From owner-chemistry@ccl.net Wed Aug 17 00:39:01 2011 From: "A Anglea a.anglea90]|[yahoo.com" To: CCL Subject: CCL:G: MOPAC output - please help Message-Id: <-45268-110816210834-2922-5vKyCiQ684sKE273CwxLpQ- -server.ccl.net> X-Original-From: "A Anglea" Date: Tue, 16 Aug 2011 21:08:31 -0400 Sent to CCL by: "A Anglea" [a.anglea90 . yahoo.com] Dear all I am looking for calculation the molar volume and solvent-surface-accessible- area of my molecule. I used MOPAC code to get the data and want to ensure I understood the output correctly because it is the first time for me to use this code: COSMO area: is the solvent-surface-accessible-area, isn't it? COSMO volume: is the molar volume, isn't it? The output is slightly confused, how can I calculation the "interaction enthalpy" from the output? I want to compare the data with high level using Gaussian, VOLUME keyword gives me the molar volume, is there any recommendation regards the theoretical method to be used? How can I calculate the solvent-surface-accessible-area using Gaussian? What is the direct relation between the molar volume and solvent-surface- accessible-area? I would be grateful if you helped me by any mean Cheers From owner-chemistry@ccl.net Wed Aug 17 01:52:00 2011 From: "psavita:-:crlindia.com" To: CCL Subject: CCL:G: Molecular modeling of ZnO/PP composite Message-Id: <-45269-110817012052-701-Qw0ZmFsuct8Yi8MCTfh6OQ a server.ccl.net> X-Original-From: psavita a crlindia.com Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Wed, 17 Aug 2011 10:57:03 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: psavita[#]crlindia.com
Hello Daniel,

I think of two distinct methods to simulat= e optical properties of materials.
One is a quantum mechanical treatment= using time dependent Schroedinger
equation whereby you compute excited = states and transition probabilities. Being
compute intensive, this metho= d is usable for small clusters or molecules.
Gaussian or any such softwa= re may be able to do this.

The other is a classical treatment using = Maxwell equations.  It is possible
to simulate the spectral respons= e in a dielectric medium of choice. The softwares
to accomplish this are= DDSCAT and FDTD, both may be available in the
open source.

Best= wishes,

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



-----owner-chemistry+psavita= =3D=3Dcrlindia.com]_[ccl.net wrote: -----

To: "Pundlik, Savita Sunil " <psa= vita]_[crlindia.com>
From: "Daniel Glossman-Mitnik dglossman]-[gmai= l.com" <owner-chemistry]_[ccl.net>
Sent by: owner-chemistry+psavita=3D=3Dcrlindia.com]_[ccl.net
Date: 08/= 16/2011 10:10PM
Subject: CCL: Molecular modeling of ZnO/PP composite
=
Dear netters:

I have been asked to try to simulate t= he optical properties of ZnO nanoparticles of varying size
in a m= atrix of polypropilene (PP). I would like to know if you can give me hints = about the
=0D
appropiate methods and/or software to accomplish thi= s task, and also about any reference to
previous work in the subj= ect.

Thanks in advance. Best regards,
Daniel
=0D

***************************= ***************************************************************************= *********
Dr. Daniel Glossman-Mitnik
Centro de Investigaci=F3n en Mat= eriales Avanzados, SC
Departamento de Simulaci=F3n Computacional y Model= ado Molecular
=0DMiguel de Cervantes 120 - Comp. Ind. Chihuahua - Chihua= hua, Chih 31109, Mexico
Phone: +52 614 4391151   Secretary/FAX= : +52 614 4391130    Lab: +52 614 4394805
E-mail:  daniel.glossman . cimav.edu.mx          = dglossman . gmail.com
=0DWWW:  http://www.cimav.edu.mx/cv/daniel.glossman
&n= bsp;             http://blogs.cimav.edu.mx/daniel.glossman
= =0D************************************************************************= ***************************************
=0D
=0D=0D

=
= From owner-chemistry@ccl.net Wed Aug 17 03:26:00 2011 From: "Andreas Klamt klamt],[cosmologic.de" To: CCL Subject: CCL:G: MOPAC output - please help Message-Id: <-45270-110817020605-7217-lYDZr3o/cwEl91QUN2Cxdw : server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 17 Aug 2011 08:06:04 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt . cosmologic.de] Dear Anglea, I am Andreas Klamt, and I wrote the COSMO part of MOPAC. I am afraid that there is no simple answer to your question: - First one needs to know which version of MOPAC you are using, since the cavity defintions have changed during the past 15 years. I newer versions (with closed cavity) you can interpret as the solvent-excluded surface, according to the defintions given under "solvent-accessible area" in wikepedia. It is the surface which can be touched by the roliing ball, where in COSMO always a ball of radius 1.3 Angstrom is used. The detailed costruction made in MOPAC is slightly different in oder to have a reasonably simple and differentiable dependence of the surface area on the molecular coordinates. - The COSMO volume is just the volume included in the COSMO surface. To first order it is close to the molar volume. - The COSMO output does give nothing else than the dielectric interaction energy between the solute and the solvent. - Be aware that all implicit solvation models are trained for free energies of solvation. They do not give the solvation enthalpy. - Only the COSMO-RS method, which is a statistical thermodynamics post-processing of the COSMO polarization charge densities, clearly splits enthalpy and entropy of solvation. For further information see: A. Klamt, COSMO-RS- From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design, Elsevier, 2005 or the recent review COSMO and COSMO-RS, which is currently freely available under http://onlinelibrary.wiley.com/doi/10.1002/wcms.56/abstract Best regards Andreas Am 17.08.2011 03:08, schrieb A Anglea a.anglea90]|[yahoo.com: > Sent to CCL by: "A Anglea" [a.anglea90 . yahoo.com] > Dear all > I am looking for calculation the molar volume and solvent-surface-accessible- > area of my molecule. > I used MOPAC code to get the data and want to ensure I understood the output > correctly because it is the first time for me to use this code: > COSMO area: is the solvent-surface-accessible-area, isn't it? > COSMO volume: is the molar volume, isn't it? > The output is slightly confused, how can I calculation the "interaction > enthalpy" from the output? > I want to compare the data with high level using Gaussian, VOLUME keyword gives > me the molar volume, is there any recommendation regards the theoretical method > to be used? > How can I calculate the solvent-surface-accessible-area using Gaussian? > What is the direct relation between the molar volume and solvent-surface- > accessible-area? > I would be grateful if you helped me by any mean > Cheers> > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt/./cosmologic.de web www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Wed Aug 17 05:28:00 2011 From: "A Anglea a.anglea90%yahoo.com" To: CCL Subject: CCL: CCL MOPAC output - please help Message-Id: <-45271-110817052707-16064-cvaocfg4VKboJcBhkRAXNA_-_server.ccl.net> X-Original-From: "A Anglea" Date: Wed, 17 Aug 2011 05:27:04 -0400 Sent to CCL by: "A Anglea" [a.anglea90^yahoo.com] Dear Dr. Andreas Thanks a lot for your helpful reply. Your reply (and your posts on CCL about COSMO) was more than helpful for me. In case, I'd like to calculate the SASA and Vmol at higher level using Gaussain, what theoretical method would you recommend? For the interaction enthalpy, I saw in a paper, the author calculated the interaction enthalpy of A + B --> C reaction using MOPAC2009. Is there a keyword in MOPAC to calculate the interaction enthalpy directly? For the second time, thanks for your reply. Cheers By the way, I am using MOPAC2009 Sent to CCL by: Andreas Klamt [klamt . cosmologic.de] Dear Anglea, I am Andreas Klamt, and I wrote the COSMO part of MOPAC. I am afraid that there is no simple answer to your question: - First one needs to know which version of MOPAC you are using, since the cavity defintions have changed during the past 15 years. I newer versions (with closed cavity) you can interpret a solvens thet-excluded surface, according to the defintions given under "solvent-accessible area" in wikepedia. It is the surface which can be touched by the roliing ball, where in COSMO always a ball of radius 1.3 Angstrom is used. The detailed costruction made in MOPAC is slightly different in oder to have a reasonably simple and differentiable dependence of the surface area on the molecular coordinates. - The COSMO volume is just the volume included in the COSMO surface. To first order it is close to the molar volume. - The COSMO output does give nothing else than the dielectric interaction energy between the solute and the solvent. - Be aware that all implicit solvation models are trained for free energies of solvation. They do not give the solvation enthalpy. - Only the COSMO-RS method, which is a statistical thermodynamics post-processing of the COSMO polarization charge densities, clearly splits enthalpy and entropy of solvation. For further information see: A. Klamt, COSMO-RS- From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design, Elsevier, 2005 or the recent review COSMO and COSMO-RS, which is currently freely available under http://onlinelibrary.wiley.com/doi/10.1002/wcms.56/abstract Best regards From owner-chemistry@ccl.net Wed Aug 17 09:18:00 2011 From: "jaleel uc jaleel.uc_._gmail.com" To: CCL Subject: CCL: Molecular modeling of ZnO/PP composite Message-Id: <-45272-110817021434-21426-xS4O7mpTks+17w57CgAFfg+*+server.ccl.net> X-Original-From: jaleel uc Content-Type: multipart/alternative; boundary=bcaec52994d7e1647c04aaad673c Date: Wed, 17 Aug 2011 11:44:15 +0530 MIME-Version: 1.0 Sent to CCL by: jaleel uc [jaleel.uc{:}gmail.com] --bcaec52994d7e1647c04aaad673c Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear sir I expect the following link will help http://www.ifm.liu.se/physchem/courses/NKEC18/ JALEEL UC MCC CALICUT On Tue, Aug 16, 2011 at 10:10 PM, Daniel Glossman-Mitnik dglossman]-[ gmail.com wrote: > Dear netters: > > I have been asked to try to simulate the optical properties of ZnO > nanoparticles of varying size > in a matrix of polypropilene (PP). I would like to know if you can give m= e > hints about the > appropiate methods and/or software to accomplish this task, and also abou= t > any reference to > previous work in the subject. > > Thanks in advance. Best regards, > > Daniel > > > *************************************************************************= ************************************** > Dr. Daniel Glossman-Mitnik > Centro de Investigaci=F3n en Materiales Avanzados, SC > Departamento de Simulaci=F3n Computacional y Modelado Molecular > Miguel de Cervantes 120 - Comp. Ind. Chihuahua - Chihuahua, Chih 31109, > Mexico > Phone: +52 614 4391151 Secretary/FAX: +52 614 4391130 Lab: +52 614 > 4394805 > E-mail: daniel.glossman . cimav.edu.mx dglossman . gmail.com > WWW: http://www.cimav.edu.mx/cv/daniel.glossman > http://blogs.cimav.edu.mx/daniel.glossman > > *************************************************************************= ************************************** > --=20 JALEEL --bcaec52994d7e1647c04aaad673c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear sir

I=A0 expect the following link will help

http://www.ifm.liu.se/phys= chem/courses/NKEC18/


JALEEL UC

MCC CALICUT

On Tue, Aug 16, 2011 at 10:10 PM, Daniel Glossma= n-Mitnik dglossman]-[gmail.com <owner-chemistry+*+ccl= .net> wrote:
Dear netters:
I have been asked to try to simulate the optical properties= of ZnO nanoparticles of varying size
in a matrix of polypropilene (PP). I would like to know if you can giv= e me hints about the
appropiate methods and/or software to accomplish this task, and also a= bout any reference to
previous work in the subject.
Thanks in advance. Best regards,

Daniel

*******************************************************= ********************************************************
Dr. Daniel Glos= sman-Mitnik
Centro de Investigaci=F3n en Materiales Avanzados, SC
Departamento de Simulaci=F3n Computacional y Modelado Molecular
Miguel de Cervantes 120 - Comp. Ind. Chihuahua - Chihuahua, Chih 31109, Mex= ico
Phone: +52 614 4391151=A0=A0 Secretary/FAX: +52 614 4391130=A0 =A0 L= ab: +52 614 4394805
E-mail:=A0 daniel.glossman . cimav.edu.mx=A0 =A0 =A0 = =A0 =A0 dglossma= n . gmail.com
WWW:=A0 http://www.cimav.edu.mx/cv/daniel.glossman
=A0 =A0 =A0 =A0 =A0= =A0 =A0 http://blogs.cimav.edu.mx/daniel.glossman
***************************************************************************= ************************************



--
=A0JALEEL

--bcaec52994d7e1647c04aaad673c-- From owner-chemistry@ccl.net Wed Aug 17 11:39:00 2011 From: "Andreas Klamt klamt{:}cosmologic.de" To: CCL Subject: CCL: CCL MOPAC output - please help Message-Id: <-45273-110817113741-13631-9ngqROrenuClZSlR1/cW7w,,server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 17 Aug 2011 17:37:40 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt###cosmologic.de] Dear Dr. Anglea, (turning the names in the right order) I do not think that calculation of SASA and VMmol on higher level quantum mthods will be of any benefit, because usually the geometries are already rather converged at DFT level, and the values for SASA and Vmol do much more depend on the details of the construction (radii, smooting radius and smootihnig algorithm) than they do on the QM level. As I said in my previous e-mail, there is no "enthalpy keyword" together with COSMO in MOPAC, as there is no such option in PCM or in any dielectric continuum solvation model. If one considers the dielectric interaction energy as an enthalpy, then obviously on can calculate the reaction enthalpy with COSMO in MOPAC. But since the model as any solvation model is trained on free energies, it is questionable whether the assumption is right. Regards Andreas Am 17.08.2011 11:27, schrieb A Anglea a.anglea90%yahoo.com: > Sent to CCL by: "A Anglea" [a.anglea90^yahoo.com] > Dear Dr. Andreas > Thanks a lot for your helpful reply. > Your reply (and your posts on CCL about COSMO) was more than helpful for me. > In case, I'd like to calculate the SASA and Vmol at higher level using > Gaussain, what theoretical method would you recommend? > For the interaction enthalpy, I saw in a paper, the author calculated the > interaction enthalpy of A + B --> C reaction using MOPAC2009. Is there a > keyword in MOPAC to calculate the interaction enthalpy directly? > For the second time, thanks for your reply. > Cheers > By the way, I am using MOPAC2009 > > Sent to CCL by: Andreas Klamt [klamt . cosmologic.de] > Dear Anglea, > > I am Andreas Klamt, and I wrote the COSMO part of MOPAC. I am afraid that > there is no simple answer to your question: - First one needs to know which > version of MOPAC you are using, since the cavity defintions have changed > during the past 15 years. I newer versions (with closed cavity) you can > interpret a solvens thet-excluded surface, according to the defintions given > under "solvent-accessible area" in wikepedia. It is the surface which can be > touched by the roliing ball, where in COSMO always a ball of radius 1.3 > Angstrom is used. The detailed costruction made in MOPAC is slightly > different in oder to have a reasonably simple and differentiable dependence > of the surface area on the molecular coordinates. - The COSMO volume is just > the volume included in the COSMO surface. To first order it is close to the > molar volume. - The COSMO output does give nothing else than the dielectric > interaction energy between the solute and the solvent. - Be aware that all > implicit solvation models are trained for free energies of solvation. They do > not give the solvation enthalpy. - Only the COSMO-RS method, which is a > statistical thermodynamics post-processing of the COSMO polarization charge > densities, clearly splits enthalpy and entropy of solvation. > > For further information see: A. Klamt, COSMO-RS- From Quantum Chemistry to > Fluid Phase Thermodynamics and Drug Design, Elsevier, 2005 or the recent > review COSMO and COSMO-RS, which is currently freely available under > http://onlinelibrary.wiley.com/doi/10.1002/wcms.56/abstract > Best regards> > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt:+:cosmologic.de web www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Wed Aug 17 12:13:01 2011 From: "Brian B Masek brian.masek*_*certara.com" To: CCL Subject: CCL: New version - KNIME extensions from Tripos Message-Id: <-45274-110817121135-2352-vwfZl1HNQJqJYsgQ95bsMA#,#server.ccl.net> X-Original-From: "Brian B Masek" Date: Wed, 17 Aug 2011 12:11:32 -0400 Sent to CCL by: "Brian B Masek" [brian.masek^_^certara.com] A new set of KNIME nodes, Tripos Chemistry Extensions for KNIME v 2.3.x and 2.4, is available now from Tripos. This latest release supports KNIME v2.4 and includes a new node that performs topomer similarity searching, released at the request of many customers. The Tripos Chemistry Extensions package introduces chemical intelligence to the KNIME platform, providing researchers with chemical structure manipulation, visualization, and other important analysis features. The Tripos Chemistry Extensions package complements KNIMEs existing capabilities by providing access to many important cheminformatics tools, such as those used to visualize and transform molecular structures, compute molecular properties and search for functional groups. A number of basic capabilities, such as file I/O, composite score building, or fingerprint computation do not require a license, so KNIME users may download and access this functionality as a free, unsupported license. Other capabilities, such as 2D to 3D molecule conversion, superimposing molecules, UNITY searching and 3D visualization require separately licensed software in order to work. You can download the Tripos Chemistry Extensions for KNIME from www.tripos.com/download in the SYBYL section (registration is required). If youd like more information about the nodes that are available from Tripos, contact your local application scientist, or send email to me at diana.orourke ~~ certara.com