From owner-chemistry@ccl.net Thu Mar 31 00:09:00 2011 From: "Sobia Ahsan Halim sobia_halim[-]yahoo.com" To: CCL Subject: CCL: 3D chemical coordinates to 2D image Message-Id: <-44256-110330235217-5926-FWLMdzf50W7buyiUUMCtIg!=!server.ccl.net> X-Original-From: Sobia Ahsan Halim Content-Type: multipart/alternative; boundary="0-1567105149-1301543530=:20702" Date: Wed, 30 Mar 2011 20:52:10 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sobia Ahsan Halim [sobia_halim%a%yahoo.com] --0-1567105149-1301543530=:20702 Content-Type: text/plain; charset=us-ascii Hi Don You can use UCSF chimera. It is freely available and really makes very nice images. You can increase dpi of the images and get attractive images. http://www.cgl.ucsf.edu/chimera/ Hope it works for you Sobia. ________________________________ > From: Donald James Keidel dkeidel() emolecules.com To: "Halim, Sobia Ahsan " Sent: Wed, March 30, 2011 8:59:40 PM Subject: CCL: 3D chemical coordinates to 2D image Sent to CCL by: "Donald James Keidel" [dkeidel+*+emolecules.com] Hi, I am looking for an open source software or API that will allow me to convert 3D structures to 2D images (gif, png, jpg, etc.). I know I can use Marvin molconvert, but I am looking for an open source equivalent and could not find one searching the web. Any suggestion are welcome and much appreciated. Thank you Donhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-1567105149-1301543530=:20702 Content-Type: text/html; charset=us-ascii
Hi Don

You can use UCSF chimera. It is freely available and really makes
very nice images. You can increase dpi of the images and get attractive
images.

http://www.cgl.ucsf.edu/chimera/

Hope it works for you

Sobia.


From: Donald James Keidel dkeidel() emolecules.com <owner-chemistry[*]ccl.net>
To: "Halim, Sobia Ahsan " <sobia_halim[*]yahoo.com>
Sent: Wed, March 30, 2011 8:59:40 PM
Subject: CCL: 3D chemical coordinates to 2D image


Sent to CCL by: "Donald James Keidel" [dkeidel+*+emolecules.com]
Hi,

I am looking for an open source software or API that will allow me to convert 3D structures to 2D images (gif, png, jpg, etc.).  I know I can use Marvin molconvert, but I am looking for an open source equivalent and could not find one searching the web.  Any suggestion are welcome and much appreciated.

Thank you

Don



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--0-1567105149-1301543530=:20702-- From owner-chemistry@ccl.net Thu Mar 31 08:03:00 2011 From: "William F. Coleman wcoleman:+:wellesley.edu" To: CCL Subject: CCL: absolute hardness Message-Id: <-44257-110330232721-8091-ToDF8qd/JJIzbJl17rGD5w(0)server.ccl.net> X-Original-From: "William F. Coleman" Content-Type: multipart/alternative; boundary="--=_--23293be3.23293aab.c9b9a510" Date: Wed, 30 Mar 2011 23:27:12 -0400 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman : wellesley.edu] This is a multi-part message in MIME format. ----=_--23293be3.23293aab.c9b9a510 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit "CCL Subscribers" writes: >Dear all > > I need some information on the molecular absolute hardness in my >study, but I don't know how to calculate it and which data I need to >compute in gaussion 09. Therefore, I need a detail computational process, >formulas or examples on gaining the molecular absolute hardness. > Any help will be appreciated, I am looking forward to your timely >reply > > Sincerely yours > As defined by Pearson, absolute hardness is 1/2 the difference between the ionization energy and electron affinity of a substance, with the energy of the highest occupied molecular orbital being the negative of the ionization energy, and the energy of the lowest unoccupied molecular orbital being the negative of the electron affinity. So, the absolute hardness is half the difference between the HOMO and LUMO orbitals, usually expressed in eV. Hope this helps, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html http://www.flicksstuff.com/photos/pictures.html new galleries 12/23/2010 ----=_--23293be3.23293aab.c9b9a510 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>
"CCL Subscribers" <chemistry=40ccl.net> writes:
Dear all
    
    I need some information on the molecular a= bsolute hardness in my study, but I don't know how to calculate it and whic= h data I  need to compute in gaussion 09. Therefore, I need a detail c= omputational process, formulas or examples on gaining the molecular absolut= e hardness.
   Any help will be appreciated, I am looking forw= ard to your timely reply

   Sincerely yours


As defined by Pearson, absolute hardn= ess is 1/2 the difference between the ionization energy and electron affini= ty of a substance, with the energy of the highest occupied molecular orbita= l being the negative of the ionization energy, and the energy of the lowest= unoccupied molecular orbital being the negative of the electron affinity. =  So, the absolute hardness is half the difference between the HOMO and= LUMO orbitals, usually expressed in eV.

Hope this helps,

Flick


_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481



----=_--23293be3.23293aab.c9b9a510-- From owner-chemistry@ccl.net Thu Mar 31 08:38:00 2011 From: "Georg Lefkidis lefkidis ~~ physik.uni-kl.de" To: CCL Subject: CCL:G: Gaussian09 basis functions Message-Id: <-44258-110331031604-9402-6eJqrv2Hvck7ZfEz6szt+w..server.ccl.net> X-Original-From: "Georg Lefkidis" Date: Thu, 31 Mar 2011 03:16:02 -0400 Sent to CCL by: "Georg Lefkidis" [lefkidis[-]physik.uni-kl.de] Dear CCLers, I am trying to extract the exact wavefunction from Gaussian09 (SAC-CI calculations), and have some problems deciding what is what: namely 1) if the 5d (and 7f) keywords are given, then Gaussian uses pure functions. However these can be both pure cartesians (3dz2, dx2-y2, dx ,dy ,dz) and pure spherical harmonic ones (d0,d-1, d+1 etc.). From the output I would presume the second choice, since the AO are given names D-1, D+1 etc, however the density matrix (and other matrices in that respect) printed out IOP(3/33=1) is real-valued. Is it that the absolute values of the elements are printed, or am I missing something 2) in the excitations given in the SAC and SAC-CI sections for every state it is not indicated which electrons (alpha or/and beta) are excited. Of course knowing the multiplicity one can deduce a linear combination of singly excited Slater determinants, however the questions arise (i) are these coefficients CI coefficients or the amplitudes of the cummulative expansion still (I prisume they are CI expansions in the intermediate normalization, can someone confirm this?) and (ii) by the double excitations 12 20 13 45 am I write to presume that the first excitation 12->20 is a singlet excitation which couples to the second triplet excitation 13->45 ? At least this is what I understand from the SAC-CI guide of H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, and H. Nakai. Cheers George From owner-chemistry@ccl.net Thu Mar 31 09:12:00 2011 From: "Wojciech Kolodziejczyk dziecial]|[icnanotox.org" To: CCL Subject: CCL:G: Gaussian transition state Message-Id: <-44259-110331082708-8647-nG3Pwo15+Uxzf8UEA5/YBA[#]server.ccl.net> X-Original-From: Wojciech Kolodziejczyk Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 31 Mar 2011 14:27:02 +0200 MIME-Version: 1.0 Sent to CCL by: Wojciech Kolodziejczyk [dziecial]^[icnanotox.org] Hello everyone I have question. I am looking for rotational transtion states. In one case it finds different transition state than I need. I check all frequencies and I find one exactly as I need. How to make gaussian to find transition state using this frequency? Thank you for your help. Wojciech Kolodziejczyk From owner-chemistry@ccl.net Thu Mar 31 10:31:00 2011 From: "Delwar Hossain hossaind2004-#-yahoo.com" To: CCL Subject: CCL: absolute hardness Message-Id: <-44260-110331100825-2075-vZV5m8OWvZ4WXil7RPJhGg(_)server.ccl.net> X-Original-From: Delwar Hossain Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 31 Mar 2011 07:08:18 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Delwar Hossain [hossaind2004===yahoo.com] Calculation of hardness using HOMO and LUMO may not give reliable results. A nice article about hardness was published in Faraday Discussion Vol 135, 2007 page 151 . Please read also general discussion section. Another article, although it is relevant to cluster, may help you to understand in details about hardness: "Growth ability and stability indices of clusters" J. A. Alonso and M. J. Lopez, Journal of clusters sciences, Vol14, Number 1, Page 13-47. With regards, Delwar Hossain --- On Wed, 3/30/11, Kang Xiaohui huixiaokang328() 163.com wrote: > From: Kang Xiaohui huixiaokang328() 163.com > Subject: CCL: absolute hardness > To: "Hossain, Delwar " > Date: Wednesday, March 30, 2011, 9:16 PM > > Sent to CCL by: "Kang  Xiaohui" > [huixiaokang328!^!163.com] > Dear all >     >     I need some information on the molecular > absolute hardness in my study, but I don't know how to > calculate it and which data I  need to compute in > gaussion 09. Therefore, I need a detail computational > process, formulas or examples on gaining the molecular > absolute hardness. >     Any help will be appreciated, I am looking > forward to your timely reply > >     Sincerely yours > > > > -= This is automatically added to each message by the > mailing script =- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the *o* sign. You > can also> > E-mail to subscribers: CHEMISTRY*o*ccl.net > or use: >      > > E-mail to administrators: CHEMISTRY-REQUEST*o*ccl.net > or use >      >      >      > > > From owner-chemistry@ccl.net Thu Mar 31 16:17:01 2011 From: "Kshatresh Dutta Dubey kshatresh\a/gmail.com" To: CCL Subject: CCL:G: absolute hardness Message-Id: <-44261-110331090918-11531-B4jnB1a3r92AZNFFflyiRw**server.ccl.net> X-Original-From: Kshatresh Dutta Dubey Content-Type: multipart/alternative; boundary=0016363b879cb7c6d3049fc6ff86 Date: Thu, 31 Mar 2011 18:39:09 +0530 MIME-Version: 1.0 Sent to CCL by: Kshatresh Dutta Dubey [kshatresh[*]gmail.com] --0016363b879cb7c6d3049fc6ff86 Content-Type: text/plain; charset=ISO-8859-1 Dear Coleman, The absolute hardness of chemical species can be calculated simply by calculating HOMO-LUMO energy gap as stated by Parr and Pearson. You may find a lot of literature for this purpose. The calculation of HOMO-LUMO energy gap can be easily done with the help of Gaussian. On Thu, Mar 31, 2011 at 8:57 AM, William F. Coleman wcoleman:+:wellesley.edu wrote: > *"CCL Subscribers" writes:* > Dear all > > I need some information on the molecular absolute hardness in my study, > but I don't know how to calculate it and which data I need to compute in > gaussion 09. Therefore, I need a detail computational process, formulas or > examples on gaining the molecular absolute hardness. > Any help will be appreciated, I am looking forward to your timely reply > > Sincerely yours > > > As defined by Pearson, absolute hardness is 1/2 the difference between the > ionization energy and electron affinity of a substance, with the energy of > the highest occupied molecular orbital being the negative of the ionization > energy, and the energy of the lowest unoccupied molecular orbital being the > negative of the electron affinity. So, the absolute hardness is half the > difference between the HOMO and LUMO orbitals, usually expressed in eV. > > Hope this helps, > > Flick > > > _______________ > William F. Coleman > Professor of Chemistry > Wellesley College > Wellesley MA 02481 > > www.wellesley.edu/Chemistry/colemanw.html > http://www.flicksstuff.com/photos/pictures.html new galleries 12/23/2010 > > > -- ************************************************************************************************************************** Kshatresh Dutta Dubey Senior Research Fellow (SRF) Biophysics Unit, Department of Physics DDU Gorakhpur University --0016363b879cb7c6d3049fc6ff86 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Coleman,

=A0The absolute hardness of chemical = species can be calculated simply by calculating HOMO-LUMO energy gap as sta= ted by Parr and Pearson. You may find a lot of literature for this purpose.= The calculation of HOMO-LUMO energy gap can be easily done with the help o= f Gaussian.=A0

On Thu, Mar 31, 2011 at 8:57 AM, William F. = Coleman wcoleman:+:wellesley.edu <owner-chemistry= %a%ccl.net> wrote:
"CCL Subscribers" <chemistry%a%ccl.net> writes:
De= ar all
= =A0=A0=A0=A0
= =A0=A0=A0=A0I need some information on the molecular absolute hardness in m= y study, but I don't know how to calculate it and which data I =A0need = to compute in gaussion 09. Therefore, I need a detail computational process= , formulas or examples on gaining the molecular absolute hardness.
= =A0=A0=A0Any help will be appreciated, I am looking forward to your timely = reply

= =A0=A0=A0Sincerely yours


As defined by Pearson, absolute hardness is 1/2 the = difference between the ionization energy and electron affinity of a substan= ce, with the energy of the highest occupied molecular orbital being the neg= ative of the ionization energy, and the energy of the lowest unoccupied mol= ecular orbital being the negative of the electron affinity. =A0So, the abso= lute hardness is half the difference between the HOMO and LUMO orbitals, us= ually expressed in eV.

Hope this helps,

Flick


_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481






--
******= ***************************************************************************= *****************************************
Kshatresh Dutta Dubey
Senio= r Research Fellow (SRF)
Biophysics Unit,
Department of Physics
DDU Gorakhpur University

--0016363b879cb7c6d3049fc6ff86-- From owner-chemistry@ccl.net Thu Mar 31 19:45:00 2011 From: "Vlad vvv900]![anusf.anu.edu.au" To: CCL Subject: CCL: 3D chemical coordinates to 2D image Message-Id: <-44262-110331194402-10879-H4GfxyatwKBbp35/necG+g-#-server.ccl.net> X-Original-From: Vlad Content-transfer-encoding: 7BIT Content-type: text/html; CHARSET=US-ASCII Date: Fri, 01 Apr 2011 10:43:47 +1100 MIME-version: 1.0 Sent to CCL by: Vlad [vvv900[A]anusf.anu.edu.au] Hi Donald,

I suggest you to try
Jamberoo.

You have several options in Jamberoo.

1) You can create the jpeg or png image of your molecular scene.

2) For the high quality graphics you can create input file for the PovRay.

3) Finally, you can create a file in the VRML format and use it for creation of the 3D PDF documents.

Regards,
Vlad

>> From: Donald James Keidel dkeidel() emolecules.com
>> <owner-chemistry() ccl.net>
> To: "Halim, Sobia Ahsan " <sobia_halim() yahoo.com> Sent: Wed, March
> 30, 2011 8:59:40 PM Subject: CCL: 3D chemical coordinates to 2D
> image
>
>
> Sent to CCL by: "Donald James Keidel" [dkeidel+*+emolecules.com] Hi,
>
> I am looking for an open source software or API that will allow me
> to convert 3D structures to 2D images (gif, png, jpg, etc.). I know
> I can use Marvin molconvert, but I am looking for an open source
> equivalent and could not find one searching the web. Any suggestion
> are welcome and much appreciated.
>
> Thank you
>
> Donhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-1567105149-1301543530=:20702
From owner-chemistry@ccl.net Thu Mar 31 22:08:00 2011 From: "Guenter Grethe ggrethe[A]att.net" To: CCL Subject: CCL: Last reminder - abstract submission for CINF scholarships extended Message-Id: <-44263-110331214341-25040-URcHXv9sM5EJYwyJCPyRSw#server.ccl.net> X-Original-From: "Guenter Grethe" Date: Thu, 31 Mar 2011 21:43:39 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe(!)att.net] Please note: the deadline to submit short abstracts for the 2011 CINF scholarship awards has been extended to April 8, 2011 2011 CINF Scholarship for Scientific Excellence Sponsored by FIZ Chemie Berlin The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by FIZ Chemie Berlin is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to three scholarships valued at $1,000 each will be presented at the 242th ACS National Meeting in Denver, CO, August 28 September 1, 2011. Applicants must be enrolled at a certified college or university, and they will present a poster during the Welcoming Reception of the division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through PACS, the abstract submission system of ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe||att.net, that you are applying for a scholarship. Submit your abstract to http://abstracts.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract for CINF Scholarship for Scientific Excellence. The deadline for submitting an abstract to PACS is April 8, 2011. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by June30, 2010. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked Winner of FIZ Chemie-CINF Scholarship for Scientific Excellence at the poster session. Guenter Grethe