From owner-chemistry@ccl.net Wed Mar 23 01:46:00 2011 From: "neeraj misra neerajmisra^^hotmail.com" To: CCL Subject: CCL: electron transport Message-Id: <-44177-110323014438-9596-bQVNL7jnqiiDfdA/hUKhvg:+:server.ccl.net> X-Original-From: "neeraj misra" Date: Wed, 23 Mar 2011 01:44:36 -0400 Sent to CCL by: "neeraj misra" [neerajmisra(-)hotmail.com] Dear All, How to study the electron transport in a doped fullerene,, any free software ? I mean the bias dependent electron transmission and current. Thanks in advance NM From owner-chemistry@ccl.net Wed Mar 23 08:36:00 2011 From: "Roman Affentranger roman+/-douglasconnect.com" To: CCL Subject: CCL: OpenTox Series of Online Tutorials Message-Id: <-44178-110323075553-25531-PkAWw4B4jCRhVRzVEDNddQ]![server.ccl.net> X-Original-From: Roman Affentranger Content-Type: multipart/alternative; boundary=bcaec53f9069803131049f250a6c Date: Wed, 23 Mar 2011 12:55:45 +0100 MIME-Version: 1.0 Sent to CCL by: Roman Affentranger [roman#douglasconnect.com] --bcaec53f9069803131049f250a6c Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All: OpenTox is pleased to announce a series of online seminars and interactive tutorials on topics related to predictive toxicology using a virtual conferencing system supporting desktop sharing and voice. The tutorials are part of the EU FP7 project OpenTox (www.opentox.org), which aims at developing an interoperable open source predictive toxicology framework which may be used as an enabling platform for the creation of predictive toxicology applications. The first tutorial will be held Wednesday, 30 March, at 15:00 CET, and aiming at Java developers who want to learn how to build an OpenTox API compliant Web service (some acquaintance with Restlet, http://www.restlet.org, and basic knowledge of the OpenTox REST API, http://opentox.org/dev/apis/api-1.2, is necessary). Participation in these online events involves no registration fee. For more information, as well as to register, visit http://www.opentox.org/meet/opentoxonline. Best regards, Roman Affentranger -- Roman Affentranger PhD R&D Activity Coordinator Douglas Connect (OpenTox Coordinator) B=E4rmeggenweg 14 4314 Zeiningen Switzerland --bcaec53f9069803131049f250a6c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All:

OpenTox is pleased to announce a series of online seminars= and interactive tutorials on topics related to predictive toxicology using= a virtual conferencing system supporting desktop sharing and voice. The tu= torials are part of the EU FP7 project OpenTox (www.opentox.org), which aims at developing an interoperable ope= n source predictive toxicology framework=A0which may be used as an enabling= =A0platform for the creation of predictive toxicology applications.

The first tutorial will be held Wednesday, 30 March, at 15:00 CET, and aiming at Java developers=20 who want to learn how to build an OpenTox API compliant Web service=20 (some acquaintance with Restlet, http://www.restlet.org, and basic knowledge of the OpenTox = REST API, http://opentox.org/dev/apis/api-1.2, is=20 necessary).

Participation in these online events involves no registr= ation fee. For more information, as well as to register, visit http://www.open= tox.org/meet/opentoxonline.


Best regards,
Roman Affentranger


--
Roman Affentranger PhD
R&D Activit= y Coordinator
Douglas Connect (OpenTox Coordinator)
B=E4rmeggenweg 14
4314 Zeiningen
Switzerland --bcaec53f9069803131049f250a6c-- From owner-chemistry@ccl.net Wed Mar 23 09:11:00 2011 From: "Vaithy gct vaidees_208]-[rediff.com" To: CCL Subject: CCL:G: Unable to project occupied orbitals ! Message-Id: <-44179-110323012832-8109-ITTQdtb08NrjJge69yAzrA],[server.ccl.net> X-Original-From: "Vaithy gct" Date: Wed, 23 Mar 2011 01:28:30 -0400 Sent to CCL by: "Vaithy gct" [vaidees_208(~)rediff.com] My G03 job terminated with the following error message. Guess basis will be translated and rotated to current coordinates.Unable to project occupied orbitals !Error termination via Lnk1e in /usr/users/g03/l401.exe. I have used geom=allcheck and guess=read for reading the coordinates from the previous calculation. How to overcome this error. From owner-chemistry@ccl.net Wed Mar 23 09:46:01 2011 From: "pascal boulet pascal.boulet::univ-provence.fr" To: CCL Subject: CCL: electron transport Message-Id: <-44180-110323040802-7117-6sXkud2z1eAQSu4OJYRHSQ()server.ccl.net> X-Original-From: pascal boulet Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=ISO-8859-1 Date: Wed, 23 Mar 2011 09:07:52 +0100 MIME-Version: 1.0 Sent to CCL by: pascal boulet [pascal.boulet+*+univ-provence.fr]
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Hash: SHA1

Hello,

Maybe OpenMX is suitable for your needs.  It is free of charge.

http://www.openmx-square.org/

Pascal

Le 23/03/2011 06:44, neeraj misra neerajmisra^^hotmail.com a écrit :
> Sent to CCL by: "neeraj misra" [neerajmisra(-)hotmail.com]
>
> Dear All,
> How to study the electron transport in a doped fullerene,, any free software ? I mean the bias dependent electron transmission and current.
>
> Thanks in advance
> NM
>
>
>
>
>
>
>
>
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!!!!WARNING: my phone number has CHANGED!!!!

Dr. pascal Boulet, computational chemist
University of Aix-Marseille I
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From owner-chemistry@ccl.net Wed Mar 23 10:21:00 2011 From: "Morad El-Hendawy m80elhendawy]*[yahoo.com" To: CCL Subject: CCL: electron transport Message-Id: <-44181-110323043855-29526-1eylyLt+3Bdx8NrluE8rkw{=}server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-312200457-1300869526=:40055" Date: Wed, 23 Mar 2011 01:38:46 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy(!)yahoo.com] --0-312200457-1300869526=:40055 Content-Type: text/plain; charset=us-ascii As far as I know, there are two free programs: 1-Siesta is distributed freely for academics. It uses the combined DFT-NEGF to calculate the current, transmission, etc. http://www.icmab.es/siesta/Academic-License-Individuals 2-Huckel IV 3.0 can be used as well, but it uses thecombined Extended Huckel-NEGF to calculate the current, transmission, etc. http://nanohub.org/resources/2951 Regards, Morad ________________________________ > From: neeraj misra neerajmisra^^hotmail.com To: "El-Hendawy, Morad Metwally " Sent: Wed, March 23, 2011 5:44:36 AM Subject: CCL: electron transport Sent to CCL by: "neeraj misra" [neerajmisra(-)hotmail.com] Dear All, How to study the electron transport in a doped fullerene,, any free software ? I mean the bias dependent electron transmission and current. Thanks in advance NMhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-312200457-1300869526=:40055 Content-Type: text/html; charset=us-ascii
As far as I know, there are two free programs:

1-Siesta is distributed freely for academics. It uses the combined DFT-NEGF to calculate the current, transmission, etc.
http://www.icmab.es/siesta/Academic-License-Individuals

2-Huckel IV 3.0 can be used as well, but it uses thecombined Extended Huckel-NEGF to calculate the current, transmission, etc.
http://nanohub.org/resources/2951

Regards,
Morad
From: neeraj misra neerajmisra^^hotmail.com <owner-chemistry..ccl.net>
To: "El-Hendawy, Morad Metwally " <m80elhendawy..yahoo.com>
Sent: Wed, March 23, 2011 5:44:36 AM
Subject: CCL: electron transport


Sent to CCL by: "neeraj  misra" [neerajmisra(-)hotmail.com]

Dear All,
How to study the electron transport in a doped fullerene,, any free software ? I mean the bias dependent electron transmission and current.

Thanks in advance
NM



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--0-312200457-1300869526=:40055-- From owner-chemistry@ccl.net Wed Mar 23 10:56:00 2011 From: "Deskins, N Aaron nadeskins,WPI.EDU" To: CCL Subject: CCL: Correctly drawing aromatic compounds Message-Id: <-44182-110323085931-12175-sZ/TZLOmlwyZ9FwZObvHPQ===server.ccl.net> X-Original-From: "Deskins, N Aaron" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 23 Mar 2011 08:58:41 -0400 MIME-Version: 1.0 Sent to CCL by: "Deskins, N Aaron" [nadeskins*o*WPI.EDU] Hello all, I'm trying to draw (2-D) some aromatic compounds but can't seem to get them right. For instance, all the pictures of coronene I've seen show 12 C=C bonds (see for example en.wikipedia.org/wiki/File:Coronene_structure.png). But I tried making coronene in ChemSketch but it puts draws a structure with 10-11 C=C bonds depending on the order I put the benzene rings together. Same problem with pyrene. My drawings show 7 C=C bonds, while I believe it should have 8. More importantly, I'd like to figure out how many C=C bonds different large aromatic compounds have for a series of isodesmic reactions I'm interested in. Any ideas? Thank you, N. Aaron Deskins Assistant Professor Chemical Engineering Department Worcester Polytechnic Institute http://users.wpi.edu/~nadeskins From owner-chemistry@ccl.net Wed Mar 23 11:31:00 2011 From: "vihar vihgeo|*|chem.gla.ac.uk" To: CCL Subject: CCL: electron transport Message-Id: <-44183-110323100307-472-gK1ftkuwBwW0CU+N/IJaxg+/-server.ccl.net> X-Original-From: vihar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 Mar 2011 14:03:48 +0000 MIME-Version: 1.0 Sent to CCL by: vihar [vihgeo::chem.gla.ac.uk] Hi Neeraj, they are few free programs such as: Smeagol: http://www.smeagol.tcd.ie/ Siesta: http://www.icmab.es/siesta/ gDFTB: http://icode.eln.uniroma2.it/tools/simulators/gdftb Probably they are few more but all of them are similar. The commercials software is very nice and it can be downloaded from : http://quantumwise.com/ I hope that this information will be helpful for you. Regards, Vihar On 23/03/11 05:44, neeraj misra neerajmisra^^hotmail.com wrote: > Sent to CCL by: "neeraj misra" [neerajmisra(-)hotmail.com] > > Dear All, > How to study the electron transport in a doped fullerene,, any free software ? I mean the bias dependent electron transmission and current. > > Thanks in advance > NM> > From owner-chemistry@ccl.net Wed Mar 23 12:06:00 2011 From: "Michael Shokhen shokhen-,-mail.biu.ac.il" To: CCL Subject: CCL: search PDB databank by a fragment of amino acid sequence Message-Id: <-44184-110323112039-11861-HX2su8UDB0Lv7A0T9JAJIA:server.ccl.net> X-Original-From: "Michael Shokhen" Date: Wed, 23 Mar 2011 11:20:36 -0400 Sent to CCL by: "Michael Shokhen" [shokhen,+,mail.biu.ac.il] Dear colleagues, I have a peptide (10-15 amino acids). I would appreciate if anybody could address me to a software tool aimed at searching of the PDB databank for proteins containing this amino acid fragment. Thank you, Michael From owner-chemistry@ccl.net Wed Mar 23 12:41:00 2011 From: "Ted Dibble tsdibble]_[syr.edu" To: CCL Subject: CCL: Pressure dependence in reaction rate kinetics calculations Message-Id: <-44185-110323112851-19937-Va8hSlnRb3q68lcMh2n++Q#%#server.ccl.net> X-Original-From: "Ted Dibble" Date: Wed, 23 Mar 2011 11:28:45 -0400 Sent to CCL by: "Ted Dibble" [tsdibble{:}syr.edu] The answers to your questions can be found in most textbooks. Start with a physical chemistry textbook for the basics, and look in a graduate kinetics textbook for fuller explanations. Look for the Lindeman or Lindeman-Hinshelwood mechanism. The three-body reaction is the net reaction including the third body, e.g.: ClO + NO2 + M = ClONO2 + M where M is the third body, and [M] corresponds to the total concentration of gas phase species. This is in contrast to the elementary reactions: ClO + NO2 -> ClONO2* ClONO2* -> ClO + NO2 ClONO2* + M -> ClONO2 + M Please note: TST applies where there is a Boltzmann distribution of energy, which corresponds to the high-pressure limit rather than the low-pressure limit. To calculate rate constants versus pressure, see the UNIMOL package, made available at http://www.frad.t.u-tokyo.ac.jp/miyoshi/ssumes/index.html Good luck! Theodore S. Dibble Chemistry Department SUNY-Environmental Science and Forestry 1 Forestry Drive Syracuse, NY 13210 (315) 470-6596 (315) 470-6856 (fax) http://www.esf.edu/chemistry/faculty/dibble.htm > "RD Miles rdmsgl!A!gmail.com" wrote: > > Sent to CCL by: RD Miles [rdmsgl^gmail.com] > --0015173fe52af75fe4049efe5381 > Content-Type: text/plain; charset=ISO-8859-1 > > I have been working on calculating reaction rate constants at the low > pressure limit using TST type methodologies. However, I need to understand > how to transition into calculations for high pressure systems. > > Could you recommend any references that deal specifically with the pressure > dependence of reaction rate constants, and how it is addressed in > computational chemistry? > > Questions I have are: > > - Can TST based methods be adapted to high pressure systems? > - What is meant by "3 body reactions" in many kinetics mechanisms? > - What is meant by the pressure dependence "fall-off" in some reaction > rate constant descriptions? > > Any help on this subject would be greatly appreciated. > > -RD From owner-chemistry@ccl.net Wed Mar 23 13:16:00 2011 From: "Miguel Quiliano Meza rifaximina===gmail.com" To: CCL Subject: CCL: Carbocation calculations, an approach Message-Id: <-44186-110322181548-25722-d5OLZeI7SYbVDAvxxrcthg(~)server.ccl.net> X-Original-From: Miguel Quiliano Meza Content-Type: multipart/alternative; boundary=bcaec51ddac199b2aa049f199419 Date: Tue, 22 Mar 2011 18:15:22 -0400 MIME-Version: 1.0 Sent to CCL by: Miguel Quiliano Meza [rifaximina]-[gmail.com] --bcaec51ddac199b2aa049f199419 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear colleagues. My apologies if I disturb you with a couple of questions. I have never worked with carbocations, but now I have a good case to start I would like to answer some chemicals questions using computational chemistry, but unfortunately I obtained rare energy values. Could you tell me please, what should I do? or what kind of chemistry model should I use?. I want to answer some questions: *Which reaction is the most probable to happen? *What energy is necessary to reach transitional compounds before obtained products? I have performed some calculations using this: # opt=3Dtight freq b3lyp/6-31+g scf=3Dqc with the respect spin multiplicit= y, but my calculations told me that compound A is most stable than B, besides compound C is most stable than A and B. I stopped here because I think that is impossible. A: is a carbocation very similar in structure like B B is not a carbocation C is a carbocation product of A+B Final energy for A =3D -195.60813 Final energy for B =3D -195.27260 Final energy for C =3D -390.92315 Thank in advance for your time. Maybe if you don=B4t have time please recom= men me one good paper or good tutorial. Best regards. Miguel. --bcaec51ddac199b2aa049f199419 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear colleagues.

My apologies if I disturb you with a couple of ques= tions.

I have never worked with carbocations, but now I have a good = case to start

I would like to answer some chemicals questions using = computational chemistry, but unfortunately I obtained rare energy values.
Could you tell me please, what should I do? or what kind of chemistry m= odel should I use?.

I want to answer some questions:

*Which = reaction is the most probable to happen?
*What energy is necessary to reach transitional compounds before obtained products?

I have perfo= rmed some calculations using this:

# opt=3Dtight freq b3lyp/6-31+g scf=3Dqc=A0 with the respect spin multiplici= ty, but my calculations told me that compound A is most stable than B,=20 besides compound C is most stable than A and B. I stopped here because I think that is=20 impossible.

A: is a carbocation very similar in structure like B
= =A0B is not a carbocation
C is a carbocation product of A+B

Final= energy for A =3D -195.60813

Final energy for B =3D -195.27260

Final energy for C =3D -390.92315

Thank in advance for your time. Ma= ybe if you don=B4t have time please recommen me one good paper or good tuto= rial.

Best regards.
Miguel.


--bcaec51ddac199b2aa049f199419-- From owner-chemistry@ccl.net Wed Mar 23 13:51:00 2011 From: "Vincent Leroux vincent.leroux]^[loria.fr" To: CCL Subject: CCL: search PDB databank by a fragment of amino acid sequence Message-Id: <-44187-110323134501-22525-Rvzsb2Isti43yk1KUovmsA_._server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 Mar 2011 18:44:49 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux:+:loria.fr] http://www.pdb.org/pdb/search/advSearch.do?st=SequenceQuery Le 23/03/11 16:20, Michael Shokhen shokhen-,-mail.biu.ac.il a écrit : > Sent to CCL by: "Michael Shokhen" [shokhen,+,mail.biu.ac.il] > Dear colleagues, > > I have a peptide (10-15 amino acids). > I would appreciate if anybody could address me to a software tool > aimed at searching of the PDB databank for proteins containing > this amino acid fragment. > > Thank you, > Michael> > > From owner-chemistry@ccl.net Wed Mar 23 14:26:01 2011 From: "Radoslaw Kaminski rkaminski.rk*gmail.com" To: CCL Subject: CCL: d-orbital populations for a transition metal Message-Id: <-44188-110323135948-3599-Gv0dSkACF+VUjYZbmvNKmA _ server.ccl.net> X-Original-From: "Radoslaw Kaminski" Date: Wed, 23 Mar 2011 13:59:45 -0400 Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk^^gmail.com] Hi All, I have calculated an electronic structure of my Ni complex using ADF package. I have also collected and fully analyzed the X-ray-derived electron density distribution based on the Bader's QTAIM applying the Hansen-Coppens formalism. From experiment I have obtained the d-orbital populations of Ni atoms in respect to some given coordinate system. Is it possible somehow to extract information of d-orbital populations from calculations? I was thinking that it could be related to Mulliken population scheme or NPA. How it would be related to my chosen coordinate system? Appreciate help very much. Regards, Radek From owner-chemistry@ccl.net Wed Mar 23 15:00:00 2011 From: "Wolf Ihlenfeldt wdi++xemistry.com" To: CCL Subject: CCL: Correctly drawing aromatic compounds Message-Id: <-44189-110323123747-20298-pn+ZGqAgxEFDqIVJSDK/rA]=[server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=000e0cd5c70e608e9f049f28fa90 Date: Wed, 23 Mar 2011 17:37:34 +0100 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi[]xemistry.com] --000e0cd5c70e608e9f049f28fa90 Content-Type: text/plain; charset=UTF-8 Why don't you just merge cyclohexane rings and then later change the bond orders if your drawing software cannot figure it out on its own? Or you retrieve the compound data in some format without Kekule bond orders, and use a chemistry toolkit which can resolve it for your operations. In Cactvs - www.xemistry.com, free for academic users) you can easily do something like cactvs>ens create c2c7c1c6c5c4c3c1c(c2)ccc3ccc4ccc5ccc6cc7 ens0 cactvs>ens bonds ens0 {arobond doublebond} count 12 cactvs> On Wed, Mar 23, 2011 at 1:58 PM, Deskins, N Aaron nadeskins,WPI.EDU < owner-chemistry|-|ccl.net> wrote: > > Sent to CCL by: "Deskins, N Aaron" [nadeskins*o*WPI.EDU] > Hello all, > > I'm trying to draw (2-D) some aromatic compounds but can't seem to get > them right. For instance, all the pictures of coronene I've seen show 12 C=C > bonds (see for example en.wikipedia.org/wiki/File:Coronene_structure.png). > But I tried making coronene in ChemSketch but it puts draws a structure with > 10-11 C=C bonds depending on the order I put the benzene rings together. > Same problem with pyrene. My drawings show 7 C=C bonds, while I believe it > should have 8. > > More importantly, I'd like to figure out how many C=C bonds different > large aromatic compounds have for a series of isodesmic reactions I'm > interested in. > > Any ideas? > > Thank you, > > N. Aaron Deskins > Assistant Professor > Chemical Engineering Department > Worcester Polytechnic Institute > http://users.wpi.edu/~nadeskins> > > -- Wolf-D. Ihlenfeldt, Xemistry GmbH www.xemistry.com --000e0cd5c70e608e9f049f28fa90 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Why don't you just merge cyclohexane rings and then later change th= e bond orders if your drawing software cannot figure it out on its own?
=
Or you retrieve the compound data in some format without Kekule bond or= ders, and use a chemistry toolkit which can resolve it for your operations.=

In Cactvs - www.xemistry.com, f= ree for academic users) you can easily do something like

cactvs>e= ns create c2c7c1c6c5c4c3c1c(c2)ccc3ccc4ccc5ccc6cc7
ens0
cactvs>ens= bonds ens0 {arobond doublebond} count
12
cactvs>





On Wed, = Mar 23, 2011 at 1:58 PM, Deskins, N Aaron nadeskins,WPI.EDU <owner-chemistry|-|ccl.net> wrote:

Sent to CCL by: "Deskins, N Aaron" [nadeskins*o*WPI.EDU]
Hello all,

=C2=A0I'm trying to draw (2-D) some aromatic compounds but can't s= eem to get them right. For instance, all the pictures of coronene I've = seen show 12 C=3DC bonds (see for example =C2=A0en.wikipedia.or= g/wiki/File:Coronene_structure.png). But I tried making coronene in Che= mSketch but it puts draws a structure with 10-11 C=3DC bonds depending on t= he order I put the benzene rings together. Same problem with pyrene. My dra= wings show 7 C=3DC bonds, while I believe it should have 8.

=C2=A0More importantly, I'd like to figure out how many C=3DC bonds di= fferent large aromatic compounds have for a series of isodesmic reactions I= 'm interested in.

=C2=A0Any ideas?

=C2=A0Thank you,

N. Aaron Deskins
Assistant Professor
Chemical Engineering Department
Worcester Polytechnic Institute
http://user= s.wpi.edu/~nadeskins



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--
Wolf-D. Ihlenfeldt, Xem= istry GmbH
www.xem= istry.com

--000e0cd5c70e608e9f049f28fa90-- From owner-chemistry@ccl.net Wed Mar 23 15:36:00 2011 From: "Marco Milanesio marco.milanesio[a]mfn.unipmn.it" To: CCL Subject: CCL: School on combining computing tools with diffraction and spectroscopy Message-Id: <-44190-110323120818-25870-hx4LfQuH6hy8o2OB5JKhww=-=server.ccl.net> X-Original-From: "Marco Milanesio" Date: Wed, 23 Mar 2011 12:08:15 -0400 Sent to CCL by: "Marco Milanesio" [marco.milanesio[#]mfn.unipmn.it] Dear members of CCL, We remind that the deadline for registering to the AIC School 2011 school on combined diffraction, spectroscopy and computational tool, to be held in Camerino (Italy) on July 4-8, 2011 is approaching. The school deals with the use of molecular mechanics and first principle computational tools in combination with experimental methods (X-ray and elecron diffraction, PDF methods, NMR, X-ray absorption, vibrational spectroscopies). The school aims at showing how combined experimental and computational tools can be used to treat samples too complicated for a technique alone Practical sessions, including montecarlo simulation and an introduction to the use of CRYSTAL software will be held. IN PARTICULAR NOTE THAT the deadline for bursary request for the AICS2011 school is very close (Friday, March 25th). Please find all the information on the website: www.unicam.it/geologia/aics2011. Thanks a lot and best regards Marco Milanesio and Mchele Zema, chairs From owner-chemistry@ccl.net Wed Mar 23 16:11:01 2011 From: "Dr David N Haney haney^edusoft-lc.com" To: CCL Subject: CCL: Correctly drawing aromatic compounds Message-Id: <-44191-110323131823-28025-AwYmHlWwywaDr900rWo5Hw=server.ccl.net> X-Original-From: Dr David N Haney Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 23 Mar 2011 10:18:04 -0700 Mime-Version: 1.0 Sent to CCL by: Dr David N Haney [haney~~edusoft-lc.com] Prof Deskins, Actually the Fisher-type or Kekule-type projections of aromatic compounds that contain double bonds are a representation of a struction that is very misleading. In these structures all the bonds are of identical length (slightly longer than an alkene double bond) and thus such stuctures are best represented by circles (or a line and dashes). The best way to identify a bond type is by the bond length. In this case the bond would be classified as a partial double bond. If you want to give it a value it would be 1.5 not 2. On Wed, Mar 23, 2011 at 08:58:41AM -0400, Deskins, N Aaron nadeskins,WPI.EDU wrote: > > Sent to CCL by: "Deskins, N Aaron" [nadeskins*o*WPI.EDU] > Hello all, > > I'm trying to draw (2-D) some aromatic compounds but can't seem to get them right. For instance, all the pictures of coronene I've seen show 12 C=C bonds (see for example en.wikipedia.org/wiki/File:Coronene_structure.png). But I tried making coronene in ChemSketch but it puts draws a structure with 10-11 C=C bonds depending on the order I put the benzene rings together. Same problem with pyrene. My drawings show 7 C=C bonds, while I believe it should have 8. > > More importantly, I'd like to figure out how many C=C bonds different large aromatic compounds have for a series of isodesmic reactions I'm interested in. > > Any ideas? > > Thank you, > > N. Aaron Deskins > Assistant Professor > Chemical Engineering Department > Worcester Polytechnic Institute > http://users.wpi.edu/~nadeskins> -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney{:}edusoft-lc.com # ################# ##################### From owner-chemistry@ccl.net Wed Mar 23 16:45:01 2011 From: "Marcin Feder Marcin.Feder*adamed.com.pl" To: CCL Subject: CCL: ODP: search PDB databank by a fragment of amino acid sequence Message-Id: <-44192-110323151149-9275-Y1mcJdjh87nID/ukXR2+og^-^server.ccl.net> X-Original-From: Marcin Feder Content-Language: pl-PL Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-2" Date: Wed, 23 Mar 2011 20:11:29 +0100 MIME-Version: 1.0 Sent to CCL by: Marcin Feder [Marcin.Feder%x%adamed.com.pl] Pieñków Email: mailto:Marcin.Feder(!)adamed.com.pl Dear Michael, you can use regular BLAST for this purpouse i.e. the one at http://blast.ncbi.nlm.nih.gov/Blast.cgi . Just select the "protein blast" as a program to use and set database to "Protein Data Bank proteins (PDB)". Hope this helps, Marcin Feder ________________________________________ Od: owner-chemistry+marcin.feder==adamed.com.pl(!)ccl.net [owner-chemistry+marcin.feder==adamed.com.pl(!)ccl.net] w imieniu Michael Shokhen shokhen-,-mail.biu.ac.il [owner-chemistry(!)ccl.net] Wys³ano: 23 marca 2011 16:20 Do: Marcin Feder Temat: CCL: search PDB databank by a fragment of amino acid sequence Sent to CCL by: "Michael Shokhen" [shokhen,+,mail.biu.ac.il] Dear colleagues, I have a peptide (10-15 amino acids). I would appreciate if anybody could address me to a software tool aimed at searching of the PDB databank for proteins containing this amino acid fragment. Thank you, Michaelhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtis a limited company registered in England and Wales. Registered number: Registration No. ###### Registered office: ###### Registered Address , Pieñków, This message (and any associated files) is intended only for the use of the individual or entity to which it is addressed and may contain information that is confidential, subject to copyright or constitutes a trade secret. If you are not the intended recipient you are hereby notified that any dissemination, copying or distribution of this message, or files associated with this message, is strictly prohibited. If you have received this message in error, please notify us immediately by replying to the message and deleting it from your computer. Messages sent to and from us may be monitored. Internet communications cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. Therefore, we do not accept responsibility for any errors or omissions that are present in this message, or any attachment, that have arisen as a result of e-mail transmission. If verification is required, please request a hard-copy version. Any views or opinions presented are solely those of the author and do not necessarily represent those of the company. From owner-chemistry@ccl.net Wed Mar 23 17:21:00 2011 From: "Pedro Silva pedros.:.ufp.edu.pt" To: CCL Subject: CCL:G: Carbocation calculations, an approach Message-Id: <-44193-110323160800-30348-oZBUyPv8/vM20EafaGSO5A\a/server.ccl.net> X-Original-From: Pedro Silva Content-Type: multipart/alternative; boundary=0016e6475664d2b234049f2be868 Date: Wed, 23 Mar 2011 20:07:25 +0000 MIME-Version: 1.0 Sent to CCL by: Pedro Silva [pedros_-_ufp.edu.pt] --0016e6475664d2b234049f2be868 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Your reaction is: A+B -> C Therefore the reaction energy is: Energy(C) -Energy(A+B), which (neglecting BSSE) is equal to energy (C) -(energy (a) + energy (b) ) =3D -390.92315 - (-195.60813 + (-195.27260) ) =3D -0.04242 hartree =3D -26.6 kcal.mol-1 "Exploring Chemistry with electronic structure Methods" is a good book to start understanding computational chemistry. It used to be distributed alon= g with Gaussian, so probably there is a copy somewhere in your lab :-) Pedro S. On Tue, Mar 22, 2011 at 10:15 PM, Miguel Quiliano Meza rifaximina=3D=3D=3D gmail.com wrote: > Dear colleagues.y(C) > > My apologies if I disturb you with a couple of questions. > > I have never worked with carbocations, but now I have a good case to star= t > > I would like to answer some chemicals questions using computational > chemistry, but unfortunately I obtained rare energy values. > > Could you tell me please, what should I do? or what kind of chemistry mod= el > should I use?. > > I want to answer some questions: > > *Which reaction is the most probable to happen? > *What energy is necessary to reach transitional compounds before obtained > products? > > I have performed some calculations using this: > > # opt=3Dtight freq b3lyp/6-31+g scf=3Dqc with the respect spin multiplic= ity, > but my calculations told me that compound A is most stable than B, beside= s > compound C is most stable than A and B. I stopped here because I think th= at > is impossible. > > A: is a carbocation very similar in structure like B > B is not a carbocation > C is a carbocation product of A+B > > Final energy for A =3D -195.60813 > > Final energy for B =3D -195.27260 > > Final energy for C =3D -390.92315 > > Thank in advance for your time. Maybe if you don=B4t have time please > recommen me one good paper or good tutorial. > > Best regards. > Miguel. > > > --=20 Pedro J. Silva Associate Professor Universidade Fernando Pessoa Porto - Portugal http://www2.ufp.pt/~pedros/science/science.htm --0016e6475664d2b234049f2be868 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Your reaction is:

A+B -> C

Therefore the reaction energy i= s:

Energy(C) -Energy(A+B), which (neglecting BSSE) is equal to
<= br>energy (C) -(energy (a) + energy (b) ) =3D

-390.92315 - (-195.608= 13 + (-195.27260) ) =3D -0.04242 hartree =3D -26.6 kcal.mol-1


"Exploring Chemistry with electronic structure Methods" i= s a good book to start understanding computational chemistry. It used to be= distributed along with Gaussian, so probably there is a copy somewhere in = your lab :-)

Pedro S.

On Tue, Mar 22, 2011 at 10:1= 5 PM, Miguel Quiliano Meza rifaximina=3D=3D=3D= gmail.com <owner-chemistry[*]ccl.net> wrote:
Dear colleagues.y= (C)

My apologies if I disturb you with a couple of questions.
I have never worked with carbocations, but now I have a good case to start<= br>
I would like to answer some chemicals questions using computational = chemistry, but unfortunately I obtained rare energy values.

Could you tell me please, what should I do? or what kind of chemistry m= odel should I use?.

I want to answer some questions:

*Which = reaction is the most probable to happen?
*What energy is necessary to reach transitional compounds before obtained products?

I have perfo= rmed some calculations using this:

# opt=3Dtight freq b3lyp/6-31+g scf=3Dqc=A0 with the respect spin multiplici= ty, but my calculations told me that compound A is most stable than B,=20 besides compound C is most stable than A and B. I stopped here because I think that is=20 impossible.

A: is a carbocation very similar in structure like B
= =A0B is not a carbocation
C is a carbocation product of A+B

Final= energy for A =3D -195.60813

Final energy for B =3D -195.27260

Final energy for C =3D -390.92315

Thank in advance for your time. Ma= ybe if you don=B4t have time please recommen me one good paper or good tuto= rial.

Best regards.
Miguel.





--
Pedro J. SilvaAssociate Professor
Universidade Fernando Pessoa
Porto - Portugalhttp://www2.ufp.pt/~pedros/science/science.htm
--0016e6475664d2b234049f2be868-- From owner-chemistry@ccl.net Wed Mar 23 17:55:00 2011 From: "Deskins, N Aaron nadeskins]-[WPI.EDU" To: CCL Subject: CCL: Correctly drawing aromatic compounds Message-Id: <-44194-110323165803-13176-+pru4QUvyy939xBuOOOiAQ=server.ccl.net> X-Original-From: "Deskins, N Aaron" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Wed, 23 Mar 2011 16:57:36 -0400 MIME-Version: 1.0 Sent to CCL by: "Deskins, N Aaron" [nadeskins---WPI.EDU] Thank you all for your suggestions. I’m looking into other software (ChemDraw) that may do a better job drawing some of these aromatics. But a more fundamental question is how do you predict the number of double bonds? I don’t want to have to assume that a particular program is drawing the structure right, unless absolutely necessary. Much better is to determine the number of C=C bonds myself (as mentioned in my first email, I want to run some isodesmic reactions on these). Coronene and other small aromatics are easy because there are plenty of references on these structures. But I’d like to look at other large compounds for which there is likely little data available. Someone must have some theory/method to determining the ideal number of double bonds in an aromatic structure. Any more ideas? N. Aaron Deskins Assistant Professor Chemical Engineering Department Worcester Polytechnic Institute http://users.wpi.edu/~nadeskins From owner-chemistry@ccl.net Wed Mar 23 20:45:00 2011 From: "Jason D Acchioli jdacchio|*|gmail.com" To: CCL Subject: CCL: Correctly drawing aromatic compounds Message-Id: <-44195-110323204327-733-Jk4LJqnQ/mUw6F1yBxONZw*_*server.ccl.net> X-Original-From: "Jason D'Acchioli" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Wed, 23 Mar 2011 19:43:14 -0500 Mime-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: "Jason D'Acchioli" [jdacchio###gmail.com] Aaron, It seems to me like the best way to approach your problem is from a simple Lewis-structure perspective. Perhaps I'm being naive--colleagues, please correct me if I'm mistaken--but even for a structure like coronene, you can predict double bonds with pen and paper. Are you using coronene to model larger "sheets" or extended nanostructures? Be well, Jason On Mar 23, 2011, at 3:57 PM, Deskins, N Aaron nadeskins]-[WPI.EDU wrote: > > Sent to CCL by: "Deskins, N Aaron" [nadeskins---WPI.EDU] > Thank you all for your suggestions. I’m looking into other software (ChemDraw) that may do a better job drawing some of these aromatics. > > But a more fundamental question is how do you predict the number of double bonds? I don’t want to have to assume that a particular program is drawing the structure right, unless absolutely necessary. Much better is to determine the number of C=C bonds myself (as mentioned in my first email, I want to run some isodesmic reactions on these). Coronene and other small aromatics are easy because there are plenty of references on these structures. But I’d like to look at other large compounds for which there is likely little data available. Someone must have some theory/method to determining the ideal number of double bonds in an aromatic structure. > > Any more ideas? > > N. Aaron Deskins > Assistant Professor > Chemical Engineering Department > Worcester Polytechnic Institute > http://users.wpi.edu/~nadeskins> > ******************************************* Jason D'Acchioli Assistant Professor of Chemistry University of Wisconsin-Stevens Point 2001 Fourth Avenue Stevens Point, WI 54481 http://chemdac.uwsp.edu From owner-chemistry@ccl.net Wed Mar 23 21:38:00 2011 From: "Nuno A. G. Bandeira nuno.bandeira()ist.utl.pt" To: CCL Subject: CCL: d-orbital populations for a transition metal Message-Id: <-44196-110323153946-3286-NjblqZL+k7zjQU36+ZF/sA|*|server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 Mar 2011 20:39:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira###ist.utl.pt] On 23-03-2011 18:59, Radoslaw Kaminski rkaminski.rk*gmail.com wrote: > Is it possible somehow to extract information of d-orbital populations from calculations? I was thinking that it could be related to Mulliken population scheme or NPA. How it would be related to my chosen coordinate system? I don't understand your problem. You can extract d orbital populations > from any ADF calculation. -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN --