Dear All,<= /span>

I would li= ke to ask about solvents effect on symmetric molecule. I took simple molecu= le, BH4 -. Then I did geometry optimisation in water and THF using PCM mode= l. The total energy without any symmetry constraint (e.g. in water: -27.375= 2502) is higher in energy than the total energy using symmetry constraint (= Td) (-27.3753128). In case of loose symmetry, BH4 - is end up with one B-H = bond is more longer than the others (c3v point group). I did the calculations using Gaussian 09.

<= /span>

I perform the calculations in order to unders= trand the IR & Raman spectrum in solution. Does anyone can explain me t= he solvents effect on vibrational spectra? Which calculation should I rely = on with or without symmetry?

Thank you very much before for your help!

Best regards,

= ;

Daniel
PhD student
Universit=E9 de Gen=E8ve, Switzerland<= br>

---1211669884-2007290576-1364898036=:62521-- From owner-chemistry@ccl.net Tue Apr 2 08:25:00 2013 From: "Prasun Dutta prasundutta87.:.gmail.com" To: CCL Subject: CCL: Difference between Tanimoto Coef. and Davis index Message-Id: <-48507-130402020924-12480-mpnnPQq8pbjI8iPlhYI9kA/./server.ccl.net> X-Original-From: "Prasun Dutta" Date: Tue, 2 Apr 2013 02:09:23 -0400 Sent to CCL by: "Prasun Dutta" [prasundutta87-$-gmail.com] Could someone explain me the difference between tanimoto coefficient and the Davis index? And when each of them should they be used? From owner-chemistry@ccl.net Tue Apr 2 09:00:00 2013 From: "Jan H Jensen jhjensen^chem.ku.dk" To: CCL Subject: CCL: Computational Chemistry Highlights: March issue Message-Id: <-48508-130402040917-28526-DirA09aeh+G0dAgpzKU8yA..server.ccl.net> X-Original-From: "Jan H Jensen" Date: Tue, 2 Apr 2013 04:09:16 -0400 Sent to CCL by: "Jan H Jensen" [jhjensen::chem.ku.dk] The March issue of Computational Chemistry Highlights is out. http://www.compchemhighlights.org/2013_03_01_archive.html CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here. Table of content for this issue features contributions from CCH editors Steven Bachrach, Ric Baron and Jan Jensen: Anharmonic Vibrational Frequency Calculations Are Not Worthwhile for Small Basis Sets http://www.compchemhighlights.org/2013/03/anharmonic-vibrational-frequency.html Calculation of Molecular Entropies Using Temperature Integration http://www.compchemhighlights.org/2013/03/calculation-of-molecular-entropies.html Free Fructose is Conformationally Locked http://www.compchemhighlights.org/2013/03/free-fructose-is-conformationally-locked.html Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements http://www.compchemhighlights.org/2013/03/are-protein-force-fields-getting-better.html The Fold-In Approach to Bowl-Shaped Aromatic Compounds: Synthesis of Chrysaoroles http://www.compchemhighlights.org/2013/03/the-fold-in-approach-to-bowl-shaped.html Musings about C2 http://www.compchemhighlights.org/2013/03/musings-about-c2.html Interested in more? There are many ways to subscribe to CCH updates. http://www.compchemhighlights.org/p/get-cch-updates.html From owner-chemistry@ccl.net Tue Apr 2 09:35:00 2013 From: "Rajarshi Guha rajarshi.guha _ gmail.com" To: CCL Subject: CCL: CINF Lightning Talks - CINFLash (ACS National Meeting, New Orleans, Spring 2013) Message-Id: <-48509-130402083909-22301-1NZwHioIRXlSkqcjZVBJMQ(a)server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 2 Apr 2013 08:39:01 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha=-=gmail.com] With the Spring ACS less than week away, we are running CINFlash once again - a session of 8 minute lightning talks on any aspect of chemical information and cheminformatics. It's going to run from 12:30pm - 2pm on Sunday, April 7 (Room 350, Morial Convention Center). As before, we aren't using PACS - so there's still time to send in a brief (< 100 words) abstract to cinf.flash:_:gmail.com - I'll be looking for abstracts up til April 5 Visit http://acscinf.org/content/cinf-symposia-245-cinf-flash-call-papers for more details. If you have any questions feel free to mail me at rajarshi.guha:_:gmail.com -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science From owner-chemistry@ccl.net Tue Apr 2 10:10:00 2013 From: "Guha, Rajarshi (NIH/NCATS) C guhar|,|mail.nih.gov" To: CCL Subject: CCL: CINF Lightning Talks - CINFLash (ACS National Meeting, New Orleans, Spring 2013) Message-Id: <-48510-130402091623-12698-++WUUbFq+TBCYyXTIq1BFg|,|server.ccl.net> X-Original-From: "Guha, Rajarshi (NIH/NCATS) [C]" Content-ID: <4F18456080A7314CA35720D7B5FA6ABE|,|mail.nih.gov> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 2 Apr 2013 13:16:11 +0000 MIME-Version: 1.0 Sent to CCL by: "Guha, Rajarshi (NIH/NCATS) [C]" [guhar[A]mail.nih.gov] With the Spring ACS less than week away, we are running CINFlash once again - a session of 8 minute lightning talks on any aspect of chemical information and cheminformatics. It's going to run from 12:30pm - 2pm on Sunday, April 7 (Room 350, Morial Convention Center). As before, we aren't using PACS - so there's still time to send in a brief (< 100 words) abstract to cinf.flash++gmail.com - I'll be looking for abstracts up til April 5 Visit http://acscinf.org/content/cinf-symposia-245-cinf-flash-call-papers for more details. If you have any questions feel free to mail me at rajarshi.guha++gmail.com -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science From owner-chemistry@ccl.net Tue Apr 2 12:40:00 2013 From: "Soumen Ghosh soumenrkmrc08,gmail.com" To: CCL Subject: CCL: Calculating percentage contribution of an excitation from TDDFT output Message-Id: <-48511-130402123843-4812-gvYzmRPICXn7A6GVaHdnhA[]server.ccl.net> X-Original-From: "Soumen Ghosh" Date: Tue, 2 Apr 2013 12:38:42 -0400 Sent to CCL by: "Soumen Ghosh" [soumenrkmrc08{=}gmail.com] Dear All, I am doing TDDFT calculation on a dinuclear metal complex with each metal having unpaired electrons.In TDDFT output in G09 software the coefficients for each excitation is printed. So, I think the square of that coefficient multiplied by 100 should give the percentage contribution of that excitation. However, sometimes this coefficient is coming out as more than 1. What does it signify and how can I handle such situations? Regards Soumen Ghosh Soumen Ghosh soumenrkmrc08 ~~ gmail.com IITB,India From owner-chemistry@ccl.net Tue Apr 2 13:53:00 2013 From: "Mohammad Halim mhalim4=-=uwo.ca" To: CCL Subject: CCL: Calculating percentage contribution of an excitation from TDDFT output Message-Id: <-48512-130402133556-16437-i/zFGsH0VoQlUseq2EigBg^_^server.ccl.net> X-Original-From: Mohammad Halim Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_KPfDgoLAAgCdGFSZVU5EOA)" Date: Tue, 02 Apr 2013 13:35:49 -0400 MIME-version: 1.0 Sent to CCL by: Mohammad Halim [mhalim4(!)uwo.ca] This is a multi-part message in MIME format. --Boundary_(ID_KPfDgoLAAgCdGFSZVU5EOA) Content-type: text/plain; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Content-disposition: inline Dear Soumen, Follow the procedure already discussed in CCL: If you want the percentage contribution from the pertinent singlet configuration, you must square the printed coefficient and multiply it by 2 x 100. For instance, the contribution from the 129 -> 138 excitation in the first of your examples amounts to 0.45069^2 x 2 x 100 = 40.62%. In your second example, you get for the 130 -> 132 excitation 0.67417^2 x 2 x 100 = 90.90%. take care, ......................................................................................... Mohammad A. Halim PhD Candidate Department of Chemistry(http://www.uwo.ca/chem/) The University of Western Ontario(http://www.uwo.ca/) London, ON, Canada, N6A 5B7 Ph: (519) 661-2111 ext. 86667 Home page: http://ahalim.host56.com/ ............................................................................................. On 04/02/13, "Soumen Ghosh soumenrkmrc08,gmail.com" wrote: > > Sent to CCL by: "Soumen Ghosh" [soumenrkmrc08{=}gmail.com] > Dear All, > I am doing TDDFT calculation on a dinuclear metal complex with each > metal having unpaired electrons.In TDDFT output in G09 software the > coefficients for each excitation is printed. So, I think the square of that > coefficient multiplied by 100 should give the percentage contribution of that > excitation. However, sometimes this coefficient is coming out as more than 1. > What does it signify and how can I handle such situations? > > Regards > Soumen Ghosh > > Soumen Ghosh > soumenrkmrc08*o*gmail.com > IITB,India> > > > -- --Boundary_(ID_KPfDgoLAAgCdGFSZVU5EOA) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: quoted-printable Content-disposition: inline =3Ctt=3E Dear Soumen=2C=3Cbr /=3E=3Cbr /=3EFollow the procedure already = discussed in CCL=3A=3Cbr /=3E=3Cbr /=3EIf you want the percentage =3C/tt=3E=3Ctt=3Econtribution from the pertinent singlet configuration=2C= you must square =3C/tt=3E=3Ctt=3Ethe printed coefficient and multiply it by 2 x 100=2E = For instance=2C the =3C/tt=3E=3Ctt=3Econtribution from the 129 -=26gt=3B 138 excitation in = the first of your =3C/tt=3E=3Ctt=3Eexamples amounts to =3C/tt=3E=3Cpre style=3D=22margin=3A 0em=3B=22=3E 0=2E45069=5E2 x 2 x 1= 00 =3D 40=2E62=25=2E In your second example=2C you get for the 130 -=26gt=3B 132 excitation 0=2E67417=5E2 x 2 x 100 =3D 90=2E90=25=2E=3Cbr /=3E=3Cbr /=3Etake care=2C= =3Cbr /=3E=3C/pre=3E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E= =2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E= =2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E= =2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E= =3Cbr /=3EMohammad A=2E Halim=3Cbr /=3EPhD Candidate=3Cbr /=3E=3Ca href=3D= =22http=3A//www=2Euwo=2Eca/chem/=22=3EDepartment of Chemistry=3C/a=3E=3C= br /=3E=3Ca href=3D=22http=3A//www=2Euwo=2Eca/=22=3EThe University of We= stern Ontario=3C/a=3E=3Cbr /=3ELondon=2C ON=2C Canada=2C N6A 5B7=3Cbr /=3E= Ph=3A=3Cspan class=3D=22fixed=22=3E (519) 661-2111 ext=2E 86667=3C/span=3E= =3Cbr /=3EHome page=3A =3Ca href=3D=22http=3A//ahalim=2Ehost56=2Ecom/=22= =3Ehttp=3A//ahalim=2Ehost56=2Ecom/=3C/a=3E=3Cbr /=3E=2E=2E=2E=2E=2E=2E=2E= =2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E= =2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E= =2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E= =2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=2E=3Cbr /=3E=3Cbr /=3E=3Cspan=3E= On 04/02/13=2C =3Cb class=3D=22name=22=3E=26quot=3BSoumen Ghosh soumenrk= mrc08=2Cgmail=2Ecom=26quot=3B =3C/b=3E =26lt=3Bowner-chemistry=40ccl=2En= et=26gt=3B wrote=3A=3C/span=3E=3Cblockquote cite=3D=22mid=3A =26lt=3B-id= =233bt-48511-130402123843-4812-JKaPts2tStVu+ElWoEvH4A=40server=2Eccl=2En= et=22 class=3D=22iwcQuote=22 style=3D=22border-left=3A 1px solid =2300F=3B= padding-left=3A 13px=3B margin-left=3A 0=3B=22 type=3D=22cite=22=3E=3Cd= iv class=3D=22mimepart text plain=22=3E=3Cbr /=3ESent to CCL by=3A =26qu= ot=3BSoumen=A0 Ghosh=26quot=3B =5Bsoumenrkmrc08=7B=3D=7Dgmail=2Ecom=5D=3C= br /=3EDear All=2C=3Cbr /=3E=A0=A0=A0=A0=A0=A0=A0 I am doing TDDFT calcu= lation on a dinuclear metal complex with each =3Cbr /=3Emetal having unp= aired electrons=2EIn TDDFT output in G09 software the =3Cbr /=3Ecoeffici= ents for each excitation is printed=2E So=2C I think the square of that = =3Cbr /=3Ecoefficient multiplied by 100 should give the percentage contr= ibution of that =3Cbr /=3Eexcitation=2E However=2C sometimes this coeffi= cient is coming out as more than 1=2E =3Cbr /=3EWhat does it signify and= how can I handle such situations=3F=3Cbr /=3E=3Cbr /=3ERegards=3Cbr /=3E= Soumen Ghosh=3Cbr /=3E=3Cbr /=3ESoumen Ghosh=3Cbr /=3Esoumenrkmrc08*o*gm= ail=2Ecom=3Cbr /=3EIITB=2CIndia=3Cbr /=3E=3Cbr /=3E=3Cbr /=3E=3Cbr /=3E-= =3D This is automatically added to each message by the mailing script =3D= -=3Cbr /=3ETo recover the email address of the author of the message=2C = please change=3Cbr /=3Ethe strange characters on the top line to the =40= sign=2E You can also=3Cbr /=3Elook up the X-Original-From=3A line in th= e mail header=2E=3Cbr /=3E=3Cbr /=3EE-mail to subscribers=3A CHEMISTRY=40= ccl=2Enet or use=3A=3Cbr /=3E=A0=A0=A0=A0=A0 =3Ca href=3D=22http=3A//www= 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href=3D=22http=3A//server=2Eccl=2Enet/chemistry/announcements/conferen= ces/=22 target=3D=22l=22=3Ehttp=3A//server=2Eccl=2Enet/chemistry/announc= ements/conferences/=3C/a=3E=3Cbr /=3E=3Cbr /=3ESearch Messages=3A =3Ca h= ref=3D=22http=3A//www=2Eccl=2Enet/chemistry/searchccl/index=2Eshtml=22 t= arget=3D=22l=22=3Ehttp=3A//www=2Eccl=2Enet/chemistry/searchccl/index=2Es= html=3C/a=3E=3Cbr /=3E=3Cbr /=3EIf your mail bounces from CCL with 5=2E7= =2E1 error=2C check=3A=3Cbr /=3E=A0=A0=A0=A0=A0 =3Ca href=3D=22http=3A//= www=2Eccl=2Enet/spammers=2Etxt=22 target=3D=22l=22=3Ehttp=3A//www=2Eccl=2E= net/spammers=2Etxt=3C/a=3E=3Cbr /=3E=3Cbr /=3ERTFI=3A =3Ca href=3D=22htt= p=3A//www=2Eccl=2Enet/chemistry/aboutccl/instructions/=22 target=3D=22l=22= =3Ehttp=3A//www=2Eccl=2Enet/chemistry/aboutccl/instructions/=3C/a=3E=3Cb= r /=3E=3Cbr /=3E=3Cbr /=3E=3C/div=3E=3C/blockquote=3E--=3Cbr signature=3D= =22separator=22 /=3E --Boundary_(ID_KPfDgoLAAgCdGFSZVU5EOA)-- From owner-chemistry@ccl.net Tue Apr 2 15:02:00 2013 From: "Gabriel Aires Urquiza Carvalho urquizagabes{}gmail.com" To: CCL Subject: CCL:G: Electron Density cubic grid generation Message-Id: <-48513-130402144841-17150-lD6i6EqPRCgCdvB8ceIobQ(_)server.ccl.net> X-Original-From: "Gabriel Aires Urquiza Carvalho" Date: Tue, 2 Apr 2013 14:48:41 -0400 Sent to CCL by: "Gabriel Aires Urquiza Carvalho" [urquizagabes a gmail.com] Dear CCL subscribers, Is there any way I could get volumetric data of electron density in the form of a cubic voxelized grid? I have tried the gaussian "cubegen" utility but it doesn't neccessarily generates cubic grids, and I need those to be cubic because the other programs I'm using for my analysis can only cubic binary inputs and I'd rather not go through rewritting their code unless I really have to. It doesn't have to write the voxels in binary, I can convert them to a binary stream as an extra step in the process by writing a minor Fortran utility, I just need something to generate the voxels for me, in a cubic arrangement. Thanks in advance! Gabriel Aires Urquiza Carvalho urquizagabes(~)gmail.com Programa de Ps-Graduao em Qumica Departamento de Qumica Universidade Federal da Paraba - Brazil From owner-chemistry@ccl.net Tue Apr 2 16:23:01 2013 From: "Gabriel Aires Urquiza Carvalho gabrielcarvalho%quimica.ufpb.br" To: CCL Subject: CCL:G: Electron Density cubic grid generation Message-Id: <-48514-130402143757-11953-tG+6s6i+CvhtFEqHQcwAyg_._server.ccl.net> X-Original-From: "Gabriel Aires Urquiza Carvalho" Date: Tue, 2 Apr 2013 14:37:56 -0400 Sent to CCL by: "Gabriel Aires Urquiza Carvalho" [gabrielcarvalho**quimica.ufpb.br] Dear CCL subscribers, Is there any way I could get volumetric data of electron density in the form of a cubic voxelized grid? I have tried the gaussian "cubegen" utility but it doesn't neccessarily generates cubic grids, and I need those to be cubic because the other programs I'm using for my analysis can only cubic binary inputs and I'd rather not go through rewritting their code unless I really have to. It doesn't have to write the voxels in binary, I can convert them to a binary stream as an extra step in the process by writing a minor Fortran utility, I just need something to generate the voxels for me, in a cubic arrangement. Thanks in advance! Gabriel Aires Urquiza Carvalho gabrielcarvalho~~quimica.ufpb.br Programa de Ps-Graduao em Qumica Departamento de Qumica Universidade Federal da Paraba - Brazil From owner-chemistry@ccl.net Tue Apr 2 20:38:00 2013 From: "Hanneke Jansen johanna.jansen/./novartis.com" To: CCL Subject: CCL: Join TDT at the ACS meeting in New Orleans Message-Id: <-48515-130402195707-32307-GEcRoDcxk3esp/mdQRMMMQ() server.ccl.net> X-Original-From: "Hanneke Jansen" Date: Tue, 2 Apr 2013 19:57:06 -0400 Sent to CCL by: "Hanneke Jansen" [johanna.jansen::novartis.com] Update from Teach-Discover-Treat (TDT): join us in New Orleans! Networking Event & Award Presentation: Monday, April 8th from 5:30-7:30pm The District, 711 Tchoupitoulas Show your ACS badge for drinks & snacks Award Symposium: Wednesday, April 10th 1:30-5:35pm Morial Convention Center, Room 357 Summary: The first round of the TDT competition opened up 4 challenges for the community and a total of 6 submissions were received. The judging panel selected an overall winner and awarded 3 runner-up awards. The tutorials will be publicly available on www.teach-discover-treat.org at the time of the Award Symposium. Whats next: A second competition is being considered and we want to hear your comments regarding the first competition and your suggestions for a next one. Please join us at the networking event, the award symposium, the panel discussion after the symposium, or engage us through social media: http://www.teach-discover-treat.org/get-involved The TDT Steering Committee Hanneke Jansen, Rommie Amaro, Jane Tseng, Wendy Cornell