D This workflow keeps you free from the trouble of spendi= ng time in =0Dunderstanding the =0Dtool. This workflow performs all the ste= ps by itself and give you =0Dresults and detailed analysis of docked poses.= I will be happy to know =0Dmore about your requirement if you are interest= ed in commercial workflow=0D for protein-ligand docking.



Reg= ards,

Dr. Arundhati Saraph
arundhati-.-crlind= ia.com

Savita Pundlik
Computational Materials = Applied Research Group
Computational Research Laboratories Ltd.,
Taco House, Damle Path, Off Law College Road
= Pune - 411004, India.


-----owner-che= mistry+psavita=3D=3Dcrlindia.com-.-ccl.net wrote: -----

To: "Pundlik, Savita Sunil = " <psavita-.-crlindia.com>
From: "Kaamini Raithatha raithat= ha.kaamini..gmail.com" <owner-chemistry-.-ccl.net>
Sent by: owner-chemistry+psavita=3D=3Dcrlindia.com-.-ccl.net<= /a>
Date: 09/12/2011 07:37PM
Subject: CCL: Ligand Protein docking
=

Sent to CCL= by: "Kaamini  Raithatha" [raithatha.kaamini ~~ gmail.com]
Can Any1= tell me about the Ligand-Protein docking using Autodock4.1 its bit
dif= ficult to use..aor any other software



-=3D This is automatic= ally added to each message by the mailing script =3D-
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=0D
= From owner-chemistry@ccl.net Wed Sep 14 09:41:01 2011 From: "shabbir muhammad shabbir193rb(~)gmail.com" To: CCL Subject: CCL:G: ask for help about solvation in Gaussian09 Message-Id: <-45446-110913231131-16141-Y/CfhuqqNRrwa6girKrkog*o*server.ccl.net> X-Original-From: "shabbir muhammad" Date: Tue, 13 Sep 2011 23:11:28 -0400 Sent to CCL by: "shabbir muhammad" [shabbir193rb-*-gmail.com] Dear Haibin, Referee's comments are straight forward: Q1. For solvation calculations u shd clear either you have reoptimized the system or not.Bc geometry sometimes, slightly relaxes in solvation calculations. So just clarify this point. Q2.I guess, for Tio2-Dye model u have to consider the part of energy arise from TiO2 itself during solvation.please check following links. http://pubs.acs.org/doi/abs/10.1021/jz200191u http://pubs.acs.org/doi/abs/10.1021/jp911663k hope to help u out! Good luck! Dr. Shabbir > "Haibin Scopus lihb734_-_yahoo.com" wrote: > > Sent to CCL by: Haibin Scopus [lihb734.:.yahoo.com] > Dear CCLers, > I need your help about solvation model in Gaussian09. In our work, we stuied the absorption spectra of some dyes, also the spectra change upon the dyes adsorbed onto TiO2 nanoparticle by means ofCPCM implemented in Gaussian 09. As for spectra, the referee give us two clues to improve our manuscript, however, I can not follow his/her kind suggestion. So, could you help me out of these puzzle? > > Suggestion given by Referee: > Q1: For solvation calculations (CPCM), it appears that only single points have been done, but this is not entirely clear from the computational details. Please clarify. > > My understanding for Q1: The referee thinked that we did not give a clear description on computational details, so we should rewrite computational details to clarify this ambiguous description. > > Q2: I am not sure whether TiO2dye models have been used with CPCM solvation, and if so, how the authors deal with the fact that a spurious part of the solvation energy arises from their model, i.e. the solvation of (backside of) the Ti cluster. Please comment on this aspect. > My understanding for Q2: Sorry, I can not follow the referee, in particular "a spurious part of the solvation energy arises from their model, i.e. the solvation of (backside of) the Ti cluster." I really need your help to understand exactly the meaning of this senctence and whatIshould do to figure out this suggestion. > > > Thank you very much for your suggestion. Looking forward to your reply. > > your sincerely, > Haibin Li > > Institute of Functional Material Chemistry, Faculty of Chemistry > Northeast Normal University > changchun, Jilin, 130024 PR CHINA > E-mail: lihb734|-|nenu.edu.cn; lihb734|-|yahoo.com > http://www.nenu.edu.cn > > From owner-chemistry@ccl.net Wed Sep 14 10:16:00 2011 From: "Victor Nemykin victor_nemykin~!~yahoo.com" To: CCL Subject: CCL:G: Iron Fhthalocyanine opt + freq Message-Id: <-45447-110914010457-17896-2vasMp3RUHLwpnQKvALTKA---server.ccl.net> X-Original-From: Victor Nemykin Content-Type: multipart/mixed; boundary="0-2067429040-1315976687=:17436" Date: Tue, 13 Sep 2011 22:04:47 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Victor Nemykin [victor_nemykin||yahoo.com] --0-2067429040-1315976687=:17436 Content-Type: multipart/alternative; boundary="0-672713717-1315976687=:17436" --0-672713717-1315976687=:17436 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Diogo:=0AA couple of comments on your calculations. First, the coordin= ates you attached to the original message belong to C2 symmetry and non-pla= nar structure of MPcs. Although (if everything will go well) you will get D= 4h symmetries for NiPc and FePc after optimization, optimization will go fa= ster if you start from D4h symmetry and planar MPc geometry,=A0 assuming th= at you use Gaussian 03 or 09 program or any other program, which takes adva= ntage of molecular symmetry. In our experience with MPcs calculations, exch= ange-correlation functionals with a 20 - 25% of Hartree-Fock exchange usual= ly result in good agreement between theoretical and experimental geometries= (try, for instance, b3lyp or pbe1pbe). The choice of a basis set would pri= marily depends on the availability of computational resources. If you have = limited time on a single workstation, then LANL2DZ could be a good starting= point. If time is not a problem and you have an access to reasonable multiprocessor workstation or cluster, then you can try full-electron basi= s set (say Wachters basis set coded as 6-311+G in Gaussian) for central ato= m (Ni or Fe) and 6-31G(d) basis set for all other atoms. To simplify your l= ife, I have attached NiPc file (D4h symmetry) to this message. Also, you sh= ould be aware of the ground state of FePc. Experimentally, FePc system is a= triplet, so you have to use unrestricted DFT formalism (i.e. ub3lyp or upb= e1pbe). It is also wise to test an initial guess by using guess=3Dread opti= on because depending on the initial geometry you can end up with the differ= ent electronic configurations. The final question you have to answer is why= would you like to conduct those calculations. Indeed, semi-empirical, ab i= nitio, and DFT calculations on NiPc and FePc systems in terms of their elec= tronic structures are well-documented. Theoretical interpretation of UV-vis= and MCD spectra of these complexes have also been explored to some extent. There are also several publications on calculations of Mossbauer s= pectra parameters in FePc and analogue systems...=A0=0ABest wishes,=0AVicto= r=0A=0A=0A*****=0ADr. Victor N.Nemykin=0A=0Ae-mail: vnemykin|,|d.umn.edu=0A**= ***=0A=0A=0A________________________________=0AFrom: Diogo Volpati volpati.= :.fct.unesp.br =0ATo: "Nemykin, Victor " <= victor_nemykin|,|yahoo.com>=0ASent: Friday, September 9, 2011 9:01 AM=0ASubje= ct: CCL: Iron Fhthalocyanine opt + freq=0A=0A=0ASent to CCL by: "Diogo=A0 V= olpati" [volpati~!~fct.unesp.br]=0AHello everyone!=0A=0AI am trying to opti= mize the structure of metal phthalocyanines (Ni and Fe), =0Abut I always fo= und problems related to optimization steps or basis set used.=0AI am an exp= erimental researcher and I have no familiarity with these =0Atheoretical ca= lculations.=A0 I would be grateful if someone sends me the input =0Aconfigu= ration that works well to opt + freq calculations=A0 of Ni and Fe =0Aphthal= ocyanines .=A0 Below is a matrix with coordinates that I have used.=0AMany = thanks once again!!!=0A=0ADiogo Volpati...=0A=0AMetal=A0 =A0 =A0 =A0 =A0 = =A0 =A0 0.00000000=A0 =A0 0.00000000=A0 =A0 0.65530108=0AC=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 4.29700168=A0 -1.86013050=A0 =A0 0.15490288=0AC=A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0 4.64929293=A0 -0.50278709=A0 =A0 0.29140839= =0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 5.97289377=A0 -0.10643299=A0 =A0 0= .41459690=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 6.96329028=A0 -1.09099803= =A0 =A0 0.18919017=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 6.59865295=A0 -2= .43193139=A0 -0.13805642=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 5.24106831= =A0 -2.82883345=A0 -0.15266140=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 2.7= 6367101=A0 -1.99287676=A0 =A0 0.44194894=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 3.33890039=A0 =A0 0.32014732=A0 =A0 0.31640878=0AH=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 6.23362161=A0 =A0 0.90281237=A0 =A0 0.65608582=0AH=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 7.99764889=A0 -0.82620245=A0 =A0 0.2589656= 8=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 7.36123885=A0 -3.14653063=A0 -0.= 36764770=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 4.95600362=A0 -3.83535881= =A0 -0.37746984=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 0.53761938=A0 =A0 4= .60569820=A0 -0.28063809=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1.89985280= =A0 =A0 4.22844312=A0 -0.42873667=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 2= .89605517=A0 =A0 5.15821520=A0 -0.69336202=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 2.50835224=A0 =A0 6.51197568=A0 -0.80956047=0AC=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 1.14373920=A0 =A0 6.89582065=A0 -0.66106966=0AC=A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 0.14253573=A0 =A0 5.93308965=A0 -0.39420902=0A= C=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -0.32250124=A0 =A0 3.32813214=A0 -0.0012= 7854=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1.97593661=A0 =A0 2.69859773=A0= -0.25068617=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 3.91793407=A0 =A0 4.86= 123496=A0 -0.80499518=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 3.24822463=A0= =A0 7.25808852=A0 -1.01161350=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 0.87= 289906=A0 =A0 7.92686814=A0 -0.75296998=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= -0.88321039=A0 =A0 6.21693025=A0 -0.28371959=0AC=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 -4.64929293=A0 =A0 0.50278709=A0 =A0 0.29140839=0AC=A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 -4.29700168=A0 =A0 1.86013050=A0 =A0 0.15490288=0AC=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 -5.24106831=A0 =A0 2.82883345=A0 -0.15266140= =0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -6.59865295=A0 =A0 2.43193139=A0 -0.1= 3805642=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -6.96329028=A0 =A0 1.09099803= =A0 =A0 0.18919017=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -5.97289377=A0 =A0 0= .10643299=A0 =A0 0.41459690=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -3.33890039= =A0 -0.32014732=A0 =A0 0.31640878=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.7= 6367101=A0 =A0 1.99287676=A0 =A0 0.44194894=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 -4.95600362=A0 =A0 3.83535881=A0 -0.37746984=0AH=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 -7.36123885=A0 =A0 3.14653063=A0 -0.36764770=0AH=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 -7.99764889=A0 =A0 0.82620245=A0 =A0 0.25896568=0AH=A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0 -6.23362161=A0 -0.90281237=A0 =A0 0.65608582= =0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -1.89985280=A0 -4.22844312=A0 -0.428= 73667=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -0.53761938=A0 -4.60569820=A0 -= 0.28063809=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -0.14253573=A0 -5.93308965= =A0 -0.39420902=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -1.14373920=A0 -6.895= 82065=A0 -0.66106966=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.50835224=A0 -= 6.51197568=A0 -0.80956047=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.89605517= =A0 -5.15821520=A0 -0.69336202=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -1.975= 93661=A0 -2.69859773=A0 -0.25068617=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 0.32250124=A0 -3.32813214=A0 -0.00127854=0AH=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 0.88321039=A0 -6.21693025=A0 -0.28371959=0AH=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 -0.87289906=A0 -7.92686814=A0 -0.75296998=0AH=A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 -3.24822463=A0 -7.25808852=A0 -1.01161350=0AH=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 -3.91793407=A0 -4.86123496=A0 -0.80499518=0A= N=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 3.00223428=A0 =A0 1.72619181=A0 -0.38= 614310=0AN=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -1.90688145=A0 =A0 3.11519005=A0= =A0 0.15322528=0AN=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -3.00223428=A0 -1.7261= 9181=A0 -0.38614310=0AN=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1.90688145=A0 = -3.11519005=A0 =A0 0.15322528=0AN=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.486765= 61=A0 =A0 0.62348355=A0 =A0 1.06217133=0AN=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 2.48676561=A0 -0.62348355=A0 =A0 1.06217133=0AN=A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 -0.58288872=A0 -2.41834055=A0 =A0 0.05292827=0AN=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 0.58288872=A0 =A0 2.41834055=A0 =A0 0.05292827=0A=0A=0A= =0A-=3D This is automatically added to each message by the mailing script = =3D-=0ATo recover the email address of the author of the message, please ch= ange=0A= =0A=0A=0AE-mail to sub= scribers: CHEMISTRY|,|ccl.net or use:=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bi= n/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST|,|ccl= .net or use=0A=A0 =A0 =A0= =0A=0A=0A=A0 =A0 =A0 http://www.ccl.net/chemistry/su= b_unsub.shtml=0A=0A= =0A=0A=0AConferences: http://server.ccl.net/ch= emistry/announcements/conferences/=0A=0ASearch Messages: http://www.ccl.net= /chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from CCL with 5.= 7.1 error, check:=0A=A0 =A0 =A0=0A=0ARTFI: = http://www.ccl.net/chemistry/aboutccl/instructions/ --0-672713717-1315976687=:17436 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Diogo:
A couple of comments on your calculations. First, the coordi= nates you attached to the original message belong to C2 symmetry and non-pl= anar structure of MPcs. Although (if everything will go well) you will get = D4h symmetries for NiPc and FePc after optimization, optimization will go f= aster if you start from D4h symmetry and planar MPc geometry,  assumin= g that you use Gaussian 03 or 09 program or any other program, which takes = advantage of molecular symmetry. In our experience with MPcs calculations, = exchange-correlation functionals with a 20 - 25% of Hartree-Fock exchange u= sually result in good agreement between theoretical and experimental geomet= ries (try, for instance, b3lyp or pbe1pbe). The choice of a basis set would primarily depends on the availability of computational resources. If you h= ave limited time on a single workstation, then LANL2DZ could be a good star= ting point. If time is not a problem and you have an access to reasonable m= ultiprocessor workstation or cluster, then you can try full-electron basis = set (say Wachters basis set coded as 6-311+G in Gaussian) for central atom = (Ni or Fe) and 6-31G(d) basis set for all other atoms. To simplify your lif= e, I have attached NiPc file (D4h symmetry) to this message. Also, you shou= ld be aware of the ground state of FePc. Experimentally, FePc system is a t= riplet, so you have to use unrestricted DFT formalism (i.e. ub3lyp or upbe1= pbe). It is also wise to test an initial guess by using guess=3Dread option= because depending on the initial geometry you can end up with the differen= t electronic configurations. The final question you have to answer is why w= ould you like to conduct those calculations. Indeed, semi-empirical, ab initio, and DFT calculations on NiPc and FePc systems in terms of their= electronic structures are well-documented. Theoretical interpretation of U= V-vis and MCD spectra of these complexes have also been explored to some ex= tent. There are also several publications on calculations of Mossbauer spec= tra parameters in FePc and analogue systems... 
Best wishes,
Victor
=
*****
Dr. Victor N.Nemykin
e-mail: = vnemykin|,|d.umn.edu
*****
From:<= /b> Diogo Volpati volpati.:.fct.unesp.br <owner-chemistry|,|ccl.net>To: "Nemykin, Victor " <= ;victor_nemykin|,|yahoo.com>
Sent= : Friday, September 9, 2011 9:01 AM
Subject: CCL: Iron Fhthalocyanine opt + freq


Sent to CCL by: "Diogo  Volpati" [volpati~!~fct.unesp.br]<= br>Hello everyone!

I am trying to optimize the structure of metal ph= thalocyanines (Ni and Fe),
but I always found problems related to optim= ization steps or basis set used.
I am an experimental researcher and I h= ave no familiarity with these
theoretical calculations.  I would b= e grateful if someone sends me the input
configuration that works well = to opt + freq calculations  of Ni and Fe
phthalocyanines .  B= elow is a matrix with coordinates that I have used.
Many thanks once aga= in!!!

Diogo Volpati...

Metal              0.00000000    0.00000000    0.655= 30108
C                  4= .29700168  -1.86013050    0.15490288
C    &nb= sp;             4.64929293  -0.50278709=     0.29140839
C            &nb= sp;     5.97289377  -0.10643299    0.41459690
= C                  6.96329028=   -1.09099803    0.18919017
C       = ;           6.59865295  -2.43193139  -= 0.13805642
C                &nb= sp; 5.24106831  -2.82883345  -0.15266140
C    &nb= sp;             2.76367101  -1.99287676=     0.44194894
C                  3.33890039    0.32014732   = ; 0.31640878
H                &= nbsp; 6.23362161    0.90281237    0.65608582
H = ;                 7.99764889  = -0.82620245    0.25896568
H         = ;         7.36123885  -3.14653063  -0.36764= 770
H                  4.9= 5600362  -3.83535881  -0.37746984
C      &nb= sp;           0.53761938    4.60569820&n= bsp; -0.28063809
C              &nb= sp;   1.89985280    4.22844312  -0.42873667
C = ;                 2.89605517  =   5.15821520  -0.69336202
C                  2.50835224    6.511975= 68  -0.80956047
C             =     1.14373920    6.89582065  -0.66106966
C&= nbsp;                 0.14253573&nb= sp;   5.93308965  -0.39420902
C        &= nbsp;       -0.32250124    3.32813214  -0.0= 0127854
C                 = 1.97593661    2.69859773  -0.25068617
H    &= nbsp;             3.91793407    4.8= 6123496  -0.80499518
H            &= nbsp;     3.24822463    7.25808852  -1.01161350 H                  0.872899= 06    7.92686814  -0.75296998
H                -0.88321039    6.2169= 3025  -0.28371959
C            &nbs= p;   -4.64929293    0.50278709    0.29140839
= C                -4.29700168 =   1.86013050    0.15490288
C       =         -5.24106831    2.82883345  -0= .15266140
C                -6.= 59865295    2.43193139  -0.13805642
C    &nbs= p;           -6.96329028    1.09099803&= nbsp;   0.18919017
C            &nbs= p;   -5.97289377    0.10643299    0.41459690
= C                -3.33890039 = -0.32014732    0.31640878
C                -2.76367101    1.99287676&nb= sp;   0.44194894
H             =   -4.95600362    3.83535881  -0.37746984
H =               -7.36123885   = 3.14653063  -0.36764770
H          &nbs= p;     -7.99764889    0.82620245    0.258965= 68
H                -6.2336216= 1  -0.90281237    0.65608582
C      &nbs= p;         -1.89985280  -4.22844312  -0.42= 873667
C                -0.537= 61938  -4.60569820  -0.28063809
C       = ;         -0.14253573  -5.93308965  -0.394= 20902
C               =20 -1.14373920  -6.89582065  -0.66106966
C     = ;           -2.50835224  -6.51197568  = -0.80956047
C                = -2.89605517  -5.15821520  -0.69336202
C     =           -1.97593661  -2.69859773  = -0.25068617
C                &n= bsp; 0.32250124  -3.32813214  -0.00127854
H    &n= bsp;             0.88321039  -6.2169302= 5  -0.28371959
H              =   -0.87289906  -7.92686814  -0.75296998
H   = ;             -3.24822463  -7.25808852=   -1.01161350
H              &= nbsp; -3.91793407  -4.86123496  -0.80499518
N                  3.00223428  &= nbsp; 1.72619181  -0.38614310
N         =       -1.90688145    3.11519005    0.1= 5322528
N                -3.00= 223428  -1.72619181  -0.38614310
N      &nbs= p;           1.90688145  -3.11519005  &= nbsp; 0.15322528
N              &nbs= p; -2.48676561    0.62348355    1.06217133
N =                 2.48676561  = -0.62348355    1.06217133
N         =       -0.58288872  -2.41834055    0.052928= 27
N                  0.58= 288872    2.41834055    0.05292827



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NTEgMS4wDQogMzYgNTIgMS4wDQogMzcgMzggMS41IDUzIDEuMA0KIDM4IDU0 IDEuMA0KIDM5IDQwIDEuNSA1NSAxLjANCiA0MCA1NiAxLjANCiA0MQ0KIDQy DQogNDMNCiA0NA0KIDQ1DQogNDYNCiA0Nw0KIDQ4DQogNDkNCiA1MA0KIDUx DQogNTINCiA1Mw0KIDU0DQogNTUNCiA1Ng0KIDU3DQoNCk5pIDANCjYtMzEx K0cNCioqKioNCkMgTiBIIDANCjYtMzFHKGQpDQoqKioqDQoNCg0K --0-2067429040-1315976687=:17436-- From owner-chemistry@ccl.net Wed Sep 14 11:08:00 2011 From: "Sergio Manzetti sergio.manzetti^^^gmail.com" To: CCL Subject: CCL:G: Question on Charge distribution Gaussian Message-Id: <-45448-110914110720-11176-bJK43DAxQVgwk+Yv/FSDDw/./server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=20cf3071cd346dc53304ace81d96 Date: Wed, 14 Sep 2011 17:07:12 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti]~[gmail.com] --20cf3071cd346dc53304ace81d96 Content-Type: text/plain; charset=ISO-8859-1 Marcelo, sorry for the confusion, but I included the example of a non-charge variant which is completely running fine. I wanted basically to include the settings for the Ar-NH+ run. In order to show you the exact file for the charged variant here it is: %Mem=1900MB #P B3LYP/6-311+G* # Opt # polar # Gfinput IOP(6/7=3) Pop=full Density Test # Units(Ang,Deg) Input file generated by gabedit... 1 1 C 0 3.660609 0.062684 -0.055216 C 0 1.307244 -1.631340 0.059945 C 0 1.170487 -0.169562 0.031325 C 0 2.301480 0.653081 0.001556 C 0 -0.135160 0.412793 0.012876 C 0 -1.309095 -0.419808 -0.020969 C 0 -1.132231 -1.862188 -0.010636 C 0 0.094703 -2.419354 0.026699 H 0 -2.006512 -2.493442 -0.040192 C 0 2.154020 2.057523 -0.023195 C 0 -0.259838 1.834345 0.013191 C 0 0.909727 2.632740 -0.002590 H 0 0.805942 3.713275 -0.002350 C 0 -1.553070 2.418646 0.030481 C 0 -2.547190 0.229138 -0.016917 C 0 -2.672197 1.633154 0.033417 H 0 -3.663629 2.064808 0.059241 H 0 -1.645704 3.499523 0.039276 H 0 0.192896 -3.500656 0.043701 N 0 -3.821518 -0.509124 -0.050102 O 0 -4.778414 0.005116 0.520821 O 0 -3.876347 -1.573835 -0.659021 H 0 3.051896 2.662178 -0.053512 C 0 2.526362 -2.209914 0.152378 H 0 2.607107 -3.292696 0.192983 N 0 4.653782 0.816006 -0.340374 H 0 5.528681 0.288307 -0.362329 C 0 3.786190 -1.418235 0.267624 H 0 4.593806 -1.883995 0.548544 On Wed, Sep 14, 2011 at 2:58 PM, Marcelo Puiatti wrote: > Sergio there is a mistake in your setting. > > before the coordinates you should include the charge and multiplicity, > in your case it should be > > 1 1 > > instead of 0 1 > > > Marcelo > > > > On 14 September 2011 13:50, Sergio Manzetti sergio.manzetti ~ > gmail.com wrote: > > Dear CCLrs. I am running calculations on a nitrenium molecule, with the > > positively charge Ar-NH+ using Gaussian. The charge is assigned on the > > Nitrogen atom in the input file ( in accord to literature), however in > the > > results it becomes localized on neighbour atoms, at times as distance as > a > > phenyl ring away. Is this the peculiar nature of the charged molecules, > or > > am I running the wrong setting? > > > > The input is: > > > > #P B3LYP/6-311+G* > > # Opt > > # polar > > # Gfinput IOP(6/7=3) Pop=full Density Test > > # Units(Ang,Deg) > > > > Dinitropyrene > > > > 0 1 > > C 1.18010000 -0.27278000 -0.00014000 > > C 2.60899000 -0.24741000 -0.00009000 > > C 1.13615000 2.20214000 0.00041000 > > C 2.56505000 2.22752000 0.00080000..... > > > > > > Thanks > > > > Sergio > > > --20cf3071cd346dc53304ace81d96 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Marcelo, sorry for the confusion, but I included the example of a non-charg= e variant which is completely running fine. I wanted basically to include t= he settings for the Ar-NH+ run. In order to show you the exact file for the= charged variant here it is:

%Mem=3D1900MB
#P B3LYP/6-311+G*
# Opt
#=A0 polar
# Gfinput= IOP(6/7=3D3)=A0 Pop=3Dfull=A0 Density=A0 Test
# Units(Ang,Deg)

= Input file generated by gabedit...

1 =A0=A0=A0 1 =A0=A0=A0
C=A0= =A0=A0 0=A0=A0=A0 3.660609=A0=A0=A0 0.062684=A0=A0=A0 -0.055216
C=A0=A0=A0 0=A0=A0=A0 1.307244=A0=A0=A0 -1.631340=A0=A0=A0 0.059945
C=A0= =A0=A0 0=A0=A0=A0 1.170487=A0=A0=A0 -0.169562=A0=A0=A0 0.031325
C=A0=A0= =A0 0=A0=A0=A0 2.301480=A0=A0=A0 0.653081=A0=A0=A0 0.001556
C=A0=A0=A0 0= =A0=A0=A0 -0.135160=A0=A0=A0 0.412793=A0=A0=A0 0.012876
C=A0=A0=A0 0=A0= =A0=A0 -1.309095=A0=A0=A0 -0.419808=A0=A0=A0 -0.020969
C=A0=A0=A0 0=A0=A0=A0 -1.132231=A0=A0=A0 -1.862188=A0=A0=A0 -0.010636
C= =A0=A0=A0 0=A0=A0=A0 0.094703=A0=A0=A0 -2.419354=A0=A0=A0 0.026699
H=A0= =A0=A0 0=A0=A0=A0 -2.006512=A0=A0=A0 -2.493442=A0=A0=A0 -0.040192
C=A0= =A0=A0 0=A0=A0=A0 2.154020=A0=A0=A0 2.057523=A0=A0=A0 -0.023195
C=A0=A0= =A0 0=A0=A0=A0 -0.259838=A0=A0=A0 1.834345=A0=A0=A0 0.013191
C=A0=A0=A0 0=A0=A0=A0 0.909727=A0=A0=A0 2.632740=A0=A0=A0 -0.002590
H=A0= =A0=A0 0=A0=A0=A0 0.805942=A0=A0=A0 3.713275=A0=A0=A0 -0.002350
C=A0=A0= =A0 0=A0=A0=A0 -1.553070=A0=A0=A0 2.418646=A0=A0=A0 0.030481
C=A0=A0=A0 = 0=A0=A0=A0 -2.547190=A0=A0=A0 0.229138=A0=A0=A0 -0.016917
C=A0=A0=A0 0= =A0=A0=A0 -2.672197=A0=A0=A0 1.633154=A0=A0=A0 0.033417
H=A0=A0=A0 0=A0=A0=A0 -3.663629=A0=A0=A0 2.064808=A0=A0=A0 0.059241
H=A0= =A0=A0 0=A0=A0=A0 -1.645704=A0=A0=A0 3.499523=A0=A0=A0 0.039276
H=A0=A0= =A0 0=A0=A0=A0 0.192896=A0=A0=A0 -3.500656=A0=A0=A0 0.043701
N=A0=A0=A0 = 0=A0=A0=A0 -3.821518=A0=A0=A0 -0.509124=A0=A0=A0 -0.050102
O=A0=A0=A0 0= =A0=A0=A0 -4.778414=A0=A0=A0 0.005116=A0=A0=A0 0.520821
O=A0=A0=A0 0=A0=A0=A0 -3.876347=A0=A0=A0 -1.573835=A0=A0=A0 -0.659021
H= =A0=A0=A0 0=A0=A0=A0 3.051896=A0=A0=A0 2.662178=A0=A0=A0 -0.053512
C=A0= =A0=A0 0=A0=A0=A0 2.526362=A0=A0=A0 -2.209914=A0=A0=A0 0.152378
H=A0=A0= =A0 0=A0=A0=A0 2.607107=A0=A0=A0 -3.292696=A0=A0=A0 0.192983
N=A0=A0=A0 = 0=A0=A0=A0 4.653782=A0=A0=A0 0.816006=A0=A0=A0 -0.340374
H=A0=A0=A0 0=A0=A0=A0 5.528681=A0=A0=A0 0.288307=A0=A0=A0 -0.362329
C=A0= =A0=A0 0=A0=A0=A0 3.786190=A0=A0=A0 -1.418235=A0=A0=A0 0.267624
H=A0=A0= =A0 0=A0=A0=A0 4.593806=A0=A0=A0 -1.883995=A0=A0=A0 0.548544


On Wed, Sep 14, 2011 at 2:58 PM, Marcelo Puiatt= i <marcel= o.puiatti_-_gmail.com> wrote:
Sergio there is a mistake in your setting.<= br>
before the coordinates you should include the charge and multiplicity,
in your case it should be

1 1

instead of 0 1


Marcelo



On 14 September 2011 13:50, Sergio Manzetti sergio.manzetti ~
gmail.com <owner-chemistry_-_ccl.net> wrote:
> Dear CCLrs. I am running calculations on a nitrenium molecule, with th= e
> positively charge Ar-NH+ using Gaussian. The charge is assigned on the=
> Nitrogen atom in the input file ( in accord to literature), however in= the
> results it becomes localized on neighbour atoms, at times as distance = as a
> phenyl ring away. Is this the peculiar nature of the charged molecules= , or
> am I running the wrong=A0 setting?
>
> The input is:
>
> #P B3LYP/6-311+G*
> # Opt
> #=A0 polar
> # Gfinput IOP(6/7=3D3)=A0 Pop=3Dfull=A0 Density=A0 Test
> # Units(Ang,Deg)
>
> Dinitropyrene
>
> 0 1
> =A0C=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.18010000=A0= =A0 -0.27278000=A0=A0 -0.00014000
> =A0C=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.60899000=A0= =A0 -0.24741000=A0=A0 -0.00009000
> =A0C=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.13615000=A0= =A0=A0 2.20214000=A0=A0=A0 0.00041000
> =A0C=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.56505000=A0= =A0=A0 2.22752000=A0=A0=A0 0.00080000.....
>
>
> Thanks
>
> Sergio
>



--20cf3071cd346dc53304ace81d96-- From owner-chemistry@ccl.net Wed Sep 14 11:55:01 2011 From: "Jason D Acchioli jdacchio]_[gmail.com" To: CCL Subject: CCL: Pure DFT functionals and ORCA Message-Id: <-45449-110914115342-13799-EyKEL0Uy92B9fDZaKfwoew]^[server.ccl.net> X-Original-From: "Jason D'Acchioli" Content-Type: multipart/alternative; boundary="Apple-Mail=_FCE411C8-5F0A-458F-8394-75CD28AAE3EC" Date: Wed, 14 Sep 2011 10:53:22 -0500 Mime-Version: 1.0 (Apple Message framework v1244.3) Sent to CCL by: "Jason D'Acchioli" [jdacchio()gmail.com] --Apple-Mail=_FCE411C8-5F0A-458F-8394-75CD28AAE3EC Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Hi all, I posted the following question on the ORCA forum, but haven't = heard anything (yet), so I'll throw it out here. The output file is = below the message.=20 Jason Hi all,=20 I'm trying to run a single point / TDDFT calc on a metal-organic system. = However, the SCF does not converge after 125 cycles. I've tried the PBE, = RPBE, and revPBE XC functionals, and the same thing happens-I get an = oscillating SCF cycle. The same thing happens when I try the hybrid = B3LYP/G functional and the RIJCOSX approximation. However, if I do a = B3LYP/G without the RIJCOSX, convergence is fine.=20 What am I doing wrong? If it is a problem with RI, can I still use any = of PW91 or PBE XC functionals (which, I believe, require auxiliary basis = sets?)? The input is attached as a zip file.=20 Thanks,=20 Jason !RKS PW91 def2-SVP def2-SVP/J TightSCF PrintMOs Grid5 %output Print[P_OrbPopMO_M] 1 Print[P_FragPopMO_M] 1 end %rel method ZORA #or IORA modelpot 1,1,1,1 modeldens rhoZORA velit 137.0359895 #speed of light used end %tddft nroots 15 maxdim 64 end ! PAL4 * xyz 0 1 H(1) -4.56675 -2.48229 -0.00028 C(1) -4.57359 -1.39699 -0.00028 C(1) -5.77738 -0.69952 -0.00035 H(1) -6.71624 -1.24540 -0.00040 C(1) -5.77739 0.69938 -0.00034 H(1) -6.71628 1.24523 -0.00039 C(1) -4.57363 1.39688 -0.00028 H(1) -4.56682 2.48218 -0.00029 C(1) -3.34414 0.71339 -0.00022 C(1) -2.12293 1.43662 -0.00018 C(1) -3.34412 -0.71346 -0.00021 C(1) -2.12289 -1.43666 -0.00014 C(1) -1.05872 2.02393 -0.00013 C(1) 0.16183 2.74774 -0.00010 C(1) -1.05866 -2.02394 -0.00006 C(1) 0.16190 -2.74772 -0.00004 C(1) 0.16567 4.15310 -0.00038 C(1) 0.16578 -4.15308 -0.00027 H(1) -0.78318 -4.67691 -0.00043 C(1) 1.37444 -4.83715 -0.00028 H(1) -0.78331 4.67691 -0.00066 C(1) 1.37431 4.83720 -0.00031 C(1) 2.56419 4.10860 0.00002 H(1) 1.38849 5.92301 -0.00055 C(1) 2.49611 2.71947 0.00026 H(1) 3.53196 4.59786 0.00008 N(1) 1.33136 2.05360 0.00019 H(1) 3.38890 2.10605 0.00051 C(1) 2.56430 -4.10851 -0.00008 H(1) 1.38865 -5.92296 -0.00045 C(1) 2.49618 -2.71939 0.00013 H(1) 3.53208 -4.59774 -0.00008 N(1) 1.33141 -2.05354 0.00016 H(1) 3.38895 -2.10595 0.00028 Pd(2) 1.33817 -0.00000 0.00023 newgto "def2-TZVP" = "def2-TZVP/J" end Cl(3) 1.43325 -0.00001 -2.35531 Cl(3) 1.43091 0.00002 2.35584 * ******************************************* Jason D'Acchioli Assistant Professor of Chemistry University of Wisconsin-Stevens Point 2001 Fourth Avenue Stevens Point, WI 54481 http://chemdac.uwsp.edu --Apple-Mail=_FCE411C8-5F0A-458F-8394-75CD28AAE3EC Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Hi = all,

I posted the following question = on the ORCA forum, but haven't heard anything (yet), so I'll throw it = out here. The output file is below the = message. 

Jason

Hi = all,I'm trying to = run a single point / TDDFT calc on a metal-organic system. However, the = SCF does not converge after 125 cycles. I've tried the PBE, RPBE, and = revPBE XC functionals, and the same thing happens-I get an oscillating = SCF cycle. The same thing happens when I try the hybrid B3LYP/G = functional and the RIJCOSX approximation. However, if I do a B3LYP/G = without the RIJCOSX, convergence is fine.What am I = doing wrong? If it is a problem with RI, can I still use any of PW91 or = PBE XC functionals (which, I believe, require auxiliary basis sets?)? = The input is attached as a zip file. 

Jason

!RKS PW91 def2-SVP = def2-SVP/J TightSCF PrintMOs Grid5
%output
Print[P_OrbPopMO_M] 1
Print[P_FragPopMO_M] 1
end
%rel method ZORA #or = IORA
modelpot 1,1,1,1
modeldens rhoZORA
velit 137.0359895 #speed of light = used
end
%tddft nroots 15
maxdim 64
end
! PAL4
* xyz 0 1
H(1)         -4.56675   =     -2.48229       = -0.00028
C(1)         -4.57359       = -1.39699       -0.00028
C(1)         -5.77738   =     -0.69952       = -0.00035
H(1)         -6.71624       = -1.24540       -0.00040
C(1)         -5.77739   =      0.69938       = -0.00034
H(1)         -6.71628       =  1.24523       = -0.00039
C(1)         -4.57363       =  1.39688       = -0.00028
H(1)         -4.56682       =  2.48218       = -0.00029
C(1)         -3.34414       =  0.71339       = -0.00022
C(1)         -2.12293       =  1.43662       = -0.00018
C(1)         -3.34412       = -0.71346       -0.00021
C(1)         -2.12289   =     -1.43666       = -0.00014
C(1)         -1.05872       =  2.02393       = -0.00013
C(1)          0.16183     =    2.74774       = -0.00010
C(1)         -1.05866       = -2.02394       -0.00006
C(1)          0.16190 =       -2.74772       = -0.00004
C(1)          0.16567     =    4.15310       = -0.00038
C(1)          0.16578     =   -4.15308       = -0.00027
H(1)         -0.78318       = -4.67691       -0.00043
C(1)          1.37444 =       -4.83715       = -0.00028
H(1)         -0.78331       =  4.67691       = -0.00066
C(1)         1.37431       =  4.83720       = -0.00031
C(1)          2.56419     =    4.10860       =  0.00002
H(1)          1.38849     =    5.92301       = -0.00055
C(1)          2.49611     =    2.71947       =  0.00026
H(1)          3.53196     =    4.59786       =  0.00008
N(1)          1.33136     =    2.05360       =  0.00019
H(1)          3.38890     =    2.10605       =  0.00051
C(1)          2.56430     =   -4.10851       = -0.00008
H(1)          1.38865     =   -5.92296       = -0.00045
C(1)          2.49618     =   -2.71939       =  0.00013
H(1)          3.53208     =   -4.59774       = -0.00008
N(1)          1.33141     =   -2.05354       =  0.00016
H(1)          3.38895     =   -2.10595       =  0.00028
Pd(2)         1.33817       = -0.00000        0.00023 newgto "def2-TZVP" = "def2-TZVP/J" end
Cl(3)         1.43325       = -0.00001       -2.35531
Cl(3)         1.43091   =      0.00002       =  2.35584
*


*******************************************
Jason = D'Acchioli
Assistant Professor of Chemistry
University of = Wisconsin-Stevens Point
2001 Fourth Avenue
Stevens Point, WI = 54481
http://chemdac.uwsp.edu


= --Apple-Mail=_FCE411C8-5F0A-458F-8394-75CD28AAE3EC-- From owner-chemistry@ccl.net Wed Sep 14 12:30:00 2011 From: "Olasunkanmi Lukman Olawale walecomuk#yahoo.co.uk" To: CCL Subject: CCL: MOPAC and standard free energy of formation Message-Id: <-45450-110914115018-11494-6dtiy4uxCAkbua1JnR+NRg * server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="1815230994-456340306-1316015408=:51665" Date: Wed, 14 Sep 2011 16:50:08 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk#yahoo.co.uk] --1815230994-456340306-1316015408=:51665 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello everyone,=0AI need to solve this quickly please. How do I get the sta= ndard free energy of formation from MOPAC thermo calculation results.=0AFor= a single molecule like CH3Cl: I will get the following results:=0A=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 CALCULATED THERMODYNAMI= C PROPERTIES=0A=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 *=0A=A0=A0 = TEMP. (K)=A0=A0 PARTITION FUNCTION=A0=A0=A0=A0=A0=A0 H.O.F.=A0=A0=A0 =A0=A0= =A0=A0ENTHALPY=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0HEAT CAPACITY=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0ENTROPY=0A=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0KCAL/MOL=A0=A0 =A0=A0=A0=A0CAL/MOLE=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0CAL/K/MOL=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0CAL/K/MOL=0A=A0298.00=A0 VIB.=A0=A0=A0=A0 0.1049D+01=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0126.4045=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A01.9784=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.5185=0A= =A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0 ROT.=A0=A0=A0=A0 0.1745D+04=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0888.2813=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A02.9808=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 17.81= 45=0A=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0 INT.=A0=A0=A0=A0 0.1830D+04=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A01014.6= 858=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 4.9592=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A018.333= 0=0A=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0 TRA.=A0=A0=A0=A0 0.3468D+27=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A01480.4688=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 4.9680=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 37.6786=0A=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 TOT.=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0-15.060=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A02495.1547=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0 9.9272=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A056.0116=0ABut how will i get DG from it.=0AMore so, for molecules= =A0of polychlorinated polyaromatic/polyheteroaromatic compounds, I think on= e can resolve to using isodesmic reactions, however, I got the following li= ne from MOPAC manual:=0AStandard Gibbs free-energy of formation (DG) can be= calculated by taking the difference from that for the isomer or that at di= fferent temperature:=0ADG=3D (DH - TDS) (for the state under consideration)= - (DH - TDS) (for reference state).=0ATo me, this does not seem applicable= to getting DG of formation for an=A0isolated molecule.=0AI really need you= suggestions and contributions on this issue. Thank you all.=A0=0A=0AOlasun= kanmi Lukman Olawale=0ACurrent Address:=0ADepartment of Chemistry,=0AObafem= i Awolowo University,=0AIle-Ife, Osun State.=0ANigeria.=0A=0A+234-0-80-5240= 1564 Or +234-0-80-67161091=0A --1815230994-456340306-1316015408=:51665 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello everyone,
I need to solve this= quickly please. How do I get the standard free energy of formation from MO= PAC thermo calculation results.
For a single molecul= e like CH3Cl: I will get the following results:
   &n= bsp;            = ;    CALCULATED THERMODYNAMIC PROPERTIES
  &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp; *
   TEMP. (K)   PARTITION FUNCTION  = ;     H.= O.F.      =   ENTHALPY       &= nbsp;     =  HEAT CAPACITY          &nb= sp;  ENTROPY
    &nbs= p;            &= nbsp;           &nbs= p;     &nb= sp;     &n= bsp;     <= SPAN style=3D"RIGHT: auto" class=3Dtab>                &nbs= p;   KCAL/MOL       CAL/MOLE&= nbsp;     =       = ;    CAL/K/MOL  &nb= sp;     &n= bsp;     <= /SPAN>CAL/K/MOL
 298.00  V= IB.     0.1049D+01      &= nbsp;           &nbs= p;                &n= bsp;     &= nbsp;     = 126.4045   =       = ;                1.9784 &n= bsp;     &= nbsp;                 0.5= 185
            ROT.&n= bsp;    0.1745D+04       =                                             = 888.2813         &= nbsp;     =       = ;2.9808           &nbs= p;     &nb= sp;       &n= bsp; 17.8145
          &nbs= p;  INT.     0.1830D+04    &nb= sp;            =                       &nb= sp;     &n= bsp;    = 1014.6858   = ;              &nb= sp;   4.9592    <= SPAN style=3D"RIGHT: auto" class=3Dtab>                &nbs= p;   18.3330
 &nb= sp;          TRA.   =   0.3468D+27         &nbs= p;                 &= nbsp;          &nb= sp;     &n= bsp;     <= /SPAN>1480.4688  = ;               &= nbsp;     =              37= .6786
           =   TOT.          &nbs= p;            &= nbsp;                     &nbs= p;  -15.060  =       = ;      2495.1547&nb= sp;                    9.9272  &n= bsp;     <= SPAN style=3D"RIGHT: auto" class=3Dtab>                56.0116
But how will i get D= G from it.
More so, for molecul= es of polychlorinated polyaromatic/polyh= eteroaromatic compounds, I think one can resolve to using isodesmic reactio= ns, however, I got the following line from MOPAC manual:
Standard Gibbs free-= energy of formation (DG) can be calculated by taking the difference from th= at for the isomer or that at different temperature:
DG=3D (DH - TDS) (fo= r the state under consideration) - (DH - TDS) (for reference state).=
To me, this does not= seem applicable to getting DG of formation for an isolated molecule.<= /SPAN>
I really need you su= ggestions and contributions on this issue. Thank you all.
 
 
Olasunkanmi Luk= man Olawale
Current = Address:
D= epartment of Chemistry,
Obafemi Awol= owo University,
= Ile-Ife, Osun State.=
Nigeria.
+234-0-80-52401564 Or +234-0-80-6= 7161091
--1815230994-456340306-1316015408=:51665-- From owner-chemistry@ccl.net Wed Sep 14 13:04:00 2011 From: "=?ISO-8859-1?Q?Jo=E3o_Henriques?= jmhenriques=fc.ul.pt" To: CCL Subject: CCL:G: Question on Charge distribution Gaussian Message-Id: <-45451-110914112802-28971-leDWIcBBsCxz1Ipre6cvIQ{:}server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jo=E3o_Henriques?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 14 Sep 2011 16:27:53 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jo=E3o_Henriques?= [jmhenriques ~ fc.ul.pt] Dear Sergio, Have you tried doing the calculations with an implicit solvent model? A part from that, many other things may be causing the reported undesired effect (theory level, basis set, geometry, etc). Yet, your settings seem adequate to your system... I did not take a look at your system, so it's always a good idea to recheck the charge and spin multiplicity. Sorry I cannot help you much more than this. Surely, more experienced users will come up with an answer to your problem. Best regards, On Wed, Sep 14, 2011 at 12:50 PM, Sergio Manzetti sergio.manzetti ~ gmail.com wrote: > Dear CCLrs. I am running calculations on a nitrenium molecule, with the > positively charge Ar-NH+ using Gaussian. The charge is assigned on the > Nitrogen atom in the input file ( in accord to literature), however in the > results it becomes localized on neighbour atoms, at times as distance as a > phenyl ring away. Is this the peculiar nature of the charged molecules, or > am I running the wrong  setting? > > The input is: > > #P B3LYP/6-311+G* > # Opt > #  polar > # Gfinput IOP(6/7=3)  Pop=full  Density  Test > # Units(Ang,Deg) > > Dinitropyrene > > 0 1 >  C                  1.18010000   -0.27278000   -0.00014000 >  C                  2.60899000   -0.24741000   -0.00009000 >  C                  1.13615000    2.20214000    0.00041000 >  C                  2.56505000    2.22752000    0.00080000..... > > > Thanks > > Sergio > -- Joćo Henriques, MSc in Biochemistry Faculty of Science of the University of Lisbon Department of Chemistry and Biochemistry C8 Building, Room 8.5.47 Campo Grande, 1749-016 Lisbon, Portugal E-mail: joao.henriques.32353||gmail.com / jmhenriques||fc.ul.pt http://intheochem.fc.ul.pt/members/joaoh.html From owner-chemistry@ccl.net Wed Sep 14 13:40:01 2011 From: "Jason D Acchioli jdacchio-,-gmail.com" To: CCL Subject: CCL: Pure DFT functionals and ORCA Message-Id: <-45452-110914132850-14571-nhEyffwV37fMKFClgKhehw#,#server.ccl.net> X-Original-From: "Jason D'Acchioli" Content-Type: multipart/alternative; boundary="Apple-Mail=_045690B7-65EA-44A4-85A8-31880E08C6B4" Date: Wed, 14 Sep 2011 12:28:36 -0500 Mime-Version: 1.0 (Apple Message framework v1244.3) Sent to CCL by: "Jason D'Acchioli" [jdacchio---gmail.com] --Apple-Mail=_045690B7-65EA-44A4-85A8-31880E08C6B4 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Sorry; I meant input file! Jason On Sep 14, 2011, at 10:53 AM, Jason D Acchioli jdacchio]_[gmail.com = wrote: > Hi all, >=20 > I posted the following question on the ORCA forum, but haven't = heard anything (yet), so I'll throw it out here. The output file is = below the message.=20 >=20 > Jason >=20 > Hi all,=20 >=20 > I'm trying to run a single point / TDDFT calc on a metal-organic = system. However, the SCF does not converge after 125 cycles. I've tried = the PBE, RPBE, and revPBE XC functionals, and the same thing happens-I = get an oscillating SCF cycle. The same thing happens when I try the = hybrid B3LYP/G functional and the RIJCOSX approximation. However, if I = do a B3LYP/G without the RIJCOSX, convergence is fine.=20 > What am I doing wrong? If it is a problem with RI, can I still use any = of PW91 or PBE XC functionals (which, I believe, require auxiliary basis = sets?)? The input is attached as a zip file.=20 >=20 > Thanks,=20 >=20 > Jason >=20 > !RKS PW91 def2-SVP def2-SVP/J TightSCF PrintMOs Grid5 > %output > Print[P_OrbPopMO_M] 1 > Print[P_FragPopMO_M] 1 > end > %rel method ZORA #or IORA > modelpot 1,1,1,1 > modeldens rhoZORA > velit 137.0359895 #speed of light used > end > %tddft nroots 15 > maxdim 64 > end > ! PAL4 > * xyz 0 1 > H(1) -4.56675 -2.48229 -0.00028 > C(1) -4.57359 -1.39699 -0.00028 > C(1) -5.77738 -0.69952 -0.00035 > H(1) -6.71624 -1.24540 -0.00040 > C(1) -5.77739 0.69938 -0.00034 > H(1) -6.71628 1.24523 -0.00039 > C(1) -4.57363 1.39688 -0.00028 > H(1) -4.56682 2.48218 -0.00029 > C(1) -3.34414 0.71339 -0.00022 > C(1) -2.12293 1.43662 -0.00018 > C(1) -3.34412 -0.71346 -0.00021 > C(1) -2.12289 -1.43666 -0.00014 > C(1) -1.05872 2.02393 -0.00013 > C(1) 0.16183 2.74774 -0.00010 > C(1) -1.05866 -2.02394 -0.00006 > C(1) 0.16190 -2.74772 -0.00004 > C(1) 0.16567 4.15310 -0.00038 > C(1) 0.16578 -4.15308 -0.00027 > H(1) -0.78318 -4.67691 -0.00043 > C(1) 1.37444 -4.83715 -0.00028 > H(1) -0.78331 4.67691 -0.00066 > C(1) 1.37431 4.83720 -0.00031 > C(1) 2.56419 4.10860 0.00002 > H(1) 1.38849 5.92301 -0.00055 > C(1) 2.49611 2.71947 0.00026 > H(1) 3.53196 4.59786 0.00008 > N(1) 1.33136 2.05360 0.00019 > H(1) 3.38890 2.10605 0.00051 > C(1) 2.56430 -4.10851 -0.00008 > H(1) 1.38865 -5.92296 -0.00045 > C(1) 2.49618 -2.71939 0.00013 > H(1) 3.53208 -4.59774 -0.00008 > N(1) 1.33141 -2.05354 0.00016 > H(1) 3.38895 -2.10595 0.00028 > Pd(2) 1.33817 -0.00000 0.00023 newgto "def2-TZVP" = "def2-TZVP/J" end > Cl(3) 1.43325 -0.00001 -2.35531 > Cl(3) 1.43091 0.00002 2.35584 > * >=20 >=20 > ******************************************* > Jason D'Acchioli > Assistant Professor of Chemistry > University of Wisconsin-Stevens Point > 2001 Fourth Avenue > Stevens Point, WI 54481 > http://chemdac.uwsp.edu >=20 >=20 ******************************************* Jason D'Acchioli Assistant Professor of Chemistry University of Wisconsin-Stevens Point 2001 Fourth Avenue Stevens Point, WI 54481 http://chemdac.uwsp.edu --Apple-Mail=_045690B7-65EA-44A4-85A8-31880E08C6B4 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii
Hi = all,

I posted the following question = on the ORCA forum, but haven't heard anything (yet), so I'll throw it = out here. The output file is below the = message. 

Jason

Hi = all,I'm trying to = run a single point / TDDFT calc on a metal-organic system. However, the = SCF does not converge after 125 cycles. I've tried the PBE, RPBE, and = revPBE XC functionals, and the same thing happens-I get an oscillating = SCF cycle. The same thing happens when I try the hybrid B3LYP/G = functional and the RIJCOSX approximation. However, if I do a B3LYP/G = without the RIJCOSX, convergence is fine.What am I = doing wrong? If it is a problem with RI, can I still use any of PW91 or = PBE XC functionals (which, I believe, require auxiliary basis sets?)? = The input is attached as a zip file. 

Jason

!RKS PW91 def2-SVP = def2-SVP/J TightSCF PrintMOs Grid5
%output
Print[P_OrbPopMO_M] 1
Print[P_FragPopMO_M] 1
end
%rel method ZORA #or = IORA
modelpot 1,1,1,1
modeldens rhoZORA
velit 137.0359895 #speed of light = used
end
%tddft nroots 15
maxdim 64
end
! PAL4
* xyz 0 1
H(1)         -4.56675   =     -2.48229       = -0.00028
C(1)         -4.57359       = -1.39699       -0.00028
C(1)         -5.77738   =     -0.69952       = -0.00035
H(1)         -6.71624       = -1.24540       -0.00040
C(1)         -5.77739   =      0.69938       = -0.00034
H(1)         -6.71628       =  1.24523       = -0.00039
C(1)         -4.57363       =  1.39688       = -0.00028
H(1)         -4.56682       =  2.48218       = -0.00029
C(1)         -3.34414       =  0.71339       = -0.00022
C(1)         -2.12293       =  1.43662       = -0.00018
C(1)         -3.34412       = -0.71346       -0.00021
C(1)         -2.12289   =     -1.43666       = -0.00014
C(1)         -1.05872       =  2.02393       = -0.00013
C(1)          0.16183     =    2.74774       = -0.00010
C(1)         -1.05866       = -2.02394       -0.00006
C(1)          0.16190 =       -2.74772       = -0.00004
C(1)          0.16567     =    4.15310       = -0.00038
C(1)          0.16578     =   -4.15308       = -0.00027
H(1)         -0.78318       = -4.67691       -0.00043
C(1)          1.37444 =       -4.83715       = -0.00028
H(1)         -0.78331       =  4.67691       = -0.00066
C(1)         1.37431       =  4.83720       = -0.00031
C(1)          2.56419     =    4.10860       =  0.00002
H(1)          1.38849     =    5.92301       = -0.00055
C(1)          2.49611     =    2.71947       =  0.00026
H(1)          3.53196     =    4.59786       =  0.00008
N(1)          1.33136     =    2.05360       =  0.00019
H(1)          3.38890     =    2.10605       =  0.00051
C(1)          2.56430     =   -4.10851       = -0.00008
H(1)          1.38865     =   -5.92296       = -0.00045
C(1)          2.49618     =   -2.71939       =  0.00013
H(1)          3.53208     =   -4.59774       = -0.00008
N(1)          1.33141     =   -2.05354       =  0.00016
H(1)          3.38895     =   -2.10595       =  0.00028
Pd(2)         1.33817       = -0.00000        0.00023 newgto "def2-TZVP" = "def2-TZVP/J" end
Cl(3)         1.43325       = -0.00001       -2.35531
Cl(3)         1.43091   =      0.00002       =  2.35584
*


*******************************************
Jason = D'Acchioli
Assistant Professor of Chemistry
University of = Wisconsin-Stevens Point
2001 Fourth Avenue
Stevens Point, WI = 54481
http://chemdac.uwsp.edu



http://chemdac.uwsp.edu


= --Apple-Mail=_045690B7-65EA-44A4-85A8-31880E08C6B4-- From owner-chemistry@ccl.net Wed Sep 14 14:25:00 2011 From: "Kacper Druzbicki kacper.druzbicki:_:uj.edu.pl" To: CCL Subject: CCL:G: Question on Molecular Electrostatic Potential in Gaussian Message-Id: <-45453-110914113655-2655-IyYvZceRebjWImuKK6BqgQ|-|server.ccl.net> X-Original-From: "Kacper Druzbicki" Date: Wed, 14 Sep 2011 11:36:52 -0400 Sent to CCL by: "Kacper Druzbicki" [kacper.druzbicki _ uj.edu.pl] Dear CCl users, I've got a question regarding molecular electrostatic potential via Gaussian. I want to get the average value of the positive electrostatic potentials on the molecular surface. I tried to redo some of the published results and I got different numbers. I do not know where I am wrong, but my results differ significantly. In order to calculate the average value of the positive electrostatic potential I generate Cube file with Gaussian Cubegen keyword and Potential=SCF keyword, I use npts corresponding to the number of points per side in the cube equal to 100^3. Next I use gsgrid program (which I strongly recommend btw) in order to extract the values from the cube. http://gsgrid.codeplex.com/releases/view/54499 I sum up all the positive values and finaly I divide the result by the total number of points which are greater than 0. To get the results in ev I multiply the value in a.u. by 27.21 eV. Could you tell me please what am I doing wrong? Is the generated cube connected with the ESP not only at the surface? How to get such a grid? Any suggestions? Thank you in advance! Best wishes, Casper From owner-chemistry@ccl.net Wed Sep 14 15:00:01 2011 From: "Kacper Druzbicki kacper.druzbicki_._uj.edu.pl" To: CCL Subject: CCL:G: Question on Molecular Electrostatic Potential in Gaussian Message-Id: <-45454-110914113818-3572-EIkz6b1vTx6xnTkLNDD5Pw(a)server.ccl.net> X-Original-From: "Kacper Druzbicki" Date: Wed, 14 Sep 2011 11:38:15 -0400 Sent to CCL by: "Kacper Druzbicki" [kacper.druzbicki+*+uj.edu.pl] Dear CCl users, I've got a question regarding molecular electrostatic potential via Gaussian. I want to get the average value of the positive electrostatic potentials on the molecular surface. I tried to redo some of the published results and I got different numbers. I do not know where I am wrong, but my results differ significantly. In order to calculate the average value of the positive electrostatic potential I generate Cube file with Gaussian Cubegen keyword and Potential=SCF keyword, I use npts corresponding to the number of points per side in the cube equal to 100^3. Next I use gsgrid program (which I strongly recommend btw) in order to extract the values from the cube. http://gsgrid.codeplex.com/releases/view/54499 I sum up all the positive values and finaly I divide the result by the total number of points which are greater than 0. To get the results in ev I multiply the value in a.u. by 27.21 eV. Could you tell me please what am I doing wrong? Is the generated cube connected with the ESP not only at the surface? How to get such a grid? Any suggestions? Thank you in advance! Best wishes, Casper From owner-chemistry@ccl.net Wed Sep 14 15:35:00 2011 From: "Kacper Druzbicki kacper.druzbicki]^[uj.edu.pl" To: CCL Subject: CCL:G: Question on Molecular Electrostatic Potential in Gaussian Message-Id: <-45455-110914114901-10669-8bfiS8nOZVYQF0AvdkhSyA=server.ccl.net> X-Original-From: "Kacper Druzbicki" Date: Wed, 14 Sep 2011 11:48:57 -0400 Sent to CCL by: "Kacper Druzbicki" [kacper.druzbicki#%#uj.edu.pl] Dear CCl users, I've got a question regarding molecular electrostatic potential in Gaussian. I want to get the average value of the positive electrostatic potentials on the molecular surface. I tried to redo some of the published results and I got different numbers. I do not know where I am wrong, but my results differ significantly. In order to calculate the average value of the positive electrostatic potential I generate Cube file with Gaussian Cubegen keyword and Potential=SCF keyword, I use npts corresponding to the number of points per side in the cube equal to 100^3. Next I use gsgrid program (which I strongly recommend btw) in order to extract the values from the cube. http://gsgrid.codeplex.com/releases/view/54499 I sum up all the positive values and finaly I divide the result by the total number of points which are greater than 0. To get the results in ev I multiply the value in a.u. by 27.21 eV. Could you tell me please what am I doing wrong? Is the generated cube connected with the ESP not only at the surface? How to get such a grid? Any suggestions? And I also have the second question. What is the most reliable way of getting molecular volume in Gaussian in your opinion? I used Volume keyword, but the results differ between particular SCF steps. I found an info that the results fail within 10% in this way. Maybe some SCRF choice would be more appropriate? Thank you in advance! Best wishes, Casper Kacper Drubicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krakw, Poland phone: +48 12 6632265 From owner-chemistry@ccl.net Wed Sep 14 16:09:00 2011 From: "Farhan Pasha pashafa(0)yahoo.co.in" To: CCL Subject: CCL:G: Problem in ONIOM calculations Message-Id: <-45456-110914150812-24506-EQwFv3o0Kmc6bEgkcRRNCg!=!server.ccl.net> X-Original-From: Farhan Pasha Content-Type: multipart/alternative; boundary="1691852587-329495572-1316027282=:61888" Date: Thu, 15 Sep 2011 00:38:02 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Farhan Pasha [pashafa/./yahoo.co.in] --1691852587-329495572-1316027282=:61888 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi I had such problem. Possible solution is to do calculation in first step just DFT and MM and re= do with 3 layer. Infirst calculation include middle layer in MM. If it is not any special case and you calculation allow you to do so I hope= It will work. =A0 Correspondence Address =0ADr. Syed Farhan Ahmad Pasha --- On Wed, 14/9/11, Krati joshi kjjulie.joshi|*|gmail.com wrote: > From: Krati joshi kjjulie.joshi|*|gmail.com Subject: CCL:G: Problem in ONIOM calculations To: "Pasha, Frahan Ahmad " Date: Wednesday, 14 September, 2011, 5:32 PM Sent to CCL by: "Krati=A0 joshi" [kjjulie.joshi]|[gmail.com] Dear all, =A0 =A0 =A0 =A0=A0=A0I have some problem in ONIOM calculations.i am doing t= hree layer ONIOM calculation. The 3 layers of ONIOM consists of following a= toms- 1.High-Si,4O,3H,Na, with 25 H2O around it-QM(DFT) 2.Middle layer-27H2O molecules-SEM(AM1) 3.Low-28H2O molecules-MM(UFF) I have selected all the layers properly by using gauss view.I am using Gau= ssian 09 for my calculations.After running for a long time say about 6-8 ho= urs my jobs crashes with the following error message- =20 "Error in internal coordinates. error termination via Lnk1e in ../../../l301.exe" I am not able to understand what is the problem with my jobs. If anybody kn= ows anything about it then pls suggest me. it will be of great help to me.T= hanks in advance.=20 > From KRATI JOSHI catalysis Division=20 NCL Pune, India email- kjjulie.joshi-at-gmail.com -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0--1691852587-329495572-1316027282=:61888 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi
I had such problem.
Possible solutio= n is to do calculation in first step just DFT and MM and redo with 3 layer.= Infirst calculation include middle layer in MM.
If it is not any specia= l case and you calculation allow you to do so I hope It will work.
 = ;

Correspondence Address
=0ADr. Syed Farhan Ahmad Pasha

--- On Wed, 14/9/11, Krati joshi kjjulie.joshi|*|gmail.com <owne= r-chemistry() ccl.net> wrote:

From= : Krati joshi kjjulie.joshi|*|gmail.com <owner-chemistry() ccl.net>
= Subject: CCL:G: Problem in ONIOM calculations
To: "Pasha, Frahan Ahmad -= id#3tt-" <pashafa() yahoo.co.in>
Date: Wednesday, 14 September, 2011= , 5:32 PM


Sent to CCL by: "Krati  = joshi" [kjjulie.joshi]|[gmail.com]
Dear all,
      &nb= sp;  I have some problem in ONIOM calculations.i am doing three l= ayer ONIOM calculation. The 3 layers of ONIOM consists of following atoms-<= br>
1.High-Si,4O,3H,Na, with 25 H2O around it-QM(DFT)
2.Middle layer-= 27H2O molecules-SEM(AM1)
3.Low-28H2O molecules-MM(UFF)

I have se= lected all the layers properly by using gauss view.I am using Gaussian 09 for my calculations.After running = for a long time say about 6-8 hours my jobs crashes with the following erro= r message-

"Error in internal coordinates.
error termination via= Lnk1e in ../../../l301.exe"

I am not able to understand what is the= problem with my jobs. If anybody knows anything about it then pls suggest = me. it will be of great help to me.Thanks in advance.


> From=
KRATI JOSHI
catalysis Division
NCL Pune, India
email- kjjulie= .joshi-at-gmail.com



-=3D This is automatically added to each= message by the mailing script =3D-
To recover the email address of the = author of the message, please change
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--1691852587-329495572-1316027282=:61888-- From owner-chemistry@ccl.net Wed Sep 14 16:45:01 2011 From: "Johannes Hachmann jh:-:chemistry.harvard.edu" To: CCL Subject: CCL:G: Question on Charge distribution Gaussian Message-Id: <-45457-110914144459-2358-2Tr6dz45KCpQC++q714UaQ:_:server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Language: en-us Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 14 Sep 2011 14:44:32 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh**chemistry.harvard.edu] Dear Sergio, How do you evaluate the partial charge distribution? Mulliken population analysis is known to regularly give unphysical results (there are a number of papers explaining its failure) - try NPA or an AIM analysis instead. Best Johannes ----------------------------------------------- Dr. Johannes Hachmann Postdoctoral Fellow Aspuru-Guzik Research Group Harvard University Department of Chemistry and Chemical Biology 12 Oxford St, Rm M104A Cambridge, MA 02138 USA eMail: jh . chemistry.harvard.edu ----------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh388==cornell.edu . ccl.net [mailto:owner- > chemistry+jh388==cornell.edu . ccl.net] On Behalf Of Joćo Henriques > jmhenriques=fc.ul.pt > Sent: Wednesday, September 14, 2011 11:28 > To: Hachmann, Johannes > Subject: CCL:G: Question on Charge distribution Gaussian > > > Sent to CCL by: =?ISO-8859-1?Q?Jo=E3o_Henriques?= [jmhenriques ~ > fc.ul.pt] > Dear Sergio, > > Have you tried doing the calculations with an implicit solvent > model? > A part from that, many other things may be causing the reported > undesired effect (theory level, basis set, geometry, etc). Yet, your > settings seem adequate to your system... I did not take a look at > your > system, so it's always a good idea to recheck the charge and spin > multiplicity. > > Sorry I cannot help you much more than this. Surely, more > experienced > users will come up with an answer to your problem. > > Best regards, > > On Wed, Sep 14, 2011 at 12:50 PM, Sergio Manzetti sergio.manzetti ~ > gmail.com wrote: > > Dear CCLrs. I am running calculations on a nitrenium molecule, > with the > > positively charge Ar-NH+ using Gaussian. The charge is assigned on > the > > Nitrogen atom in the input file ( in accord to literature), > however in the > > results it becomes localized on neighbour atoms, at times as > distance as a > > phenyl ring away. Is this the peculiar nature of the charged > molecules, or > > am I running the wrong  setting? > > > > The input is: > > > > #P B3LYP/6-311+G* > > # Opt > > #  polar > > # Gfinput IOP(6/7=3)  Pop=full  Density  Test > > # Units(Ang,Deg) > > > > Dinitropyrene > > > > 0 1 > >  C                  1.18010000   -0.27278000   -0.00014000 > >  C                  2.60899000   -0.24741000   -0.00009000 > >  C                  1.13615000    2.20214000    0.00041000 > >  C                  2.56505000    2.22752000    0.00080000..... > > > > > > Thanks > > > > Sergio > > > > > > -- > Joćo Henriques, MSc in Biochemistry > Faculty of Science of the University of Lisbon > Department of Chemistry and Biochemistry > C8 Building, Room 8.5.47 > Campo Grande, 1749-016 Lisbon, Portugal > E-mail: joao.henriques.32353]~[gmail.com / jmhenriques]~[fc.ul.pt > http://intheochem.fc.ul.pt/members/joaoh.html > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ From owner-chemistry@ccl.net Wed Sep 14 20:06:01 2011 From: "John McKelvey jmmckel%a%gmail.com" To: CCL Subject: CCL: Pure DFT functionals and ORCA Message-Id: <-45458-110914200137-16434-uUisTt9BVjBRr6nQmwBD1g(0)server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=bcaec520eb1b8cec1604acef9383 Date: Wed, 14 Sep 2011 20:01:19 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel[a]gmail.com] --bcaec520eb1b8cec1604acef9383 Content-Type: text/plain; charset=ISO-8859-1 Have you tried "very slow convergence" or something like that.. It is highly recommended in the Manual for metal complexes. I've used it and it does the job! John McKelvey On Wed, Sep 14, 2011 at 1:28 PM, Jason D Acchioli jdacchio-,-gmail.com < owner-chemistry[#]ccl.net> wrote: > Sorry; I meant *input* file! > > Jason > > On Sep 14, 2011, at 10:53 AM, Jason D Acchioli jdacchio]_[gmail.com wrote: > > Hi all, > > I posted the following question on the ORCA forum, but haven't heard > anything (yet), so I'll throw it out here. The output file is below the > message. > > Jason > > Hi all, > > I'm trying to run a single point / TDDFT calc on a metal-organic system. > However, the SCF does not converge after 125 cycles. I've tried the PBE, > RPBE, and revPBE XC functionals, and the same thing happens-I get an > oscillating SCF cycle. The same thing happens when I try the hybrid B3LYP/G > functional and the RIJCOSX approximation. However, if I do a B3LYP/G without > the RIJCOSX, convergence is fine. > What am I doing wrong? If it is a problem with RI, can I still use any of > PW91 or PBE XC functionals (which, I believe, require auxiliary basis > sets?)? The input is attached as a zip file. > > Thanks, > > Jason > > !RKS PW91 def2-SVP def2-SVP/J TightSCF PrintMOs Grid5 > %output > Print[P_OrbPopMO_M] 1 > Print[P_FragPopMO_M] 1 > end > %rel method ZORA #or IORA > modelpot 1,1,1,1 > modeldens rhoZORA > velit 137.0359895 #speed of light used > end > %tddft nroots 15 > maxdim 64 > end > ! PAL4 > * xyz 0 1 > H(1) -4.56675 -2.48229 -0.00028 > C(1) -4.57359 -1.39699 -0.00028 > C(1) -5.77738 -0.69952 -0.00035 > H(1) -6.71624 -1.24540 -0.00040 > C(1) -5.77739 0.69938 -0.00034 > H(1) -6.71628 1.24523 -0.00039 > C(1) -4.57363 1.39688 -0.00028 > H(1) -4.56682 2.48218 -0.00029 > C(1) -3.34414 0.71339 -0.00022 > C(1) -2.12293 1.43662 -0.00018 > C(1) -3.34412 -0.71346 -0.00021 > C(1) -2.12289 -1.43666 -0.00014 > C(1) -1.05872 2.02393 -0.00013 > C(1) 0.16183 2.74774 -0.00010 > C(1) -1.05866 -2.02394 -0.00006 > C(1) 0.16190 -2.74772 -0.00004 > C(1) 0.16567 4.15310 -0.00038 > C(1) 0.16578 -4.15308 -0.00027 > H(1) -0.78318 -4.67691 -0.00043 > C(1) 1.37444 -4.83715 -0.00028 > H(1) -0.78331 4.67691 -0.00066 > C(1) 1.37431 4.83720 -0.00031 > C(1) 2.56419 4.10860 0.00002 > H(1) 1.38849 5.92301 -0.00055 > C(1) 2.49611 2.71947 0.00026 > H(1) 3.53196 4.59786 0.00008 > N(1) 1.33136 2.05360 0.00019 > H(1) 3.38890 2.10605 0.00051 > C(1) 2.56430 -4.10851 -0.00008 > H(1) 1.38865 -5.92296 -0.00045 > C(1) 2.49618 -2.71939 0.00013 > H(1) 3.53208 -4.59774 -0.00008 > N(1) 1.33141 -2.05354 0.00016 > H(1) 3.38895 -2.10595 0.00028 > Pd(2) 1.33817 -0.00000 0.00023 newgto "def2-TZVP" > "def2-TZVP/J" end > Cl(3) 1.43325 -0.00001 -2.35531 > Cl(3) 1.43091 0.00002 2.35584 > * > > > ******************************************* > Jason D'Acchioli > Assistant Professor of Chemistry > University of Wisconsin-Stevens Point > 2001 Fourth Avenue > Stevens Point, WI 54481 > http://chemdac.uwsp.edu > > > > ******************************************* > Jason D'Acchioli > Assistant Professor of Chemistry > University of Wisconsin-Stevens Point > 2001 Fourth Avenue > Stevens Point, WI 54481 > http://chemdac.uwsp.edu > > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel[#]gmail.com --bcaec520eb1b8cec1604acef9383 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Have you tried "very slow convergence" or something like that..= =A0 It is highly recommended in the Manual for metal complexes.=A0 I've= used it and it does the job!

John McKelvey

On Wed, Sep 14, 2011 at 1:28 PM, Jason D Acchioli jdacchio-,-gmail.com <owner-chemistry[#]ccl.net> wrote:
Sorry; I meant input=A0file!

Jason

On Sep 14, 2011, at 10:53 AM, Jason D Acchioli jdacchio]_[gmail.com wrote:

Hi all,

I posted the following qu= estion on the ORCA forum, but haven't heard anything (yet), so I'll= throw it out here. The output file is below the message.=A0

Jason

Hi all,=A0
I'm trying to run a single point / TDDFT calc on = a metal-organic system. However, the SCF does not converge after 125 cycles= . I've tried the PBE, RPBE, and revPBE XC functionals, and the same thi= ng happens-I get an oscillating SCF cycle. The same thing happens when I tr= y the hybrid B3LYP/G functional and the RIJCOSX approximation. However, if = I do a B3LYP/G without the RIJCOSX, convergence is fine.=A0
What am I doing wrong? If it is a problem with RI, can I still use= any of PW91 or PBE XC functionals (which, I believe, require auxiliary bas= is sets?)? The input is attached as a zip file.=A0

Thanks,=A0

Jason

!RKS PW91 def2-SVP def2-SVP/J TightSCF= PrintMOs Grid5
%output
Print[P_OrbPopMO_M] 1
Print[P_FragPopMO_M] 1
end
%rel method ZORA #or IORA
modelpot 1,1,1,1
modeldens rhoZORA
velit 137.0359895 #speed of light= used
end
%tddft nroots 15
maxdim 64
end
! PAL4
* xyz 0 1
H(1) =A0 =A0 =A0 =A0 -4.56675 =A0 =A0= =A0 -2.48229 =A0 =A0 =A0 -0.00028
C(1) =A0 =A0 =A0 =A0 -4.57359 =A0= =A0 =A0 -1.39699 =A0 =A0 =A0 -0.00028
C(1) =A0 =A0 =A0 =A0 -5.77738 =A0 =A0 =A0 -0.6995= 2 =A0 =A0 =A0 -0.00035
H(1) =A0 =A0 =A0 =A0 -6.71624 =A0= =A0 =A0 -1.24540 =A0 =A0 =A0 -0.00040
C(1) =A0 =A0 =A0 =A0 -5.77739 =A0 =A0 =A0 =A00.69= 938 =A0 =A0 =A0 -0.00034
H(1) =A0 =A0 =A0 =A0 -6.71628 =A0= =A0 =A0 =A01.24523 =A0 =A0 =A0 -0.00039
C(1) =A0 =A0 =A0 =A0 -4.57363 =A0 =A0 =A0 =A01.3= 9688 =A0 =A0 =A0 -0.00028
H(1) =A0 =A0 =A0 =A0 -4.56682 =A0= =A0 =A0 =A02.48218 =A0 =A0 =A0 -0.00029
C(1) =A0 =A0 =A0 =A0 -3.34414 =A0 =A0 =A0 =A00.7= 1339 =A0 =A0 =A0 -0.00022
C(1) =A0 =A0 =A0 =A0 -2.12293 =A0= =A0 =A0 =A01.43662 =A0 =A0 =A0 -0.00018
C(1) =A0 =A0 =A0 =A0 -3.34412 =A0 =A0 =A0 -0.713= 46 =A0 =A0 =A0 -0.00021
C(1) =A0 =A0 =A0 =A0 -2.12289 =A0= =A0 =A0 -1.43666 =A0 =A0 =A0 -0.00014
C(1) =A0 =A0 =A0 =A0 -1.05872 =A0 =A0 =A0 =A02.02= 393 =A0 =A0 =A0 -0.00013
C(1) =A0 =A0 =A0 =A0 =A00.16183 = =A0 =A0 =A0 =A02.74774 =A0 =A0 =A0 -0.00010
C(1) =A0 =A0 =A0 =A0 -1.05866 =A0 =A0 =A0 -2.= 02394 =A0 =A0 =A0 -0.00006
C(1) =A0 =A0 =A0 =A0 =A00.16190 = =A0 =A0 =A0 -2.74772 =A0 =A0 =A0 -0.00004
C(1) =A0 =A0 =A0 =A0 =A00.16567 =A0 =A0 =A0 =A0= 4.15310 =A0 =A0 =A0 -0.00038
C(1) =A0 =A0 =A0 =A0 =A00.16578 = =A0 =A0 =A0 -4.15308 =A0 =A0 =A0 -0.00027
H(1) =A0 =A0 =A0 =A0 -0.78318 =A0 =A0 =A0 -4.67= 691 =A0 =A0 =A0 -0.00043
C(1) =A0 =A0 =A0 =A0 =A01.37444 = =A0 =A0 =A0 -4.83715 =A0 =A0 =A0 -0.00028
H(1) =A0 =A0 =A0 =A0 -0.78331 =A0 =A0 =A0 =A04.= 67691 =A0 =A0 =A0 -0.00066
C(1) =A0 =A0 =A0 =A0 1.37431 =A0 = =A0 =A0 =A04.83720 =A0 =A0 =A0 -0.00031
C(1) =A0 =A0 =A0 =A0 =A02.56419 =A0 =A0 =A0 =A04.= 10860 =A0 =A0 =A0 =A00.00002
H(1) =A0 =A0 =A0 =A0 =A01.38849 = =A0 =A0 =A0 =A05.92301 =A0 =A0 =A0 -0.00055
C(1) =A0 =A0 =A0 =A0 =A02.49611 =A0 =A0 =A0 = =A02.71947 =A0 =A0 =A0 =A00.00026
H(1) =A0 =A0 =A0 =A0 =A03.53196 = =A0 =A0 =A0 =A04.59786 =A0 =A0 =A0 =A00.00008
N(1) =A0 =A0 =A0 =A0 =A01.33136 =A0 =A0 =A0= =A02.05360 =A0 =A0 =A0 =A00.00019
H(1) =A0 =A0 =A0 =A0 =A03.38890 = =A0 =A0 =A0 =A02.10605 =A0 =A0 =A0 =A00.00051
C(1) =A0 =A0 =A0 =A0 =A02.56430 =A0 =A0 =A0= -4.10851 =A0 =A0 =A0 -0.00008
H(1) =A0 =A0 =A0 =A0 =A01.38865 = =A0 =A0 =A0 -5.92296 =A0 =A0 =A0 -0.00045
C(1) =A0 =A0 =A0 =A0 =A02.49618 =A0 =A0 =A0 -2.= 71939 =A0 =A0 =A0 =A00.00013
H(1) =A0 =A0 =A0 =A0 =A03.53208 = =A0 =A0 =A0 -4.59774 =A0 =A0 =A0 -0.00008
N(1) =A0 =A0 =A0 =A0 =A01.33141 =A0 =A0 =A0 -2.= 05354 =A0 =A0 =A0 =A00.00016
H(1) =A0 =A0 =A0 =A0 =A03.38895 = =A0 =A0 =A0 -2.10595 =A0 =A0 =A0 =A00.00028
Pd(2) =A0 =A0 =A0 =A0 1.33817 =A0 =A0 =A0 -0.= 00000 =A0 =A0 =A0 =A00.00023 newgto "def2-TZVP" "def2-TZVP/J= " end
Cl(3) =A0 =A0 =A0 =A0 1.43325 =A0= =A0 =A0 -0.00001 =A0 =A0 =A0 -2.35531
Cl(3) =A0 =A0 =A0 =A0 1.43091 =A0 =A0 =A0 =A00.00= 002 =A0 =A0 =A0 =A02.35584
*


*******************************************
Jason D'Acchioli
Assi= stant Professor of Chemistry
University of Wisconsin-Stevens Point
20= 01 Fourth Avenue
Stevens Point, WI 54481
http://chemdac.uwsp.edu



*******************= ************************
Jason D'Acchioli
Assistant Professor of Chemistry
University of W= isconsin-Stevens Point
2001 Fourth Avenue
Stevens Point, WI 54481
= http://chemdac.uwsp.e= du




--=
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-= 2160
jmmckel[#]gmail.com
--bcaec520eb1b8cec1604acef9383-- From owner-chemistry@ccl.net Wed Sep 14 20:46:01 2011 From: "N. Sukumar nagams{}rpi.edu" To: CCL Subject: CCL:G: Question on Molecular Electrostatic Potential in Gaussian Message-Id: <-45459-110914160926-2713-HCHoT1vyTLCChW9axkWRXQ_+_server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Wed, 14 Sep 2011 16:10:02 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams()rpi.edu] How do you determine the molecular surface? Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research http://reccr.chem.rpi.edu/ -------------------------- "Gasoline made from the tar sands gives a Toyota Prius the same impact on climate as a Hummer using gasoline made from oil." --- Al Gore ==============Original message text=============== On Wed, 14 Sep 2011 11:38:15 EDT "Kacper Druzbicki kacper.druzbicki_._uj.edu.pl" wrote: Sent to CCL by: "Kacper Druzbicki" [kacper.druzbicki+*+uj.edu.pl] Dear CCl users, I've got a question regarding molecular electrostatic potential via Gaussian. I want to get the average value of the positive electrostatic potentials on the molecular surface. I tried to redo some of the published results and I got different numbers. I do not know where I am wrong, but my results differ significantly. In order to calculate the average value of the positive electrostatic potential I generate Cube file with Gaussian Cubegen keyword and Potential=SCF keyword, I use npts corresponding to the number of points per side in the cube equal to 100^3. Next I use gsgrid program (which I strongly recommend btw) in order to extract the values from the cube. http://gsgrid.codeplex.com/releases/view/54499 I sum up all the positive values and finaly I divide the result by the total number of points which are greater than 0. To get the results in ev I multiply the value in a.u. by 27.21 eV. Could you tell me please what am I doing wrong? Is the generated cube connected with the ESP not only at the surface? How to get such a grid? Any suggestions? Thank you in advance! Best wishes, Casperhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========