From owner-chemistry@ccl.net Fri Oct 5 04:14:01 2012 From: "Robert W. Gora robert.gora[#]pwr.wroc.pl" To: CCL Subject: CCL: [CCL] Resonance energy Message-Id: <-47722-121005040436-26757-KVxv/chnu9XZDecI+fRKAw_+_server.ccl.net> X-Original-From: "Robert W. Gora" Content-type: multipart/mixed; boundary="Boundary_(ID_dH+qHKELnMWu496iq98Deg)" Date: Fri, 05 Oct 2012 10:04:27 +0200 (CEST) MIME-version: 1.0 Sent to CCL by: "Robert W. Gora" [robert.gora!^!pwr.wroc.pl] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. --Boundary_(ID_dH+qHKELnMWu496iq98Deg) Content-type: TEXT/PLAIN; charset=iso-8859-1; format=flowed Content-transfer-encoding: 8BIT >> This is particularly easy in CASVB or SCVB implemented in VB2000 (the >> two methods are in fact equivalent). > > This is not correct. First, however, I have to point out that the term > "CASVB" means different things to different people. CASVB implemented in > MOLCAS and MOLPRO by David Cooper is indeed identical to SCVB. It is > obtained by projecting out a SCVB function from a CASSCF wave function, > either using an overlap criteria or an energy minimisation criteria. Naturally I meant Coper's CASVB being virtually identical to SCVB. Actually nowadays one can use this code to perform also fully variational CASVB calculations by optimizing SCVB complement which is indeed equivalent to SCVB. Could you provide us with a couple of references to CASVB as implemented in VB2000? Best, Robert -- Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.info] [http://www.researchgate.net/profile/Robert_Gora] [http://www.researcherid.com/rid/B-3919-2010] --Boundary_(ID_dH+qHKELnMWu496iq98Deg)-- From owner-chemistry@ccl.net Fri Oct 5 06:46:00 2012 From: "Salter-Duke, Brian James - brian.james.duke|gmail.com" To: CCL Subject: CCL: [CCL] Resonance energy Message-Id: <-47723-121005054148-2145-TTv3DcpCgZwBb8M8qdVVzQ|a|server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 5 Oct 2012 19:41:36 +1000 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke _ gmail.com] On Fri, Oct 05, 2012 at 10:04:27AM +0200, Robert W. Gora robert.gora[#]pwr.wroc.pl wrote: > >>This is particularly easy in CASVB or SCVB implemented in VB2000 (the > >>two methods are in fact equivalent). > > > >This is not correct. First, however, I have to point out that the term > >"CASVB" means different things to different people. CASVB implemented in > >MOLCAS and MOLPRO by David Cooper is indeed identical to SCVB. It is > >obtained by projecting out a SCVB function from a CASSCF wave function, > >either using an overlap criteria or an energy minimisation criteria. > > Naturally I meant Coper's CASVB being virtually identical to SCVB. Actually > nowadays one can use this code to perform also fully variational CASVB > calculations by optimizing SCVB complement which is indeed equivalent to SCVB. I am not quite sure what you are saying here. Cooper's CASVB is indeed equal to SCVB, but the number of structures is much less than in the VB2000 CASVB = CASSCF [14 structures for SCVB and 1764 for VB2000 CASVB are quoted in Shaik and Hiberty's book referenced below for methane] and the SCVB energy is higher than that of VB2000 CASVB = CASSCF. Incidentally in our paper [Karadakov et al] that I referenced in my last post, calculations on benzene for SC(6) and on C5H5- and C7H7+ with our new SC approach of SCVB(6,5) and SCVB(6,7) were carried out with both VB2000 and MOLPRO giving identical results. We also give the CASSCF(6,6), CASCF(6,5) and CASSCF(6,7) energies and I think I reproduced all of these with VB2000 CASVB. I have certainly obtained identical results with VB2000 CASVB and GAMESS(US) CASSCF very many times. > Could you provide us with a couple of references to CASVB as > implemented in VB2000? There is no publication that specifically discusses the VB2000 implementation of CASVB, but it is well described in "A Chemist's Guide to Valence Bond Theory by Sason Shaik and Philippe Hiberty in the beginning of section 9.2.3 on page 243. That section then discusses the Cooper CASVB, and finally it discusses the CASVB method of Hirao et al (Int. J. Quant.Chem., 66, 157. (1998), which is I believe essentially identical to the VB2000 CASVB although the VB orbitals may not be identical. Since the set of structures is complete, the VB orbitals are invarient to transformation. VB2000 on the last iteration tries to make them as localised as possible. VB2000 CASVB(n,m) gives the same energy as CASSCF(n,m). Brian. > Best, > Robert > > -- > Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.info] > [http://www.researchgate.net/profile/Robert_Gora] > [http://www.researcherid.com/rid/B-3919-2010] -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke]=[monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia From owner-chemistry@ccl.net Fri Oct 5 07:20:00 2012 From: "Simon Cross simon _ moldiscovery.com" To: CCL Subject: CCL: PharmBench v1.0 Community Benchmarking Dataset Message-Id: <-47724-121005065508-1995-f6k7x300kWBL/VGOOAIVdg++server.ccl.net> X-Original-From: Simon Cross Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 05 Oct 2012 11:54:57 +0100 MIME-Version: 1.0 Sent to CCL by: Simon Cross [simon],[moldiscovery.com] Dear Colleagues, We would like to draw your attention to the publication of the PharmBench 1.0 dataset for the evaluation of molecular alignment and pharmacophore elucidation approaches. The dataset consists of 81 targets, containing 960 ligands in total. The dataset is based on known pharmaceutically relevant co-crystallised protein ligand complexes, which were filtered to leave high-resolution structures containing drug-like small molecule ligands, for which electron density is also available at the EDS server. For each target the structures have been aligned using the receptor backbone atoms, and then the ligands extracted and prepared by fixing their atom types and adding hydrogen atoms. The datasets therefore contain target ligands, aligned in the biologically relevant frame of reference, to act as a 'gold standard' reference set. The two-dimensional structures of these ligands are also provided. An ideal molecular alignment or pharmacophore elucidation method should be able to read the two-dimensional input structures, and output three-dimensional alignments of the ligands that are equivalent to the gold standard alignments. In the coming weeks a web service will be set up to enable user-provided alignment models to be evaluated using the same approach as described in the publication (dx.doi.org/10.1021/ci300154n). The dataset is available at pharmbench.moldiscovery.com. Kind regards, Simon -- Dr. Simon Cross Snr Scientist & Product Manager Molecular Discovery Ltd simon[at]moldiscovery[dot]com +44 7980 572278 From owner-chemistry@ccl.net Fri Oct 5 09:11:00 2012 From: "Savita Pundlik savita.pundlik!^!tcs.com" To: CCL Subject: CCL:G: Resonance energy Message-Id: <-47725-121004232004-9563-zjW5eGd/7SBBmEIsJtBDqQ(-)server.ccl.net> X-Original-From: Savita Pundlik Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="iso-8859-1" Date: Fri, 5 Oct 2012 08:49:51 +0530 MIME-Version: 1.0 Sent to CCL by: Savita Pundlik [savita.pundlik*tcs.com] Hello,

Years ago we had assessed structural characteris= tics in some fused ring systems using topographical analysis of electron de= nsity and electrostatic potential (JACS 1995, 117, 9559).
We found that = the charge pulling and pushing effects are reflected in e.g. the density at= bond critical points.
Calculation of this needs some post processing af= ter SCF.
Can these quantities serve your purpose?

Thanks and best= wishes,

Savita Pundlik
Tata Consultancy Services
Mailto: savi= ta.pundlik .. tcs.com
Website: http://www.tcs.com
______________________= ______________________
Experience certainty. IT Services
Business = Solutions
Outsourcing
____________________________________________=

-----owner-chemistry+savita.pundlik= =3D=3Dtcs.com .. ccl.net wrote: -----
To: "Pundlik, Savita Sunil " <savita.pundlik .. tcs.c= om>
From: "Sergio Manzetti sergio.manzetti]*[gmx.com"
Sent by: owner-chemistry+savita.pundlik=3D=3Dtcs.com .. ccl.net<= br>Date: 10/04/2012 05:29PM
Subject: CCL:G: Resonance energy

Robert, I ag= ree on that Truhlar (and Friedman) are central references on this. However,= how can a program (like Gaussian for isntance) be used to apply their mode= l for resonance?
= Amy's suggestion is quite interesting, and could be a way to get a glance o= f resonance for certain non-modifed PAHs for instance.
=
= Sergio
=
=

=  

=
=

= ----- = Original Message -----

=

= From: = Robert W. Gora robert.gora=3D=3D=3Dpwr.wroc.pl

=

= Sent: = 10/04/12 10:01 AM

=

= To: Ma= nzetti, Sergio

=

= Subjec= t: CCL: Resonance energy

=
=
=
=  
Dear A= my,
Dear All,

> Maybe my thinking is too simplistic. It seem= s like you could calculate the
> predicted value for the enthalpy of= complete hydrogenation of your system
> which would be N times (N= =3D# double bonds) that of one double bond). Then
> subtract the act= ual predicted value for the complete hydrogenation (which
> will be = less due to the resonance stabilization). That difference should be
>= ; the resonance energy of the system.

I don't think what you propos= e to calculate constitutes the resonance
stabilization energy even thou= gh the enthalpy of hydrogenation is obviously
somehow related.

= Apart from the recent paper by Rashid et al. I have mentioned previously, I=
could recommend a discussion in the Journal of Chemical Education that=
originated from Robert C. Kerber's paper "If It’s Resonance, Wha= t Is
Resonating?" [DOI 10.1021/ed083p223].

Personally, I am par= ticularly fond of Donald G. Truhlar's reply "The Concept
of Resonance" = ibid [DOI 10.1021/ed084p781], which captures the essence of
resonance a= s it is understood in the quantum chemistry community:

"The meaning= of resonance energy as it appears in valence bond theory is the
loweri= ng of the calculated ground state electronic energy when one improves a quantum mechanical model containing a single valence bond structure in the=
wave function to include other significant valence bond structures." W= here the
term structure corresponds to "a single set of spin orbitals w= ith a spin
coupling corresponding to a particular covalent or ionic bon= ding scheme."

Best,
Robert

PS. By the way, I apologize = Brian Salter-Duke for forgetting to mention his
excellent code ;)
<= br>--
Robert W. G=F3ra, Theoretical Chemistry Group, ICHFiT, WUT [http:= //zcht.info]
[http://www.researchgate.net/profile/Robert_Gora]
[htt= p://www.researcherid.com/rid/B-3919-2010] =
=
=
=

=  

=
=

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From owner-chemistry@ccl.net Fri Oct 5 11:15:00 2012 From: "Robert W. Gora robert.gora:-:pwr.wroc.pl" To: CCL Subject: CCL: [CCL] Resonance energy Message-Id: <-47726-121005111431-8744-F5J5nz2XhaVy5a71LFwYFQ.@.server.ccl.net> X-Original-From: "Robert W. Gora" Content-type: multipart/mixed; boundary="Boundary_(ID_RpcPOom/6fuO2sqhyw2rpw)" Date: Fri, 05 Oct 2012 17:14:23 +0200 (CEST) MIME-version: 1.0 Sent to CCL by: "Robert W. Gora" [robert.gora=-=pwr.wroc.pl] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. --Boundary_(ID_RpcPOom/6fuO2sqhyw2rpw) Content-type: TEXT/PLAIN; charset=iso-8859-1; format=flowed Content-transfer-encoding: 8BIT >> Naturally I meant Coper's CASVB being virtually identical to SCVB. Actually >> nowadays one can use this code to perform also fully variational CASVB >> calculations by optimizing SCVB complement which is indeed equivalent to SCVB. > > I am not quite sure what you are saying here. Cooper's CASVB is indeed > equal to SCVB, but the number of structures is much less than in the > VB2000 CASVB [...] Dear Brian, Thank you for the explanations and references. Regarding "variants" of CASVB originally there were two methods proposed by Thorsteinsson et al. for orbital transformation in order to obtain the representation of CASSCF wavefunction in terms of SCVB wavefunction: one maximizing the overlap of \psi_{cas} and \psi_{vb} and another one minimizing the energy functional. Now in molpro and molcas one can perform also fully variational optimization. For instance for benzene, CASSCF(6,6)/6-31G**, rumer basis, I obtain: Overlap-based optimization: -230.779129404139 Energy-based optimization: -230.779452892679 Fully variational: -230.779551675762 CASSCF(6,6) -230.787092620226 Best, Robert -- Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.info] [http://www.researchgate.net/profile/Robert_Gora] [http://www.researcherid.com/rid/B-3919-2010] --Boundary_(ID_RpcPOom/6fuO2sqhyw2rpw)-- From owner-chemistry@ccl.net Fri Oct 5 12:50:00 2012 From: "Stephen P. Molnar s.molnar**sbcglobal.net" To: CCL Subject: CCL: PharmBench v1.0 Community Benchmarking Dataset Message-Id: <-47727-121005122353-6664-hZkanY+tr7kvAhKgBC5U8Q]-[server.ccl.net> X-Original-From: "Stephen P. Molnar" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 5 Oct 2012 12:23:39 -0400 MIME-Version: 1.0 Sent to CCL by: "Stephen P. Molnar" [s.molnar*sbcglobal.net] Unfortunately, according to your web site that page cannot be found. Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 -----Original Message----- > From: owner-chemistry+s.molnar==sbcglobal.net[#]ccl.net [mailto:owner-chemistry+s.molnar==sbcglobal.net[#]ccl.net] On Behalf Of Simon Cross simon _ moldiscovery.com Sent: Friday, October 05, 2012 6:55 AM To: Molnar, Stephen P. Subject: CCL: PharmBench v1.0 Community Benchmarking Dataset Sent to CCL by: Simon Cross [simon],[moldiscovery.com] Dear Colleagues, We would like to draw your attention to the publication of the PharmBench 1.0 dataset for the evaluation of molecular alignment and pharmacophore elucidation approaches. The dataset consists of 81 targets, containing 960 ligands in total. The dataset is based on known pharmaceutically relevant co-crystallised protein ligand complexes, which were filtered to leave high-resolution structures containing drug-like small molecule ligands, for which electron density is also available at the EDS server. For each target the structures have been aligned using the receptor backbone atoms, and then the ligands extracted and prepared by fixing their atom types and adding hydrogen atoms. The datasets therefore contain target ligands, aligned in the biologically relevant frame of reference, to act as a 'gold standard' reference set. The two-dimensional structures of these ligands are also provided. An ideal molecular alignment or pharmacophore elucidation method should be able to read the two-dimensional input structures, and output three-dimensional alignments of the ligands that are equivalent to the gold standard alignments. In the coming weeks a web service will be set up to enable user-provided alignment models to be evaluated using the same approach as described in the publication (dx.doi.org/10.1021/ci300154n). The dataset is available at pharmbench.moldiscovery.com. Kind regards, Simon -- Dr. Simon Cross Snr Scientist & Product Manager Molecular Discovery Ltd simon[at]moldiscovery[dot]com +44 7980 572278http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Oct 5 14:15:00 2012 From: "Sharan sara180681]-[gmail.com" To: CCL Subject: CCL:G: Polymer Construction Message-Id: <-47728-121005134945-11344-1bWQpb8zKvQ2ihZTvsy3JQ_-_server.ccl.net> X-Original-From: Sharan Content-Type: multipart/alternative; boundary=bcaec54ee77cd87f2204cb537ee5 Date: Fri, 5 Oct 2012 23:19:37 +0530 MIME-Version: 1.0 Sent to CCL by: Sharan [sara180681()gmail.com] --bcaec54ee77cd87f2204cb537ee5 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi Gkourmpis Thomas At first i would like to thank, for you reply. In Gauss View using Periodic Boundary Conditions (PBC) one can construct Polymer unit cell, after which super cell is constructed. This resembles the whole polymer, is what my understanding. I don't think so the constrain of, number of repeating units comes into picture. But my problem is the steps given for building the unit cell is not clear to me. There are 20 steps, using these steps i want to construct a polymer of my interest. When you say "construct by hand are you referring to PBC or just regular 3D structure of a monomer? With regards Saravanan On Thu, Oct 4, 2012 at 4:02 PM, Gkourmpis, Thomas Thomas.Gkourmpis## borealisgroup.com wrote: > Hi**** > > ** ** > > Regarding the polymer in Gaussian the question is how many repeating unit= s > you need. If you need only a few units and each is small you can always > construct it by hand in GaussView. If on the other hand you want a =93pro= per=94 > chain with many units then you=92ll be better off if you use any of the > builders used in Molecular Dynamics packages and construct your system > there. Then you can convert it to any file that Gaussian can read and use > it as you see fit.**** > > ** ** > > Have I answered your question or I misunderstood something?**** > > ** ** > > Thomas**** > > ** ** > > *From:* owner-chemistry+thomas.gkourmpis=3D=3Dborealisgroup.com-x-ccl.net= [mailto: > owner-chemistry+thomas.gkourmpis=3D=3Dborealisgroup.com-x-ccl.net] *On Be= half > Of *Sharan sara180681%%gmail.com > *Sent:* Thursday, October 04, 2012 10:59 AM > *To:* Gkourmpis, Thomas > *Subject:* CCL:G: Polymer Construction**** > > ** ** > > Hi **** > > **** > > Can somebody help me in constructing Polymeric unit in Gaussian for > optimization. I am not clear on constructing the Translational vector for > polymeric unit. I went through the example given in Gaussian 03, I am not > clear on few fixed values supplied in the examples in constructing the > polymeric unit. **** > > **** > > Some helping hand will be greateful.. thanks in advance.**** > > **** > > With best regards**** > > **** > > **************************************************** > Dr. I. SARAVANAN, M.Sc., M.Phil., PGDCA., PGDHRM., Ph.D., > Consultant, ***** > This Email and any files transmitted with it are confidential and intende= d > solely for the use of the individual or the entity to whom it is addresse= d. > If you have received this Email by error, please notify the sender and > delete the material from any storage device. Borealis extends no warranti= es > and makes no representations as to the accuracy or completeness of the > information provided. It is the customer's responsibility to inspect and > test our products and technical advice in order to satisfy itself as to t= he > suitability of the products and technical advice for the customer's > particular purpose. --=20 ************************************************** Dr. I. SARAVANAN, M.Sc., M.Phil., PGDCA., PGDHRM., Ph.D., Consultant, **PerkinElmer Informatics,* UVJ Technologies Pvt.Ltd, 3rd Floor ,Plot No. 16 A, Cochin Special Economic Zone (CSEZ) Seaport Airport Road, Kakkanad, Cochin - 682 037 Kerala ************************************************** Res: No. 10, Neithal street, Solainagar, Muthialpet, Puducherry - 605 003 Cell: 9895079171 ************************************************** --bcaec54ee77cd87f2204cb537ee5 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
Hi Gkourmpis Thomas
=A0
At first i would like to t= hank, for you reply.
=A0
In Gauss View using Periodic = Boundary Conditions (PBC) one can construct Polymer unit cell, after which = super cell is constructed. This resembles the whole polymer, is what my und= erstanding. I don't think so the constrain of, number of repeating unit= s comes into picture.
=A0
=A0
But my problem is the steps given for buil= ding the unit cell is not clear to me. There are 20 steps, using these step= s=A0i want to construct a polymer of my interest.
=A0
W= hen you say "construct by hand are you referring to PBC or just regula= r 3D structure of a monomer?
=A0
With regards
Saravanan

On Thu, Oct 4, 2012 at 4:02 PM, Gkourmpis, Thomas Thomas.G= kourmpis##borealisgroup.com <owner-chemistry#,#ccl.net> wrote:
Hi

= =A0

Regarding the polymer in Gaussian the question is how many repeati= ng units you need. If you need only a few units and each is small you can a= lways construct it by hand in GaussView. If on the other hand you want a = =93proper=94 chain with many units then you=92ll be better off if you use a= ny of the builders used in Molecular Dynamics packages and construct your s= ystem there. Then you can convert it to any file that Gaussian can read and= use it as you see fit.

=A0

Have I answered your question or I misunder= stood something?

=A0

Thomas=

=A0

From: owner-chemistry+thomas.gkourmpis=3D=3Dborealisgroup.com-x-ccl.net [mailto:owner-chemistry+thomas.gkourmpis=3D=3Dborealisgroup.com-x-ccl.net] On Behalf Of Sharan sara180681%%gmail.com
Sent: Thursday, October 04, 2012 10:59 AM
To: Gkourmpis, T= homas
Subject: CCL:G: Polymer Construction

=A0

=

Hi

=A0

Can somebody help= me in constructing Polymeric unit in Gaussian for optimization. I am not c= lear on constructing the Translational vector for polymeric unit. I=A0went = through the example given in Gaussian 03, I am not clear on few fixed value= s supplied in the examples in constructing the polymeric unit.

=A0

Some helping hand will be greateful.. thanks in advance.<= /u>

=A0

=

With best regards

=A0=

******************= *******************************
Dr. I. SARAVANAN, M.= Sc., M.Phil., PGDCA., PGDHRM., Ph.D.,
Consultant,

=
This Email and any files transmitted with it are confidential and intended = solely for the use of the individual or the entity to whom it is addressed.= If you have received this Email by error, please notify the sender and del= ete the material from any storage device. Borealis extends no warranties an= d makes no representations as to the accuracy or completeness of the inform= ation provided. It is the customer's responsibility to inspect and test= our products and technical advice in order to satisfy itself as to the sui= tability of the products and technical advice for the customer's partic= ular purpose.



--
***********************= **************************
Dr. I. SARAVANAN, M.Sc., M.Phil., PGDCA., PGD= HRM., Ph.D.,
Consultant, PerkinElmer Informatics,
UVJ Technologies Pvt.Ltd, 3rd Floor ,Plot No. 16 A, Cochin Special Eco= nomic Zone (CSEZ) Seaport Airport Road, Kakkanad,
Cochin - 682 03= 7
Kerala =09
*************************************************
Re= s: No. 10, Neithal street, Solainagar, Muthialpet,
Puducherry - 605 003<= br>Cell: 9895079171
*************************************************

--bcaec54ee77cd87f2204cb537ee5--