From owner-chemistry@ccl.net Thu Jan 31 07:37:00 2013 From: "sonam bhatia sonamalerts^^^gmail.com" To: CCL Subject: CCL: ADF-Bond energy analysis query Message-Id: <-48160-130131072332-19239-7q4kQbJAoDVmMy33BG3Rng.:.server.ccl.net> X-Original-From: "sonam bhatia" Date: Thu, 31 Jan 2013 07:23:32 -0500 Sent to CCL by: "sonam bhatia" [sonamalerts|,|gmail.com] Dear all, I am interested in performing Bond energy analysis by use of ADF. I got windows version installed in our lab but I am the only one in our group using this software. As we purchased it recently and I am new to it so learning its basics. I am not quite confident in performing bond energy analysis by it. As I have performed Geometry optimization of Ph3=C=Ph3 system and in .out file in bond energy decomposition section: E pauli repulsion E steric interaction E orbital interaction above mentioned values comes. I suppose interpretation of these values give us bond energy analysis. Whether I am right? 1) But if suppose i have to do this analysis for particular no. of bonds like in Ph3=C=Ph3 system for P=C only so how I will specify this? 2) Moreover have you used *occupation* keyword in adf which is used to specify particular electronic state to individual atom. 3) if suppose for above system I have to give s2, p-sigma2, p-pie0 (perpendicular), p-pie0 (parallel) electronic configuration to carbon atom, then how with the help of occupation keyword I can assign this electronic configuration. 4) While performing bonding analysis is it mandatory to give ETS-NOCV calculations? Please help me in this regard. From owner-chemistry@ccl.net Thu Jan 31 08:12:00 2013 From: "Andreas Klamt klamt/a\cosmologic.de" To: CCL Subject: CCL: COSMO vs COSMO-RS Message-Id: <-48161-130131073524-19610-Po7VVrXiOm/fIOnJYe5r7w^server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 31 Jan 2013 13:35:15 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt=cosmologic.de] Dear Sina, there are several potential reasons for the large difference. On the one hand you used qute different basis sets for the COSMO calculations at eps=78 and the eps=infinity calculations. Admittedly I do not expect that this changes the results too much. I am not completely sure how you did the COSMO-RS reaction calculation. Did you use the thermodynamic cycle inserting the gasphase reaction energy from the b3-lyp and a def2-QZVP calculation? If so, then the latter result, i.e. GReaction-COSMO-RS-Water - GReaction-gas= -2.05 Kcal/mol should be nothing else than the dG_solvation difference of educts and products on BP-TZVP-COSMO-RS level, since GReaction-gas cancels out. Can you just check and confirm that? Please note that bare COSMO (unlike other implicit solvation models) is not parameterized for giving optimal dG-solvation values. It just trets the electrostatic component, and not the dispersion, and other non-electrosttic contributions. Hence you cannot expect good quantitative results for dG_hydrtion from using bare COSMO. COSMO-RS is my recommended method to take all these things into account. Finally it should be noted that the recommended procedure for dG_reaction calculation requires to include the vibr., rot. and transl. free energy contributions in the gasphase, which will be very important for a reaction in which the number of particles changes from 1 to 4. These can be calculated for exmple with the freeH tool in TURBOMOLE. But this contribution would appear in the gasphase as well as in the liquid phase and thus should not influence your differential results. In summary, I do not find your result too surprising. The more relible answer should be the COSMO-RS answer, but please note that your calculations are still suboptimal. Best regards Andreas Am 31.01.2013 00:13, schrieb Sina Behtash behtash!=!email.sc.edu: > Sent to CCL by: "Sina Behtash" [behtash ~ email.sc.edu] > > I am using both COSMO (implemented in Turbomole 6.0) and COSMOtherm/COSMO-RS to calculate the solvent effects on the free energy of reaction for the following reaction: > > Glucose --> HMF + 3 H2O > > First, I optimized all the reactants and products in the gas phase using b3-lyp and a def2-QZVP basis set. Next, assuming that the geometry does not change significantly in the presence of water, I used the optimized structure to run a COSMO single-point energy calculation with the same basis set and dielectric constant of water at 298 K which is 78.39. According to the COSMO calculation, > > GReaction-COSMO - GReaction-gas= -15.2 Kcal/mol > > Next, in order to generate relevant input for COSMO-RS calculations, I ran another COSMO single-point energy calculation using the BP functional and TZVP basis set. Then I used COSMOtherm/Reactions and the BP-TZVP data base to run COSMO-RS calculations for my reaction at T=298K. > > The result shows that, > > GReaction-COSMO-RS-Water - GReaction-gas= -2.05 Kcal/mol > > I was expecting that for water, the COSMO and COSMO-RS calculations should give almost the same result. However, in this case the difference in the effect of water on the free energy of reaction is around 13 Kcal/mol. Can anyone explain to me why the difference is so large? Im wondering if the effects of hydrogen bonding and electrostatic interactions can be this significant. > > Sina Behtash > Ph.D. Student > Department of Chemical Engineering > University of South Carolina > Phone: (803)777-0611 > Email: behtash-$-email.sc.edu> > > -- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt^^^cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt From owner-chemistry@ccl.net Thu Jan 31 08:46:00 2013 From: "Anna Lucia Fallacara al.fallacara{:}gmail.com" To: CCL Subject: CCL: IX European Workshop in Drug Design Message-Id: <-48162-130131054328-16345-n+Ozm/18DBLnSHt+qIhqcg~~server.ccl.net> X-Original-From: Anna Lucia Fallacara Content-Type: multipart/alternative; boundary=20cf3071cc96bc9a4d04d4934bf5 Date: Thu, 31 Jan 2013 11:43:22 +0100 MIME-Version: 1.0 Sent to CCL by: Anna Lucia Fallacara [al.fallacara_._gmail.com] --20cf3071cc96bc9a4d04d4934bf5 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable *IX EWDD Ninth European Workshop in Drug Design May, 19th =96 25th, 2013 =96 Certosa di Pontignano, Siena (Italy)* http://www3.unisi.it/EWDD/ The University of Siena is organizing the "Ninth European Workshop in Drug Design" (IX EWDD), to be held, from May, 19th to 25st 2012, in Certosa di Pontignano, on the outskirt of the beautiful city of Siena, in Tuscany. Ligand/structure based drug design, in silico ADME - Tox and metabolism, design and screening of virtual libraries, molecular modelling methodologies, cheminformatics/bioinformatics and synthetic feasibility. These topics will be covered by lectures in the mornings and exercises in the afternoon through practical case studies. The goal of the afternoon working sessions is to create an environment that is similar to what happens inside pharmaceutical Companies today. The participants will be divided into teams which will be led and coordinated by tutors who are research group leaders in their companies and Universities. Each teams will work through a different drug design case, emulating a real research team. The team's work will be focused on rational design and will include writing reports, project status reviews, and planning events of real-life research teams, as well as in-depth work with appropriate modelling software. IX EWDD will feature more than *20 well known researchers* from the University and from the Pharmaceutical Industry, including directors of research. Time for *short presentations*, from brilliant young researchers and from selected posters is avalaible (If you are interested send the topic and title at *info9ewdd(_)gmail.com**)*. *Participation to "IXEWDD" is limited to 65 attendees.* *Fee for participation (Euro 2.000,00) will include all meals and hotel accommodation in two-bed rooms for five nights (some single rooms are also available, supplementary fee Euro 200,00). **Accommodation booking will be cared by the Workshop Secretariat.* *REGISTRATION IS OPEN AND SOME FELLOWSHIPS ARE AVAILABLE* *For more info: info9ewdd(_)gmail.com* *http://www3.unisi.it/EWDD/* * * --20cf3071cc96bc9a4d04d4934bf5 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable

IX E= WDD
Ninth European Workshop in Drug Design
May, 19th =96 25th, 2013 =96 Certosa di Pontignano, S= iena (Italy)

http://www3.unisi.it/EWDD/

The Un= iversity of Siena is organizing the "Ninth European Workshop in Drug Design" (IX EWDD)= , to be held, from May, 19th to 25st 2012, in Certosa di Pontignano, on the outskirt of the beautiful city of Siena, in Tuscany.

Lig= and/structure based drug design, in silico ADME - Tox and metabolism, design and screenin= g of virtual libraries, molecular modelling methodologies, cheminformatics/bioinformatics and synthetic feasibility. These topics will= be covered by lectures in the mornings and exercises in the afternoon through practical case studies.

The goal of the afternoon working sessions is to create an environment that is similar to what happens inside pharmaceutical Companies today. The particip= ants will be divided into teams which will be led and coordinated by tutors who = are research group leaders in their companies and Universities. Each teams will work through a different drug design case, emulating a real research team. = The team's work will be focused on rational design and will include writing reports, project status reviews, and planning events of real-life research teams, as well as in-depth work with appropriate modelling software.=

IX EWD= D will feature more than 20 well known researchers from the University and from the Pharmaceutical Industry, including directors of research. Time for short presentations, > from brilliant young researchers and from selected posters is avalaible (If= you are interested send the topic and title at info9ewdd(_)g= mail.com).

Participation to "IXEWDD" is limited to 65 attendees.

Fee for participation (Euro 2.= 000,00)=A0 will include all meals and hotel accommodation in two-bed rooms for five nights (some single rooms are also available, supplementary fee Euro 200,00). Accommodation booking will be cared by the Workshop Secretaria= t.

=A0

=A0

REGISTRATION IS OPEN AND SOME FELLOWSHIPS ARE AVAILABLE

For more info: info9ewdd(_)gmail.com

http://www3.unisi.it/EWDD/



--20cf3071cc96bc9a4d04d4934bf5-- From owner-chemistry@ccl.net Thu Jan 31 09:42:00 2013 From: "Fedor Goumans goumans .. scm.com" To: CCL Subject: CCL: ADF-Bond energy analysis query Message-Id: <-48163-130131093207-690-0iJJwONwauzqU8L0Cs57tw|-|server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 31 Jan 2013 15:31:28 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans[a]scm.com] Dear Sonam, First of all, you may also send ADF questions directly to our dedicated support team (support ~~ scm.com). A good starting point for understanding energy decomposition analysis is this advanced review by von Hopffgarten and Frenking: http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS71.html To answer your questions: - Yes, the bond energy is decomposed in those three terms. - As ADF works with fragments, the bonding energy (and its decomposition) is between the fragments you defined (atoms by default). Depending on which bond you are interested in, you can run a single point calculation where you define the two fragments either side of the bond. In this case for (PH3)2C -if I understand correctly- you could define one PH3 fragment (which is present twice) and one C fragment. The bond energy that comes from this run is then twice the C-P bond. - to analyze bonding energy in terms of unrestricted fragments you can use the fragoccupations keyword. You would need the lower the spherical symmetry of this C atom fragment to something like D_inf_h or D2h to introduce the differentiation between the different pi directions (sigma, pi-parallel and pi-perpendicular in your molecule. http://www.scm.com/Doc/Doc2012/ADF/ADFUsersGuide/page65.html#keyscheme%20FRAGOCCUPATIONS Our support team will follow up on this, if you could send them their your geometry. - no you don't have to use ETS-NOCV, but it can give you additional insight in how the densities between the fragments interact and get insight in specific orbital interactions even for non-symmetric molecules, see: http://www.scm.com/Products/Capabilities/ETS-NOCV.html Hope this helps, Fedor On 1/31/2013 1:23 PM, sonam bhatia sonamalerts^^^gmail.com wrote: > Sent to CCL by: "sonam bhatia" [sonamalerts|,|gmail.com] > Dear all, > > I am interested in performing Bond energy analysis by use of ADF. I got > windows version installed in our lab but I am the only one in our > group using this software. As we purchased it recently and I am new to it > so learning its basics. I am not quite confident in performing bond energy > analysis by it. As I have performed Geometry optimization of Ph3=C=Ph3 > system and in .out file in bond energy decomposition section: > E pauli repulsion > E steric interaction > E orbital interaction > > above mentioned values comes. > I suppose interpretation of these values give us bond energy analysis. > Whether I am right? > 1) But if suppose i have to do this analysis for particular no. of bonds > like in Ph3=C=Ph3 system for P=C only so how I will specify this? > 2) Moreover have you used *occupation* keyword in adf which is used to > specify particular electronic state to individual atom. > 3) if suppose for above system I have to give s2, p-sigma2, p-pie0 > (perpendicular), p-pie0 (parallel) electronic configuration to carbon atom, > then how with the help of occupation keyword I can assign this electronic > configuration. > 4) While performing bonding analysis is it mandatory to give ETS-NOCV > calculations? > > Please help me in this regard.> > -- Dr. T. P. M. Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans ~~ scm.com http://www.scm.com From owner-chemistry@ccl.net Thu Jan 31 11:52:01 2013 From: "Belkhiri, lotfi lotfi.belkhiri++umc.edu.dz" To: CCL Subject: CCL: ADF-Bond energy analysis query Message-Id: <-48164-130131114317-4919-id/b+IpiyAG83YmFaZ91/A:+:server.ccl.net> X-Original-From: "Belkhiri, lotfi" Content-Type: multipart/alternative; boundary=001636eef47979ce1f04d4985288 Date: Thu, 31 Jan 2013 17:43:10 +0100 MIME-Version: 1.0 Sent to CCL by: "Belkhiri, lotfi" [lotfi.belkhiri _ umc.edu.dz] --001636eef47979ce1f04d4985288 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear ADF user, ADF is one of the rare quantum chemistry programs which allows a correct decomposition Bond Energy analysis, especially, for fragment-fragment calculations, i.e., for a special bond formation or like for metal-ligand interactions. In ADF,bond energy decomposition analysis, is based on the transition-state method developped by Ziegler and Morokuma et al. and reveals to be a very useful theoretical tool for predicting and investigating frag-frag bonding interactions and their covalent or ionic character. Within this scheme, the resulting total bonding energy or energy fragment = =CE=94E frag obtained from spin restricted or unrestricted calculations, can be decomposed mainly into two terms as follow: =CE=94Efrag =3D Esteric + Eorb where Esteric term is the steric interaction energy between the (RCp)3M metallic fragment and azine ligand and Eorb is the orbital (covalent) contribution to the metal-azine bond. The steric energy term (Esteric) is itself decomposed into a destabilizing term EPauli, the electronic repulsion due to the Pauli principle, and EES, the stabilizing electrostatic energy between the two fragments : Esteric =3D EPauli + EES However, it is important to remind the ADF users, that this energetic decomposition is not meaningful for a rigorous thermodynamic analysis (enthalpy-entropy parameters), but should be applied to compare the relative stability of the molecules or a specif bond formation. to be continued... Lotfi 2013/1/31 sonam bhatia sonamalerts^^^gmail.com > > Sent to CCL by: "sonam bhatia" [sonamalerts|,|gmail.com] > Dear all, > > I am interested in performing Bond energy analysis by use of ADF. I got > windows version installed in our lab but I am the only one in our > group using this software. As we purchased it recently and I am new to it > so learning its basics. I am not quite confident in performing bond energ= y > analysis by it. As I have performed Geometry optimization of Ph3=3DC=3DPh= 3 > system and in .out file in bond energy decomposition section: > E pauli repulsion > E steric interaction > E orbital interaction > > above mentioned values comes. > I suppose interpretation of these values give us bond energy analysis. > Whether I am right? > 1) But if suppose i have to do this analysis for particular no. of bonds > like in Ph3=3DC=3DPh3 system for P=3DC only so how I will specify this? > 2) Moreover have you used *occupation* keyword in adf which is used to > specify particular electronic state to individual atom. > 3) if suppose for above system I have to give s2, p-sigma2, p-pie0 > (perpendicular), p-pie0 (parallel) electronic configuration to carbon ato= m, > then how with the help of occupation keyword I can assign this electronic > configuration. > 4) While performing bonding analysis is it mandatory to give ETS-NOCV > calculations? > > Please help me in this regard. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Pr. Lotfi Belkhiri Directeur de Recherches - Groupe de Chimie Th=C3=A9orique et Mod=C3=A9lisat= ion Unit=C3=A9 de Recherche CHEMS - Universit=C3=A9 Mentouri de Constantine jct9_cne2010,yahoo.fr Fax : +213 (0)31 68 15 45 Homepage : http://www.umc.edu.dz/vf/Labo/FacScienceExact/site_lacmom/crbst_21.html --001636eef47979ce1f04d4985288 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear ADF user,

ADF is one= of the rare quantum chemistry programs which allows a correct decompositio= n Bond Energy analysis, especially, for fragment-fragment calculations, i.e= ., for a special bond formation or like for metal-ligand interactions.
In ADF,bond en= ergy decomposition analysis, is based on the transition-state method developped by Ziegler and Morokuma et al. and revea= ls to be a very useful theoretical tool for predicting and investigating frag-frag bonding interactions and their covalent or ionic character.
=09 =09 =09

Within this scheme, the resulting total bonding energy or energy fragment =CE=94Efrag obtained from spin restricted or unrestricted calcu= lations, can be decomposed mainly into two terms as follow:

=CE=94Efrag =3D Esteric + Eorb

where Esteric term is the steric interaction energy between the (RCp)3M metallic fragment and azine ligand and Eorb is the orbital (covalent) contribution to the metal-azine bond. The steric energy term (Esteric) is itself decomposed into a destabilizing term EPauli, the electronic repulsion due to the Pauli principle, and EES, the stabilizing electrostatic energy between the two fragments :

Esteric = =3D EPauli + EES

However, it is important to= remind the ADF users, that this energetic decomposition is not meaningful for a rigorous thermodynamic analysis (enthalpy-entropy parameters), but should be applied to compare the relative stability of the molecules or a specif bond formation.
to be continued...
Lotfi
=



2013/1/31 sonam bhatia sonamalerts^^^gmail.com <owner-chemistry,ccl.net>

Sent to CCL by: "sonam =C2=A0bhatia" [sonamalerts|,|gmail.com]
Dear all,

I am interested in performing Bond energy analysis by use of ADF. I got
=C2=A0windows version installed in our lab but I am the only one in our
group using this software. As we purchased it recently and I am new to it so learning its basics. I am not quite confident in performing bond energy<= br> analysis by it. As I have performed Geometry optimization of Ph3=3DC=3DPh3<= br> system and in .out file in bond energy decomposition section:
E pauli repulsion
E steric interaction
E orbital interaction

above mentioned values comes.
I suppose interpretation of these values give us bond energy analysis.
Whether I am right?
1) But if suppose i have to do this analysis for particular no. of bonds like in Ph3=3DC=3DPh3 system for P=3DC only so how I will specify this?
2) Moreover have you used *occupation* keyword in adf which is used to
specify particular electronic state to individual atom.
3) if suppose for above system I have to give =C2=A0s2, p-sigma2, p-pie0 (perpendicular), p-pie0 (parallel) electronic configuration to carbon atom,=
then how with the help of occupation keyword I can assign this electronic configuration.
4) While performing bonding analysis is it mandatory to give ETS-NOCV
calculations?

Please help me in this regard.



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--
Pr. Lotfi Belkhiri
Directeur= de Recherches -=C2=A0Groupe de Chimie Th=C3=A9orique et Mod=C3=A9lisation<= br>
Unit=C3=A9 de Recherche C= HEMS - Universit=C3=A9 Mentouri de Constantine
jct9_cne2010,yahoo.fr
Fax : +213 (0)31 68 15 45
Homepage :=C2=A0http://www.umc.edu.dz/vf/Labo/FacScienceExact/si= te_lacmom/crbst_21.html
--001636eef47979ce1f04d4985288--