From owner-chemistry@ccl.net Thu Mar 26 02:43:01 2009 From: "Jerome Kieffer jerome.Kieffer++terre-adelie.org" To: CCL Subject: CCL:G: Spin density MOPAC/Gabedit Message-Id: <-38932-090325182041-23244-jkhM/P79VAYS13fnbA61fA:-:server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Wed, 25 Mar 2009 22:20:06 +0100 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer . terre-adelie.org] Dear CCLers, I am wondering how to visualize the spin density/localization of a radical after a MOPAC2007 calculation with Gabedit ... I was already able display it using =ABcubes=BB with gaussian'03 but not with MOPAC2007. Thank you for your help, With my best regards --=20 J=E9r=F4me KIEFFER =20 http://www.terre-adelie.org From owner-chemistry@ccl.net Thu Mar 26 05:23:01 2009 From: "may abdelghani may01dz]=[yahoo.fr" To: CCL Subject: CCL: dynamic molecular calculation and fluxional behavior Message-Id: <-38933-090325145639-27595-6WBRAxGtVDVbvQBq6r8HcA-*-server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-1946176564-1238003787=:22115" Date: Wed, 25 Mar 2009 17:56:27 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz=-=yahoo.fr] --0-1946176564-1238003787=:22115 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear CCL=E2=80=99ers How the dynamic molecular calculation, can help me to treat the fluxional behavior of some fluxional molecules. What a= bout an NMR calculation? I go away from=C2=A0 any transition states search, beca= use is a very difficult task. Thanks=20 May abdelghani =C2=A0 =0A=0A=0A --0-1946176564-1238003787=:22115 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
<= link rel=3D"colorSchemeMapping" href=3D"file:///C:%5CDOCUME%7E1%5CADMINI%7E= 1%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_colorschememapping.xml"> Normal 0 21 false false false FR X-NONE AR-SA MicrosoftInternetExplorer4

Dear CCL=E2=80=99ers

How the dynamic molecular calcu= lation, can help me to treat the fluxional behavior of some fluxional molecules. What a= bout an NMR calculation? I go away from  any transition states search, beca= use is a very difficult task.

Thanks

May abdelghani

 


=0A=0A=0A=0A --0-1946176564-1238003787=:22115-- From owner-chemistry@ccl.net Thu Mar 26 07:14:01 2009 From: "veronica ferraresi veroferraresi..gmail.com" To: CCL Subject: CCL:G: L101 error Message-Id: <-38934-090326071110-10283-ZYTHldgG3BcBP2czlrZ18Q*server.ccl.net> X-Original-From: veronica ferraresi Content-Type: multipart/alternative; boundary=0016364eed54944cc1046603ab0a Date: Thu, 26 Mar 2009 08:10:56 -0300 MIME-Version: 1.0 Sent to CCL by: veronica ferraresi [veroferraresi__gmail.com] --0016364eed54944cc1046603ab0a Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, if it says "End of file in ZSymb.", you should add a blank line after your geometry specifications, at the end of your input. Ver=F3nica Ferraresi Curotto CEQUINOR-UNLP 2009/3/25 Babak Khalili khalili.babak**gmail.com > > Sent to CCL by: "Babak Khalili" [khalili.babak-,-gmail.com] > Dear all, > How can I solve the problem of L101 (Reads title and molecule > specification), in Gaussian 98 to run it. > Thanks, > Babak > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --0016364eed54944cc1046603ab0a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, if it says=A0 "End of file in ZSymb.", you should add a blank= line after your geometry specifications, at the end of your input.
Ver= =F3nica Ferraresi Curotto
CEQUINOR-UNLP

2009/3/25 Babak Khalili khalili.babak**gmail= .com <o= wner-chemistry=ccl.net>

Sent to CCL by: "Babak =A0Khalili" [khalili.babak-,-gmail.com]
Dear all,
How can I solve the problem of L101 (Reads title and molecule specification= ), in Gaussian 98 to run it.
Thanks,
Babak



-=3D This is automatically added to each message by the mailing script =3D-=
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--0016364eed54944cc1046603ab0a-- From owner-chemistry@ccl.net Thu Mar 26 07:49:00 2009 From: "allouche allouche .. lasim.univ-lyon1.fr" To: CCL Subject: CCL:G: Spin density MOPAC/Gabedit Message-Id: <-38935-090326043838-499-lpRQCuaQAG0QhC413CUmYA-*-server.ccl.net> X-Original-From: allouche Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 26 Mar 2009 08:58:13 +0100 MIME-Version: 1.0 Sent to CCL by: allouche [allouche===lasim.univ-lyon1.fr] Jerome Kieffer jerome.Kieffer++terre-adelie.org a écrit : >Sent to CCL by: Jerome Kieffer [jerome.Kieffer . terre-adelie.org] >Dear CCLers, > >I am wondering how to visualize the spin density/localization of a >radical after a MOPAC2007 calculation with Gabedit ... > >I was already able display it using «cubes» with gaussian'03 but not >with MOPAC2007. > >Thank you for your help, >With my best regards > > Hello, Try the developpement version of Gabedit (2.1.18). You can download this version from : http://sites.google.com/site/allouchear/Home/gabedit/download Best regards, -- Abdul-Rahman ALLOUCHE Tel : + (33) (0) 472431929 Fax : + (33) (0) 472431507 Email : allouche[#]lasim.univ-lyon1.fr Web : http://sites.google.com/site/allouchear/ From owner-chemistry@ccl.net Thu Mar 26 08:47:01 2009 From: "M. A. A. Ibrahim m.ibrahim1982(_)yahoo.com" To: CCL Subject: CCL:G: HEPES Solvent Specification Message-Id: <-38936-090326084537-31518-d3jRwebDKMPwr3DYJMgDWQ\a/server.ccl.net> X-Original-From: "M. A. A. Ibrahim" Date: Thu, 26 Mar 2009 08:45:33 -0400 Sent to CCL by: "M. A. A. Ibrahim" [m.ibrahim1982-*-yahoo.com] Dear CCLers I am going to do some calculations on a reation happened in HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, Organic Buffer) using SCRF and this solvent is not specified in Gaussian. So, I have to specifiy it. The problem is that I searched for its parametes (Dielectric constant, solvent radius and solvent density) and unfortunately I couldn't find any data. I have searched in some physical properties books and databases. Is there anybody can support me by HEPES's properties or direct me to a useful database or book? Thanks in advance. M. Ibrahim From owner-chemistry@ccl.net Thu Mar 26 10:11:01 2009 From: "Andreas Klamt klamt|-|cosmologic.de" To: CCL Subject: CCL:G: HEPES Solvent Specification Message-Id: <-38937-090326100022-12863-ad+1GNE3jQhWx4rW1xOZcQ/a\server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 26 Mar 2009 15:00:07 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt%cosmologic.de] Dear Ibrahim, you will never be able to model such a complicated solvent with so many different rather specific interactions by an SCRF model, even if you knew epsilon and density. COSMO-RS would be able to do that at least partially , treating solute and solvent on the same quantum chemical level, followed by a statistical thermodynamics of interacting surfaces. For further info see our website or read my papers on COSMO-RS. Best regards Andreas M. A. A. Ibrahim m.ibrahim1982(_)yahoo.com schrieb: > Sent to CCL by: "M. A. A. Ibrahim" [m.ibrahim1982-*-yahoo.com] > Dear CCLers > I am going to do some calculations on a reation happened in HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, Organic Buffer) using SCRF and this solvent is not specified in Gaussian. So, I have to specifiy it. The problem is that I searched for its parametes (Dielectric constant, solvent radius and solvent density) and unfortunately I couldn't find any data. I have searched in some physical properties books and databases. > Is there anybody can support me by HEPES's properties or direct me to a useful database or book? > Thanks in advance. > M. Ibrahim> > > > > -- -------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt[-]cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------- Please note our COSMO-RS Symposium in 2009 (For details see: http://www.cosmologic.de/Symposium/symposium.html) From owner-chemistry@ccl.net Thu Mar 26 13:00:00 2009 From: "Kikuo Harigaya harigaya : gmail.com" To: CCL Subject: CCL: symposium in ICCMSE Message-Id: <-38938-090326084444-31427-quo7FZ6FaL50Sd0rrjeG4Q%%server.ccl.net> X-Original-From: Kikuo Harigaya Content-Type: multipart/alternative; boundary=00151750eeba2d2a94046604fab8 Date: Thu, 26 Mar 2009 21:44:29 +0900 MIME-Version: 1.0 Sent to CCL by: Kikuo Harigaya [harigaya#,#gmail.com] --00151750eeba2d2a94046604fab8 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit The short circular can be found at: http://staff.aist.go.jp/k.harigaya/doc/short%20circular.pdf International Symposium "From Open-Shell Conjugated Molecules to Graphene: Theory and Experiment" International symposium on electronic properties in graphene, nanographene, and open-shell conjugated systems, will be held in the conference: "Seventh International Conference of Computational Methods in Sciences and Engineering" (http://www.iccmse.org/) at Hotel Rodos Palace, Rodos, Crete, Greece. The conference period will be September 29 - October 4, 2009. Submission of the short abstract is welcome for interested persons. See the details at the Web site: http://www.iccmse.org/. Scope "Graphene" - new carbonaceous material - is distinguished from conventional electronic systems such as graphite due to its exceptional features, e.g., a large magnetic moment around the zigzag edges and massless Dirac fermion, stimulating development of future electronic/spintronic devices. Several unique features of graphene are closely connected with the "open-shell character", which originates in the "instability of chemical bonds" in pi-conjugated system with unconventional spin states and strongly correlates with the topology of pi-electron array, especially aromatic sextet formation. This symposium focuses on recent hot topics regarding unique physical and chemical properties derived from pseudo and real spins in pi-conjugated compounds, toward collaboration between theory, computational modeling and experiment. A wide range of compounds from small conjugated/aromatic molecules and inorganic metal complexes to nano- and large-size graphenes will be covered, and origin of the open-shell character as well as functional properties such as electron conductivity, optical and magnetic properties will be concentrated as important domains in the symposium. Organizers Kikuo Harigaya, AIST; Masayoshi Nakano, Osaka University; Takashi Kubo, Osaka University Contact Kikuo Harigaya, AIST; Tel: 029-861-5151; FAX: 029-861-5375; E-mail: k.harigaya .. aist.go.jp -- Dr. Kikuo Harigaya Address: Nanotechnology Research Institute, AIST, Tsukuba 305-8568, Japan TEL: +81-29-861-5151, FAX: +81-29-861-5375 URL: http://staff.aist.go.jp/k.harigaya/ --00151750eeba2d2a94046604fab8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable The short circular can be found at:
http://staff.aist.go.= jp/k.harigaya/doc/short%20circular.pdf
I=
nternational Symposium "From Open-Shell Conjugated Molecules to

Graphene: Theory and Experiment"

International symposium on ele=
ctronic properties in graphene,
nanographene, and open-shell conjugated =
systems, will be held in the
conference: "Seventh International Con=
ference of Computational Methods

in Sciences and Engineering" (http://www.iccmse.org/) at Hotel Rodos
Palace, Rodos=
, Crete, Greece. The conference period will be September 29
- October 4,=
 2009. Submission of the short abstract is welcome for

interested persons. See the details at the Web site: http://www.iccmse.org/.

Scope
=
"Graphene" - new carbonaceous material - is distinguished from
conventional electronic systems such as graphite due to its exceptional
=
features, e.g., a large magnetic moment around the zigzag edges and
mass=
less Dirac fermion, stimulating development of future
electronic/spintro=
nic devices. Several unique features of graphene are

closely connected with the "open-shell character", which originat=
es in
the "instability of chemical bonds" in pi-conjugated sys=
tem with
unconventional spin states and strongly correlates with the top=
ology of

pi-electron array, especially aromatic sextet formation. This symposium
=
focuses on recent hot topics regarding unique physical and chemical
prop=
erties derived from pseudo and real spins in pi-conjugated compounds,

toward collaboration between theory, computational modeling and
experime=
nt. A wide range of compounds from small conjugated/aromatic
molecules a=
nd inorganic metal complexes to nano- and large-size
graphenes will be c=
overed, and origin of the open-shell character as

well as functional properties such as electron conductivity, optical andmagnetic properties will be concentrated as important domains in the
sy=
mposium.

Organizers
Kikuo Harigaya, AIST; Masayoshi Nakano, Osaka=
 University; Takashi Kubo,

Osaka University

Contact
Kikuo Harigaya, AIST; Tel: 029-861-5151;=
 FAX: 029-861-5375; E-mail:
k.harigaya .. aist.go.jp

--

Dr. Kikuo Harigaya
Address: Nanotechnology Res= earch Institute,
AIST, Tsukuba 305-8568, Japan
TEL: +81-29-861-5151, = FAX: +81-29-861-5375
URL: http://staff.aist.go.jp/k.harigaya/
--00151750eeba2d2a94046604fab8-- From owner-chemistry@ccl.net Thu Mar 26 13:35:00 2009 From: "Yan pemryan]|[yahoo.cn" To: CCL Subject: CCL: Dangling bond saturating code? Message-Id: <-38939-090326104631-32344-0O1aswGTABT4NzJmNpMu6A- -server.ccl.net> X-Original-From: Yan Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary="Boundary-00=_xh4yJYdZhyNWCPP" Date: Thu, 26 Mar 2009 21:51:38 +0800 MIME-Version: 1.0 Sent to CCL by: Yan [pemryan++yahoo.cn] --Boundary-00=_xh4yJYdZhyNWCPP Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear CCL users, Is there any dangling bond saturating code available ? I've googled but woth no luck. Thank you any information or advices. Yan -- Ren, Yan | Tel: +8610-8264-8102 Institute of Physics, Chinese Academy of Sciences, Beijing, China --Boundary-00=_xh4yJYdZhyNWCPP Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear CCL users,


Is there any dangling bond saturating code available ?
I've googled but woth no luck.


Thank you any information or advices.


Yan
--
Ren, Yan | Tel: +8610-8264-8102
Institute of Physics, Chinese Academy of Sciences, Beijing, China


--Boundary-00=_xh4yJYdZhyNWCPP-- __________________________________________________ 8O?lW"2aQE;"3,4sH]A?Cb7QSJOd? http://cn.mail.yahoo.com From owner-chemistry@ccl.net Thu Mar 26 14:12:00 2009 From: "Philippe Carbonniere philippe.carbonniere%x%univ-pau.fr" To: CCL Subject: CCL: ICCMSE 2009. sympsium : computational aspects of the modelling of vibrational properties Message-Id: <-38940-090326132611-31747-yMrb+8NexAltLQVtnXpigA]^[server.ccl.net> X-Original-From: Philippe Carbonniere Content-Type: multipart/alternative; boundary="------------080209090402020907050809" Date: Thu, 26 Mar 2009 18:23:41 +0100 MIME-Version: 1.0 Sent to CCL by: Philippe Carbonniere [philippe.carbonniere_._univ-pau.fr] This is a multi-part message in MIME format. --------------080209090402020907050809 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit *_Title:_ * *Computational aspects of the modelling of vibrational properties of gases, liquids and solids* *_ Organizer_s: _Dr. Philippe Carbonniere_ and _Prof. Claude Pouchan_, IPREM, Institut Pluridisciplinaire en Environnement et Materiaux, Groupe de Chimie Theorique, Technopole d'Helioparc, Universite de Pau et des Pays de l'Adour, Pau, France, _Prof. Mauro Causa'_, Dipartimento di Chimica "Paolo Corradini", Universita' degli Studi di Napoli Federico II, Via Cintia, 80126 Napoli, Italia * *E-mail: * *Enquiries and contributions to philippe.carbonniere**univ-pau.fr , claude.pouchan**univ-pau.fr , mauro.causa**unina.it * *_Scope and Topics:_ * * * *Vibrational spectroscopy is a particularly powerful tool for non-destructive characterisation of molecular systems. Besides routine analysis in a wide range of domains (food science, archaeology, astrophysics, medicine), numerous applications in molecular science, such as speciation, conformational analysis, molecular design and reactivity monitoring, can be based on the modelling of vibrational effects. In recent years computational chemistry provides powerful tools for the modelling of such properties in the gas, liquid and solid phase although anharmonicity, resonances, environmental and dynamic effects render the problem non-trivial. Several computational aspects will be emphasised in the present symposium: the quality of the potential electronic surface, time-dependent and time-independent approaches to the study of vibration, the treatment of the condensed phases (solvent, surfaces and bulk), the computation of intensities and possible ways to overcome actual limitations due to the size of the treated systems. The performance of modern methods will be critically reviewed and their relative merit.* -- Philippe Carbonnière, Maître de conférence Institut Pluridisciplinaire de Recherche en Environnement et Matériaux (IPREM, UMR5254) Laboratoire de Chimie Physique (LCP) F-64000 Pau Tel : 00 33 5 59 40 78 58 Fax : 00 33 5 59 40 78 62 --------------080209090402020907050809 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit

Title: Computational aspects of the modelling of vibrational properties of gases, liquids and solids

Organizers: Dr. Philippe Carbonniere and Prof. Claude Pouchan, IPREM, Institut Pluridisciplinaire en Environnement et Materiaux, Groupe de Chimie Theorique, Technopole d’Helioparc, Universite de Pau et des Pays de l’Adour, Pau, France, Prof. Mauro Causa', Dipartimento di Chimica "Paolo Corradini", Universita' degli Studi di Napoli Federico II, Via Cintia, 80126 Napoli, Italia 
 

E-mail: Enquiries and contributions to philippe.carbonniere**univ-pau.fr, claude.pouchan**univ-pau.fr,  mauro.causa**unina.it
 

Scope and Topics:

 

Vibrational spectroscopy is a particularly powerful tool for non-destructive characterisation of molecular systems. Besides routine analysis in a wide range of domains (food science, archaeology, astrophysics, medicine), numerous applications in molecular science, such as speciation, conformational analysis, molecular design and reactivity monitoring, can be based on the modelling of vibrational effects.

In recent years computational chemistry provides powerful tools for the modelling of such properties in the gas, liquid and solid phase although anharmonicity, resonances, environmental and dynamic effects render the problem non-trivial.

Several computational aspects will be emphasised in the present symposium: the quality of the potential electronic surface, time-dependent and time-independent approaches to the study of vibration, the treatment of the condensed phases (solvent, surfaces and bulk), the computation of intensities and possible ways to overcome actual limitations due to the size of the treated systems.

The performance of modern methods will be critically reviewed and their relative merit. 
-- 
Philippe Carbonnière, Maître de conférence
Institut Pluridisciplinaire de Recherche en Environnement et Matériaux (IPREM, UMR5254)
Laboratoire de Chimie Physique (LCP)
F-64000 Pau

Tel  : 00 33 5 59 40 78 58
Fax : 00 33 5 59 40 78 62
--------------080209090402020907050809-- From owner-chemistry@ccl.net Thu Mar 26 14:44:00 2009 From: "Philippe Carbonniere philippe.carbonniere%x%univ-pau.fr" To: CCL Subject: CCL: ICCMSE 2009 (29/09-03/10, rodos, greece). symposium : Computational aspects of the modelling of vibrational properties Message-Id: <-38941-090326133605-4473-yOKo9hHDmiGySfoE5RpwRQ\a/server.ccl.net> X-Original-From: Philippe Carbonniere Content-Type: multipart/alternative; boundary="------------070302030303060109000101" Date: Thu, 26 Mar 2009 18:33:29 +0100 MIME-Version: 1.0 Sent to CCL by: Philippe Carbonniere [philippe.carbonniere!^!univ-pau.fr] This is a multi-part message in MIME format. --------------070302030303060109000101 Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 8bit *_Title:_ * *Computational aspects of the modelling of vibrational properties of gases, liquids and solids* *_ Organizer_s: _Dr. Philippe Carbonniere_ and _Prof. Claude Pouchan_, IPREM, Institut Pluridisciplinaire en Environnement et Materiaux, Groupe de Chimie Theorique, Technopole d'Helioparc, Universite de Pau et des Pays de l'Adour, Pau, France, _Prof. Mauro Causa'_, Dipartimento di Chimica "Paolo Corradini", Universita' degli Studi di Napoli Federico II, Via Cintia, 80126 Napoli, Italia * *E-mail: * *Enquiries and contributions to philippe.carbonniere*univ-pau.fr , claude.pouchan*univ-pau.fr , mauro.causa*unina.it * *_Scope and Topics:_ * * * *Vibrational spectroscopy is a particularly powerful tool for non-destructive characterisation of molecular systems. Besides routine analysis in a wide range of domains (food science, archaeology, astrophysics, medicine), numerous applications in molecular science, such as speciation, conformational analysis, molecular design and reactivity monitoring, can be based on the modelling of vibrational effects. In recent years computational chemistry provides powerful tools for the modelling of such properties in the gas, liquid and solid phase although anharmonicity, resonances, environmental and dynamic effects render the problem non-trivial. Several computational aspects will be emphasised in the present symposium: the quality of the potential electronic surface, time-dependent and time-independent approaches to the study of vibration, the treatment of the condensed phases (solvent, surfaces and bulk), the computation of intensities and possible ways to overcome actual limitations due to the size of the treated systems. The performance of modern methods will be critically reviewed and their relative merit.* -- Philippe Carbonnière, Maître de conférence Institut Pluridisciplinaire de Recherche en Environnement et Matériaux (IPREM, UMR5254) Laboratoire de Chimie Physique (LCP) F-64000 Pau Tel : 00 33 5 59 40 78 58 Fax : 00 33 5 59 40 78 62 --------------070302030303060109000101 Content-Type: text/html; charset=ISO-8859-15 Content-Transfer-Encoding: 8bit

Title: Computational aspects of the modelling of vibrational properties of gases, liquids and solids

Organizers: Dr. Philippe Carbonniere and Prof. Claude Pouchan, IPREM, Institut Pluridisciplinaire en Environnement et Materiaux, Groupe de Chimie Theorique, Technopole d’Helioparc, Universite de Pau et des Pays de l’Adour, Pau, France, Prof. Mauro Causa', Dipartimento di Chimica "Paolo Corradini", Universita' degli Studi di Napoli Federico II, Via Cintia, 80126 Napoli, Italia 
 

E-mail: Enquiries and contributions to philippe.carbonniere*univ-pau.fr, claude.pouchan*univ-pau.fr,  mauro.causa*unina.it
 

Scope and Topics:

 

Vibrational spectroscopy is a particularly powerful tool for non-destructive characterisation of molecular systems. Besides routine analysis in a wide range of domains (food science, archaeology, astrophysics, medicine), numerous applications in molecular science, such as speciation, conformational analysis, molecular design and reactivity monitoring, can be based on the modelling of vibrational effects.

In recent years computational chemistry provides powerful tools for the modelling of such properties in the gas, liquid and solid phase although anharmonicity, resonances, environmental and dynamic effects render the problem non-trivial.

Several computational aspects will be emphasised in the present symposium: the quality of the potential electronic surface, time-dependent and time-independent approaches to the study of vibration, the treatment of the condensed phases (solvent, surfaces and bulk), the computation of intensities and possible ways to overcome actual limitations due to the size of the treated systems.

The performance of modern methods will be critically reviewed and their relative merit. 
-- 
Philippe Carbonnière, Maître de conférence
Institut Pluridisciplinaire de Recherche en Environnement et Matériaux (IPREM, UMR5254)
Laboratoire de Chimie Physique (LCP)
F-64000 Pau

Tel  : 00 33 5 59 40 78 58
Fax : 00 33 5 59 40 78 62
--------------070302030303060109000101-- From owner-chemistry@ccl.net Thu Mar 26 15:20:01 2009 From: "Stephen.Garrison+*+srnl.doe.gov" To: CCL Subject: CCL:G: omp_set_num_threads error Message-Id: <-38942-090326142320-9498-YlFieNXJrc2T5kex/YFVSw : server.ccl.net> X-Original-From: Stephen.Garrison],[srnl.doe.gov Content-Type: multipart/alternative; boundary="=_alternative 0064A02285257585_=" Date: Thu, 26 Mar 2009 14:19:03 -0400 MIME-Version: 1.0 Sent to CCL by: Stephen.Garrison\a/srnl.doe.gov This is a multipart message in MIME format. --=_alternative 0064A02285257585_= Content-Type: text/plain; charset="US-ASCII" Could someone tell me why I am getting the following error when I try to run a "nprocshared=8" Gaussian/G03 job on a dual-CPU quad-core (8 cores total) machine? omp_set_num_threads value (8) is invalid FYI: An "nprocshared=4" job runs just fine. Also, 'mpstat -P ALL' reports 8 CPUs/cores. Thank you. -- Stephen L. Garrison, Ph.D. Senior Engineer Engineering Modeling and Simulation Savannah River National Laboratory Savannah River Site 773-42A, Room 181 Aiken, SC 29808 803-725-2404 Stephen.Garrison:SRNL.doe.gov --=_alternative 0064A02285257585_= Content-Type: text/html; charset="US-ASCII"
Could someone tell me why I am getting the following error when I try to run a "nprocshared=8" Gaussian/G03 job on a dual-CPU quad-core (8 cores total) machine?

        omp_set_num_threads value (8) is invalid

FYI: An "nprocshared=4" job runs just fine. Also, 'mpstat -P ALL' reports 8 CPUs/cores.

Thank you.

--
Stephen L. Garrison, Ph.D.
Senior Engineer
Engineering Modeling and Simulation
Savannah River National Laboratory
Savannah River Site
773-42A, Room 181
Aiken, SC 29808
803-725-2404
Stephen.Garrison:SRNL.doe.gov
 --=_alternative 0064A02285257585_=-- From owner-chemistry@ccl.net Thu Mar 26 15:54:01 2009 From: "Babak Khalili khalili.babak__gmail.com" To: CCL Subject: CCL:G: L101 error Message-Id: <-38943-090326100117-12968-ZThP2BQfYlJGtkpeJ/XzLA{}server.ccl.net> X-Original-From: Babak Khalili Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 26 Mar 2009 16:33:52 +0430 MIME-Version: 1.0 Sent to CCL by: Babak Khalili [khalili.babak*gmail.com] Dear Veronica Thanks for your reply. The main problem is "LP" symbol in geometry specifications which is appeared due to lone electron pair formation in e.g. (-OH) and /or (-HN2). The Chem 3D makes that but the Gaussian can't recognize it. Surly omitting the lone e-pair makes my results to be invaluable. It will be your great kind if you lead me. Regads, Babak On 3/26/09, veronica ferraresi veroferraresi..gmail.com wrote: > Hi, if it says "End of file in ZSymb.", you should add a blank line afte= r > your geometry specifications, at the end of your input. > Ver=F3nica Ferraresi Curotto > CEQUINOR-UNLP > > 2009/3/25 Babak Khalili khalili.babak**gmail.com > >> >> Sent to CCL by: "Babak Khalili" [khalili.babak-,-gmail.com] >> Dear all, >> How can I solve the problem of L101 (Reads title and molecule >> specification), in Gaussian 98 to run it. >> Thanks, >> Babak >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D-> >> >> > From owner-chemistry@ccl.net Thu Mar 26 16:29:01 2009 From: "John McKelvey jmmckel]![gmail.com" To: CCL Subject: CCL: TDDFT/RPA B matrix Message-Id: <-38944-090326154634-14542-GNMRUcyRUaIRAk0WnAy9kw:+:server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=000e0cd2146cd4bb8204660ade2a Date: Thu, 26 Mar 2009 15:46:21 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel,,gmail.com] --000e0cd2146cd4bb8204660ade2a Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Folks, In RPA and TDDFT the A matrix is the same as a CIS matrix, and the B matrix is referred to a de-excitation matrix. The latter makes sense when you look compare some of the terms in each matrix. The A matrix is also referred to as a linear response. I have heard the B matrix referred to as being related to a magnetic related issue (ring currents, maybe.) I would be happy to get people's more comprehensive physical pictures of the B matrix, and if "defined" physical pictures for the A+B, and A-B matrices. Regards, John McKelvey --000e0cd2146cd4bb8204660ade2a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Folks,

In RPA and TDDFT the A matrix is the same as a CIS matrix, an= d the B matrix is referred to a de-excitation matrix.=A0 The latter makes s= ense when you look compare some of the terms in each matrix.=A0 The A matri= x is also referred to as a linear response.=A0 I have heard the B matrix re= ferred to as being related to a magnetic related issue (ring currents, mayb= e.)

I would be happy to get people's more comprehensive physical pictur= es of the B matrix, and if "defined" physical pictures for the A+= B, and A-B matrices.

Regards,

John McKelvey
--000e0cd2146cd4bb8204660ade2a-- From owner-chemistry@ccl.net Thu Mar 26 18:39:00 2009 From: "David Hose Anthrax_brothers,hotmail.com" To: CCL Subject: CCL:G: HEPES Solvent Specification Message-Id: <-38945-090326183241-2396-1dQQruvhX9oH8YpCgNXf7Q{:}server.ccl.net> X-Original-From: "David Hose" Date: Thu, 26 Mar 2009 18:32:37 -0400 Sent to CCL by: "David Hose" [Anthrax_brothers^hotmail.com] HEPES is an organic compound that is commonly added to aqueous systems to control the pH (a pH buffer). Typically it is used for biological applications where the pH needs to be controlled within the physiological pH range (6.4 - 7.2). These buffer solutions are typically in the 100 mM concentration range. Therefore as a first pass, I would just model the reaction/system you are interested in water and therefore use the Gaussian default values. Of course PCM are implicit solvation models, therefore specific solvent - solute interactions (e.g. hydrogen bonding) will not be taken into account. So if important, you might want to consider using an explicit/implicit solvation approach. btw, the addition of a buffer to the aqueous system will have an effect upon the ionic strength of the system (ca 100 mM) what you might want to consider (probably a minimal effect). IEFPCM solvation model in Gaussian can be used to specific the ionic strength (see the manual). Furthermore, if you are using HEPES then there is a good chance you are looking at biological or medicinal compounds, so you might have to consider if the compounds of interested are ionised at the pH of the buffer. Regards, Dave. -- Sent to CCL by: "M. A. A. Ibrahim" [m.ibrahim1982-*-yahoo.com] Dear CCLers I am going to do some calculations on a reation happened in HEPES (4-(2-hydroxyethyl)-1- piperazineethanesulfonic acid, Organic Buffer) using SCRF and this solvent is not specified in Gaussian. So, I have to specifiy it. The problem is that I searched for its parametes (Dielectric constant, solvent radius and solvent density) and unfortunately I couldn't find any data. I have searched in some physical properties books and databases. Is there anybody can support me by HEPES's properties or direct me to a useful database or book? Thanks in advance. M. Ibrahim From owner-chemistry@ccl.net Thu Mar 26 19:14:00 2009 From: "David Hose Anthrax_brothers!=!hotmail.com" To: CCL Subject: CCL:G: omp_set_num_threads error Message-Id: <-38946-090326183752-3166-Z5aO9c0AjjmDEDWTgx5RBw(!)server.ccl.net> X-Original-From: "David Hose" Date: Thu, 26 Mar 2009 18:37:49 -0400 Sent to CCL by: "David Hose" [Anthrax_brothers(_)hotmail.com] Stephen, I'm guessing that you are using a pre-compiled windows binary? As I understand it, the binary has been compiled to support up to 4 processors. If you want to run a calculation on all 8 cores then you'll have to get the source code and compile it yourself. Regards, Dave. -- Could someone tell me why I am getting the following error when I try to run a "nprocshared=8" Gaussian/G03 job on a dual-CPU quad-core (8 cores total) machine? omp_set_num_threads value (8) is invalid FYI: An "nprocshared=4" job runs just fine. Also, 'mpstat -P ALL' reports 8 CPUs/cores. Thank you. -- Stephen L. Garrison, Ph.D. Senior Engineer Engineering Modeling and Simulation Savannah River National Laboratory Savannah River Site 773-42A, Room 181 Aiken, SC 29808 803-725-2404 Stephen.Garrison],[SRNL.doe.gov From owner-chemistry@ccl.net Thu Mar 26 23:01:01 2009 From: "Lingyun Wang leohhq(~)sohu.com" To: CCL Subject: CCL: getting DCCM by Amber Message-Id: <-38947-090326222810-3161-2K6MI2y5FnJK2RVgDNskvA+*+server.ccl.net> X-Original-From: "Lingyun Wang" Date: Thu, 26 Mar 2009 22:28:06 -0400 Sent to CCL by: "Lingyun Wang" [leohhq]![sohu.com] Dear CCL users Recently I am trapped in how to get the dynamical cross-correlation map (DCCM). The DCCM was represented in many papers such as J.AM.CHEM.SOC.2006,128,8992-8993. But how can I get the DCCM from the trajectories of a protein MD simulation? Is it the ptraj program of AMBER suite that I can use for cross-correlated atomic fluctuations? What will I get by the ptraj command matrix correl? Thank you very much! Lingyun Wang