From owner-chemistry@ccl.net Wed Apr 19 10:42:00 2006 From: "IEJMD iejmd],[yahoo.com" To: CCL Subject: CCL: Start of CoEPrA 2006 - Data Modeling Competition Message-Id: <-31550-060418190537-19324-itSRKv7pqo9GdqlhdUFvjQ]![server.ccl.net> X-Original-From: IEJMD Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 18 Apr 2006 15:05:29 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: IEJMD [iejmd,+,yahoo.com] CoEPrA 2006 - Comparative Evaluation of Prediction Algorithms http://www.coepra.org/ CoEPrA Group http://groups.google.com/group/CoEPrA The CoEPrA 2006 data modeling competition started on April 17th, and the first two datasets are available from http://www.coepra.org/. CoEPrA (Comparative Evaluation of Prediction Algorithms) is a modeling competition organized to provide an objective testing for various classification and regression algorithms via the process of blind prediction. The problems proposed in the CoEPrA experiment are selected from cheminformatics, drug design, QSAR, bioinformatics, computational biology, medicine, toxicology, microarray gene expression data, and proteomics. The goal of the CoEPrA competition is to advance the algorithms and software for modeling chemical, biological, and medical data, with special emphasis on the prediction of physico-chemical properties and biological activities from molecular descriptors derived from the chemical structure. For details, see http://www.coepra.org/ and http://groups.google.com/group/CoEPrA Best regards, Ovidiu Ivanciuc ###################################### Ovidiu Ivanciuc Sealy Center for Structural Biology and Molecular Biophysics Department of Biochemistry and Molecular Biology University of Texas Medical Branch 301 University Boulevard Galveston, Texas 77555-0857 USA URL: http://ivanciuc.org/ Email: oiivanci:-:utmb.edu Email: iejmd:-:yahoo.com IEJMD: http://www.biochempress.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Wed Apr 19 11:17:02 2006 From: "Wendy Cornell wendy_cornell__merck.com" To: CCL Subject: CCL: Fall ACS in San Francisco - COMP abstract deadline is April 28 Message-Id: <-31551-060419101111-20594-Il+sOLxlR7+Tgke5xtYgYA{}server.ccl.net> X-Original-From: "Wendy Cornell" Date: Wed, 19 Apr 2006 10:11:08 -0400 Sent to CCL by: "Wendy Cornell" [wendy_cornell~!~merck.com] Fall 2006 ACS National Meeting, San Francisco, CA, September 10-14, 2006 The deadline for abstract submission to the COMP division for the Fall National Meeting is San Francisco has been extended to April 28. http://Oasys.acs.org The following symposia are scheduled. Contact information for organizers of individual symposia can be found on the oasys web site. Emerging Technologies in Computational Chemistry Beyond Michael Dewar's Legacy: Modern Semiempirical MO Theory Tight Binding DFT: Theory and Applications Molecular Similarity and Indexing Methods Current Trends in Molecular Docking and Virtual Screening Free Energy Computations in Drug Discovery Structure-Based Design & Development of Estrogen Receptor Modulators ADME and Property Prediction Careers for Computational Chemists in Pharma, Biotech, Patent Firms, Software Vendors, National Labs, and the National Institutes of Health General Oral Drug Discovery General Oral Molecular Mechanics and Simulation General Oral Quantum Chemistry Poster Session Regards, -Wendy Cornell COMP Program Chair Wendy Cornell, Ph.D. Director Molecular Systems Basic Chemistry Merck Research Laboratories Rahway, NJ 732-594-4954 From owner-chemistry@ccl.net Wed Apr 19 11:52:01 2006 From: "Wendy Cornell wendy_cornell~!~merck.com" To: CCL Subject: CCL: Fall ACS in San Francisco - COMP abstract deadline is April 28 Message-Id: <-31552-060419102302-22625-eu1NsLLR5OVtozQ9HU8dmg..server.ccl.net> X-Original-From: "Wendy Cornell" Date: Wed, 19 Apr 2006 10:23:01 -0400 Sent to CCL by: "Wendy Cornell" [wendy_cornell,merck.com] Fall 2006 ACS National Meeting, San Francisco, CA, September 10-14, 2006 The deadline for abstract submission to the COMP division for the Fall National Meeting is San Francisco has been extended to April 28. http://Oasys.acs.org The following symposia are scheduled. Contact information for organizers of individual symposia can be found on the oasys web site. -Emerging Technologies in Computational Chemistry -Beyond Michael Dewar's Legacy: Modern Semiempirical MO Theory -Tight Binding DFT: Theory and Applications -Molecular Similarity and Indexing Methods -Current Trends in Molecular Docking and Virtual Screening -Free Energy Computations in Drug Discovery -Structure-Based Design & Development of Estrogen Receptor Modulators -ADME and Property Prediction -Careers for Computational Chemists in Pharma, Biotech, Patent Firms, Software Vendors, National Labs, and the National Institutes of Health -General Oral Drug Discovery -General Oral Molecular Mechanics and Simulation -General Oral Quantum Chemistry -Poster Session Regards, -Wendy Cornell COMP Program Chair Wendy Cornell, Ph.D. Director Molecular Systems Basic Chemistry Merck Research Laboratories Rahway, NJ 732-594-4954 From owner-chemistry@ccl.net Wed Apr 19 12:27:00 2006 From: "Ramon Crehuet rcsqtc .. iiqab.csic.es" To: CCL Subject: CCL:G: Frequency calculation with fixed atoms. Message-Id: <-31553-060419110608-6638-6bGMPAXmeivE5Zxarqjj4w~~server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 19 Apr 2006 17:06:39 +0200 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc .. iiqab.csic.es] Dear CCLers, A few weeks ago I posted a question on how to calculate frequencies when a number of atoms are fixed. I got a solution, but now we have a related problem. I have used the ONIOM method in Gaussian 03 to optimize a transition state structure keeping several atoms fixed, but I have come up with a problem when reading a hessian. Firstly, I did a frequency calculation on the free atoms, including "-1" on frozen atoms an "0" on free atoms, and I obtained 1 negative eigenvalue: / 1 2 3 A A A Frequencies -- -41.1853 54.9227 70.3016 Red. masses -- 6.2379 7.0722 3.5451 Frc consts -- 0.0062 0.0126 0.0103 IR Inten -- 17.8501 1.2021 1.2536 Atom AN X Y Z X Y Z X Y Z 1 8 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2 6 0.01 -0.02 -0.03 0.00 0.07 0.02 0.19 0.29 -0.13 3 8 0.01 -0.01 -0.05 0.00 0.06 0.03 0.04 0.10 -0.01/ When I read the hessian from the checkpoint file (using the ReadFC keyword), in order to optimize the TS, I find that apparently the first point of the procedure does not use the previous hessian because now it has 5 negative eigenvalues: /Search for a saddle point. Step number 1 out of a maximum of 696 All quantities printed in internal units (Hartrees-Bohrs-Radians) Swaping is turned off. Second derivative matrix not updated -- first step. Eigenvalues --- -0.00345 -0.00110 -0.00033 -0.00022 -0.00004 Eigenvalues --- 0.00002 0.00004 0.00016 0.00017 0.00032 Eigenvalues --- 0.00033 0.00036 0.00041 0.00047 0.00051/ In addition, if I calculate the hessian analitically at the first point instead of reading it from a checkpoint file (using the CalcFC keyword) I obtain 4 negative eigenvalues: / Search for a saddle point. Step number 1 out of a maximum of 696 All quantities printed in internal units (Hartrees-Bohrs-Radians) Swaping is turned off. Second derivative matrix not updated -- analytic derivatives used. Eigenvalues --- -0.00053 -0.00020 -0.00014 -0.00002 0.00009 Eigenvalues --- 0.00016 0.00017 0.00018 0.00025 0.00027 Eigenvalues --- 0.00036 0.00039 0.00054 0.00066 0.00080/ It is clear that the hessian it reads is different from either the one > from the checkpoint file or the one it calculates. Why are there these differences, if they should all be the same? And, how should I carry out the TS optimization successfully? Thanks in advance, Ramon From owner-chemistry@ccl.net Wed Apr 19 13:02:02 2006 From: "Pablo Echenique Robba pnique*o*unizar.es" To: CCL Subject: CCL: orientation of the atomic orbitals Message-Id: <-31554-060419121158-12119-pZU31dnbQER9LD3vfBYgSQ[A]server.ccl.net> X-Original-From: Pablo Echenique Robba Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 19 Apr 2006 18:11:48 +0200 MIME-Version: 1.0 Sent to CCL by: Pablo Echenique Robba [pnique(_)unizar.es] Dear CCLers, I apologize in advance for a set of very basic questions: Say I have a nonsymmetrical molecule and I want to perform an ab initio Quantum Chemistry calculation (HF, MP2, ... it does not matter). Say I choose a basis set and work with Cartesian GTOs (6 d functions, 10 f functions, etc.). ¿Are, for example, all the p_x orbitals paralell in all the atoms of the molecule? ¿How are oriented the orbitals with angular momentum 1 or higher? ¿Is is trivial to prove that, say, the energy does not depend on the choice of this orientation? ¿Does the situation change in any way if I work with spherical GTOs? Thanks for your patience and regards, Pablo. -- ------------------------------------ Pablo Echenique Robba Departamento de Fisica Teorica & Instituto de Biocomputacion y Fisica de los Sistemas Complejos BIFI Universidad de Zaragoza 50009 Zaragoza Spain Tel.: 34 976761260 E-mail: pnique-#-unizar.es ------------------------------------ From owner-chemistry@ccl.net Wed Apr 19 13:39:00 2006 From: "Shobe, David dshobe**sud-chemieinc.com" To: CCL Subject: CCL:G: Frequency calculation with fixed atoms. Message-Id: <-31555-060419133449-10160-/EIvUGeVrQG+EEit3bhwEQ:server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 19 Apr 2006 19:34:36 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe]=[sud-chemieinc.com] Ramon, When you use calcfc, you un-freeze the frozen atoms. So you'll have to freeze them again. Something similar may be happenign with readfc. What exactly are you trying to do here? Have you optimized the TS using the constraints (the frozen atoms) and now you want to remove these constraints and re-optimize? Or do you want to keep the previously frozen atoms frozen? --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry*o*ccl.net [mailto:owner-chemistry*o*ccl.net] Sent: Wednesday, April 19, 2006 12:31 PM To: Shobe, David Subject: CCL:G: Frequency calculation with fixed atoms. Sent to CCL by: Ramon Crehuet [rcsqtc .. iiqab.csic.es] Dear CCLers, A few weeks ago I posted a question on how to calculate frequencies when a number of atoms are fixed. I got a solution, but now we have a related problem. I have used the ONIOM method in Gaussian 03 to optimize a transition state structure keeping several atoms fixed, but I have come up with a problem when reading a hessian. Firstly, I did a frequency calculation on the free atoms, including "-1" on frozen atoms an "0" on free atoms, and I obtained 1 negative eigenvalue: / 1 2 3 A A A Frequencies -- -41.1853 54.9227 70.3016 Red. masses -- 6.2379 7.0722 3.5451 Frc consts -- 0.0062 0.0126 0.0103 IR Inten -- 17.8501 1.2021 1.2536 Atom AN X Y Z X Y Z X Y Z 1 8 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2 6 0.01 -0.02 -0.03 0.00 0.07 0.02 0.19 0.29 -0.13 3 8 0.01 -0.01 -0.05 0.00 0.06 0.03 0.04 0.10 -0.01/ When I read the hessian from the checkpoint file (using the ReadFC keyword), in order to optimize the TS, I find that apparently the first point of the procedure does not use the previous hessian because now it has 5 negative eigenvalues: /Search for a saddle point. Step number 1 out of a maximum of 696 All quantities printed in internal units (Hartrees-Bohrs-Radians) Swaping is turned off. Second derivative matrix not updated -- first step. Eigenvalues --- -0.00345 -0.00110 -0.00033 -0.00022 -0.00004 Eigenvalues --- 0.00002 0.00004 0.00016 0.00017 0.00032 Eigenvalues --- 0.00033 0.00036 0.00041 0.00047 0.00051/ In addition, if I calculate the hessian analitically at the first point instead of reading it from a checkpoint file (using the CalcFC keyword) I obtain 4 negative eigenvalues: / Search for a saddle point. Step number 1 out of a maximum of 696 All quantities printed in internal units (Hartrees-Bohrs-Radians) Swaping is turned off. Second derivative matrix not updated -- analytic derivatives used. Eigenvalues --- -0.00053 -0.00020 -0.00014 -0.00002 0.00009 Eigenvalues --- 0.00016 0.00017 0.00018 0.00025 0.00027 Eigenvalues --- 0.00036 0.00039 0.00054 0.00066 0.00080/ It is clear that the hessian it reads is different from either the one > from the checkpoint file or the one it calculates. Why are there these differences, if they should all be the same? And, how should I carry out the TS optimization successfully? Thanks in advance, Ramonhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Wed Apr 19 16:43:01 2006 From: "Mark Zottola mzottola:_:gmail.com" To: CCL Subject: CCL: AIM charges - HF or DFT? Message-Id: <-31556-060419122251-26704-IZKjPV3rz2DzjcaaJQJZWA(a)server.ccl.net> X-Original-From: "Mark Zottola" Content-Type: multipart/alternative; boundary="----=_Part_73906_5855828.1145460402501" Date: Wed, 19 Apr 2006 11:26:42 -0400 MIME-Version: 1.0 Sent to CCL by: "Mark Zottola" [mzottola{=}gmail.com] ------=_Part_73906_5855828.1145460402501 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I have never heard this statement (see below) proffered nor defended. Are there references to substantiate this statement?? More over, it is truly difficult to believe that an RHF wavefunction provides a better wavefunctio= n than say B3LYP (at an identical basis set) for the description of electron density topology. Are there references to substantiate such an unusual claim? Mark On 4/17/06, Eduard Matito ematito_-_gmail.com wrote: > > Sent to CCL by: Eduard Matito [ematito=3D=3D=3Dgmail.com] > Dear David, > > > First of all, is a HF or a DFT wave function better? What about the > > hybrid=3D > > B3LYP?=3D20=3D20 > > > > > B3LYP geometries are far better than HF ones, but HF is actually the > best monodeterminantal wavefunction > by definition, so I would rather consider using HF wavefunction. In > addition to QTAIM charges a useful tool > for the analysis of the electron distributions are the so-called > localization/delocalization indexes (LI and DI). > See for instance the following papers: > X. Fradera, M. A. Austen, and R. F. W. Bader, J. Phys. Chem. A, 1999, > 103, 304. > J. Poater, M. Sola, M. Duran, and X. Fradera, Theo. Chem. Acc., 2002, > 107, 362. > ------=_Part_73906_5855828.1145460402501 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
I have never heard this statement (see below) proffered nor defen= ded.  Are there references to substantiate this statement??  More= over, it is truly difficult to believe that an RHF wavefunction provides a= better wavefunction than say B3LYP (at an identical basis set) for the des= cription of electron density topology.  Are there references to substa= ntiate such an unusual claim?
 

Mark
 
On 4/17/06, = Eduard Matito ematito_-_gmail.com <owner-chemistry{=}ccl.net> wrote:
Sent to CCL by: Eduard Matito [e= matito=3D=3D=3Dgmail.com]
Dear David,
> First of all, is a HF or a DFT wave function better?  = What about the
> hybrid=3D
> B3LYP?=3D20=3D20
>
>
B3LYP geomet= ries are far better than HF ones, but HF is actually the
best monodeterm= inantal wavefunction
by definition, so I would rather consider using HF = wavefunction. In
addition to QTAIM charges a useful tool
for the analysis of the elec= tron distributions are the so-called
localization/delocalization indexes= (LI and DI).
See for instance the following papers:
X. Fradera, M. A= . Austen, and R. F. W. Bader, J. Phys. Chem. A, 1999,
103, 304.
J. Poater, M. Sola, M. Duran, and X. Fradera, Theo. Chem. = Acc., 2002,
107, 362.
------=_Part_73906_5855828.1145460402501-- From owner-chemistry@ccl.net Wed Apr 19 19:33:00 2006 From: "Ana Celia Araujo Vila Verde avilaverde---engr.psu.edu" To: CCL Subject: CCL: how to prevent rotational motion in MD simulations Message-Id: <-31557-060419120313-8583-22zHL3MSjrNfJkxsgQsWzw|a|server.ccl.net> X-Original-From: "Ana Celia Araujo Vila Verde" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C663C4.24D82D20" Date: Wed, 19 Apr 2006 11:15:50 -0400 MIME-Version: 1.0 Sent to CCL by: "Ana Celia Araujo Vila Verde" [avilaverde .. engr.psu.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C663C4.24D82D20 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, =20 I'm doing molecular dynamics simulations of a single polymer chain in a = vacuum and the chain is spinning around its centre of mass. The code I = use already removes the translation of the centre of mass, but I am = concerned that too much energy is passed onto the rotational degree of = freedom and not enough energy is kept at the vibrational DOFs of the = molecule, so I'd like to remove the rotational DOF also during the MD = simulation. =20 Could anyone point me to either an article describing an algorithm or to = a freely available code that does this?=20 =20 Thank you, =20 Ana Vila Verde =20 (Penn State University, Department of Chemical Engineering) ------_=_NextPart_001_01C663C4.24D82D20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
=0A=
 
=0A=
I'm doing molecular dynamics = simulations of a =0A= single polymer chain in a vacuum and the chain is spinning around its = centre of =0A= mass. The code I use already removes the translation of the centre of = mass, but =0A= I am concerned that too much energy is passed onto the rotational degree = of =0A= freedom and not enough energy is kept at the vibrational DOFs of = the =0A= molecule, so I'd like to remove the rotational DOF also during the MD =0A= simulation.
=0A=
 
=0A=
Could anyone point me to either an = article =0A= describing an algorithm or to a freely available code that does this? =0A=
=0A=
 
=0A=
Thank you,
=0A=
 
=0A=
Ana Vila Verde
=0A=
 
=0A=
(Penn State University, Department of = Chemical =0A= Engineering)
------_=_NextPart_001_01C663C4.24D82D20-- From owner-chemistry@ccl.net Wed Apr 19 20:45:01 2006 From: "Steven Z yzhao_+_mail.sioc.ac.cn" To: CCL Subject: CCL: Where to download pdb ligand files? Message-Id: <-31558-060417232021-4808-cRue/Spwt96EjQjN31wUyA[A]server.ccl.net> X-Original-From: "Steven Z" Date: Mon, 17 Apr 2006 23:20:19 -0400 Sent to CCL by: "Steven Z" [yzhao++mail.sioc.ac.cn] Hi, CCLers I'm writing a PDB converting program and I need some diversity structures to test it. I know that there are about 6400 ligands in Protein Data Bank. Can anybody tell me where can I download those PDB ligand files? Thanks in advance. Best wishes. Steven ============================================================ State Key Lab of Bio-organic and Natural Products Chemistry Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Sciences. Addr. 354, Fenglin Road, Shanghai, China. Tel.: +86-21-54925275 Email: yzhao:mail.sioc.ac.cn From owner-chemistry@ccl.net Wed Apr 19 21:36:00 2006 From: "Chris Moth chris.moth*o*vanderbilt.edu" To: CCL Subject: CCL: Imidazoliums Message-Id: <-31559-060419153328-27875-9ZBvrVZTzxE/BeRoZ6Ga8Q+/-server.ccl.net> X-Original-From: Chris Moth Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 19 Apr 2006 13:47:33 -0500 MIME-Version: 1.0 Sent to CCL by: Chris Moth [chris.moth^^vanderbilt.edu] You might take a peek at the "HIP" (protonated histidine) residue in the AMBER force field for some inspiration/validation. See page 5190 of Cornell et. al, J. Am. Chem. SOC. 1995, 117, 5179-5197 Though, imidazolium should likely be parameterized in the context of your particular MD force field. John Daily john.daily],[colorado.edu wrote: > Sent to CCL by: John Daily [john.daily,colorado.edu] > > --Apple-Mail-3--396696999 > Content-Transfer-Encoding: 7bit > Content-Type: text/plain; > charset=US-ASCII; > delsp=yes; > format=flowed > > Folks, > > Does anyone have experience with charged imidazoliums? I am doing > molecular dynamic calculations on small droplets of ionic liquids. > Obviously as the size of the drops increases, using quantum methods > gets too expensive. However, I have not been able to find force field > parameters for N+ CCNC five member rings. In particular bond > stretching, angle bending and torsional parameters. > > Any suggestions appreciated. > > John > University of Colorado at Boulder > > > --Apple-Mail-3--396696999 > Content-Transfer-Encoding: quoted-printable > Content-Type: text/html; > charset=ISO-8859-1 > > -khtml-line-break: after-white-space; ">Folks,

class=3D"khtml-block-placeholder">
Does anyone have experience = > with charged imidazoliums? I am doing molecular dynamic calculations on = > small droplets of ionic liquids. Obviously as the size of the drops = > increases, using quantum methods gets too expensive. However, I have not = > been able to find force field parameters for N+ CCNC five member rings. = > In particular bond stretching, angle bending and torsional = > parameters.=A0

class=3D"khtml-block-placeholder">
Any suggestions = > appreciated.

class=3D"khtml-block-placeholder">
John

style=3D"margin: 0.0px 0.0px 0.0px 0.0px"> size=3D"3" style=3D"font: 12.0px Helvetica">University of Colorado at = > Boulder


class=3D"khtml-block-placeholder">= > > --Apple-Mail-3--396696999--> > > > > From owner-chemistry@ccl.net Wed Apr 19 22:44:00 2006 From: "Christopher Cramer cramer*chem.umn.edu" To: CCL Subject: CCL: AIM charges - HF or DFT? Message-Id: <-31560-060419222109-18184-RyhGKDb5O7QGC/0mkpNvdw[#]server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-1--313972720 Date: Wed, 19 Apr 2006 20:35:51 -0500 Mime-Version: 1.0 (Apple Message framework v749.3) Sent to CCL by: Christopher Cramer [cramer(_)chem.umn.edu] --Apple-Mail-1--313972720 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Actually, the claim was somewhat less than specific, which may cause confusion. I believe that what was meant was that the HF wave function is the variational minimum within the approximation of a single Slater determinant being used for the wave function. Thus, > from an energy criterion, it is clearly better than any DFT Kohn-Sham "wave function" (that is, if you evaluate the expectation value of the normal Hamiltonian over any Kohn-Sham single determinant (using the same basis set) you will always get an energy higher than the HF energy). However, that the approximate wave function is a variational minimum for the Hamiltonian in no way guarantees that the density from that wave function is more accurate than that from a DFT determinant. One would need a criterion to establish the "goodness" of a density, and such criteria are hard to come by. Experimental densities are not easily measured for isolated, gas-phase molecules, and we do not know the exact functional for most systems, so that is not a great option either. Job security for theoretical/computational folks... Cheers, Chris On Apr 19, 2006, at 4:06 PM, Mark Zottola mzottola:_:gmail.com wrote: > Sent to CCL by: "Mark Zottola" [mzottola{=}gmail.com] > ------=_Part_73906_5855828.1145460402501 > Content-Type: text/plain; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > I have never heard this statement (see below) proffered nor > defended. Are > there references to substantiate this statement?? More over, it is > truly > difficult to believe that an RHF wavefunction provides a better > wavefunctio= > n > than say B3LYP (at an identical basis set) for the description of > electron > density topology. Are there references to substantiate such an > unusual > claim? > > > Mark > > On 4/17/06, Eduard Matito ematito_-_gmail.com ccl.net> > wrote: >> >> Sent to CCL by: Eduard Matito [ematito=3D=3D=3Dgmail.com] >> Dear David, >> >>> First of all, is a HF or a DFT wave function better? What about the >>> hybrid=3D >>> B3LYP?=3D20=3D20 >>> >>> >> B3LYP geometries are far better than HF ones, but HF is actually the >> best monodeterminantal wavefunction >> by definition, so I would rather consider using HF wavefunction. In >> addition to QTAIM charges a useful tool >> for the analysis of the electron distributions are the so-called >> localization/delocalization indexes (LI and DI). >> See for instance the following papers: >> X. Fradera, M. A. Austen, and R. F. W. Bader, J. Phys. Chem. A, 1999, >> 103, 304. >> J. Poater, M. Sola, M. Duran, and X. Fradera, Theo. Chem. Acc., 2002, >> 107, 362. >> > > ------=_Part_73906_5855828.1145460402501 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > >
I have never heard this statement (see below) proffered > nor defen= > ded.  Are there references to substantiate this statement?? >   More= > over, it is truly difficult to believe that an RHF wavefunction > provides a= > better wavefunction than say B3LYP (at an identical basis set) for > the des= > cription of electron density topology.  Are there references > to substa= > ntiate such an unusual claim? >
>
 
>

Mark
 
>
On 4/17/06, class=3D"gmail_sendername">= > Eduard Matito ematito_-_gmail.com < chemistry= > %x%ccl.net">owner-chemistry%x%ccl.net> wrote: >
MARGIN: 0px 0= > px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Sent to CCL by: Eduard > Matito [e= > matito=3D=3D=3Dgmail.com]
Dear > David, r>
> First of all, is a HF or a DFT wave function better? >   = > What about the >
> hybrid=3D
> B3LYP? > =3D20=3D20
>
>
B3LYP geomet= > ries are far better than HF ones, but HF is actually the
best > monodeterm= > inantal wavefunction
by definition, so I would rather consider > using HF = > wavefunction. In >
addition to QTAIM charges a useful tool
for the analysis of > the elec= > tron distributions are the so-called
localization/delocalization > indexes= > (LI and DI).
See for instance the following papers:
X. > Fradera, M. A= > . Austen, and R. F. W. Bader, J. Phys. Chem. A, 1999, >
103, 304.
J. Poater, M. Sola, M. Duran, and X. Fradera, > Theo. Chem. = > Acc., 2002,
107, 362.
> > ------=_Part_73906_5855828.1145460402501-- > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer-,-pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-1--313972720 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Actually, the claim was somewhat = less than specific, which may cause confusion. I believe that what was = meant was that the HF wave function is the variational minimum within = the approximation of a single Slater determinant being used for the wave = function. Thus, from an energy criterion, it is clearly better than any = DFT Kohn-Sham "wave function" (that is, if you evaluate the expectation = value of the normal Hamiltonian over any Kohn-Sham single determinant = (using the same basis set) you will always get an energy higher than the = HF energy).

However, = that the approximate wave function is a variational minimum for the = Hamiltonian in no way guarantees that the density from that wave = function is more accurate than that from a DFT determinant. One would = need a criterion to establish the "goodness" of a density, and such = criteria are hard to come by. Experimental densities are not easily = measured for isolated, gas-phase molecules, and we do not know the exact = functional for most systems, so that is not a great option either. Job = security for theoretical/computational folks...

Cheers,

Chris

On Apr 19, 2006, at 4:06 PM, Mark Zottola mzottola:_:gmail.com = wrote:

Sent to CCL by: "Mark Zottola" = [mzottola{=3D}gmail.com]
Content-Type: text/plain; = charset=3DISO-8859-1
Content-Transfer-Encoding: = quoted-printable
Content-Disposition: = inline

I have never heard this statement (see below) = proffered nor defended.=A0 = Are
there references to substantiate = this statement??=A0 More = over, it is truly
difficult to believe that an RHF = wavefunction provides a better wavefunctio=3D
n
than say B3LYP (at an = identical basis set) for the description of electron
density topology.=A0 Are there references to = substantiate such an unusual



On 4/17/06, Eduard Matito ematito_-_gmail.com = <owner-chemistry%x%ccl.net>
wrote:
=
Sent to CCL by: Eduard Matito = [ematito=3D3D=3D3D=3D3Dgmail.com]
Dear = David,

=
First of all, is a HF or a = DFT wave function better?=A0 = What about the
hybrid=3D3D
B3LYP?=3D3D20=3D3D20


B3LYP = geometries are far better than HF ones, but HF is actually the
best monodeterminantal wavefunction
by definition, so I would rather consider using HF = wavefunction. In
addition to QTAIM charges a = useful tool
for the analysis of the electron = distributions are the so-called
See for instance the following papers:
X. Fradera, M. A. Austen, and R. F. W. Bader, J. = Phys. Chem. A, 1999,
103, 304.
J. Poater, M. Sola, M. Duran, and X. Fradera, Theo. = Chem. Acc., 2002,
107, 362.


Content-Type: text/html; = charset=3DISO-8859-1
Content-Transfer-Encoding: = quoted-printable
Content-Disposition: = inline

<div>I have never heard this statement (see = below)&nbsp;proffered nor defen=3D
=A0over, it is truly difficult to = believe that an RHF wavefunction provides a=3D
=A0better= wavefunction than say B3LYP (at an identical basis set) for the = des=3D
cription of electron density = topology.&nbsp; Are there references to substa=3D
ntiate such an unusual claim?
</div>
<div><span class=3D3D"gmail_quote">On = 4/17/06, <b class=3D3D"gmail_sendername">=3D
Eduard Matito ematito_-_gmail.com</b> = &lt;<a href=3D3D"mailto:owner-chemistry=3D
<blockquote = class=3D3D"gmail_quote" style=3D3D"PADDING-LEFT: 1ex; MARGIN: 0px = 0=3D
px 0px 0.8ex; BORDER-LEFT: #ccc = 1px solid">Sent to CCL by: Eduard Matito [e=3D
matito=3D3D=3D3D=3D3D<a href=3D3D"http://gmail.com">gmail.com</a>]<= ;br>Dear David,<b=3D
What about = the
<br>&gt; = hybrid=3D3D<br>&gt; = B3LYP?=3D3D20=3D3D20<br>&gt;<br>&gt;<br>B3LYP = geomet=3D
ries are far better than HF = ones, but HF is actually the<br>best monodeterm=3D
inantal wavefunction<br>by definition, so I = would rather consider using HF =3D
wavefunction. = In
<br>addition to QTAIM charges a useful = tool<br>for the analysis of the elec=3D
tron distributions are the = so-called<br>localization/delocalization indexes=3D
=A0(LI = and DI).<br>See for instance the following papers:<br>X. = Fradera, M. A=3D
. Austen, and R. F. W. Bader, J. = Phys. Chem. A, 1999,
<br>103, = 304.<br>J. Poater, M. Sola, M. Duran, and X. Fradera, Theo. Chem. = =3D
Acc., 2002,<br>107, = 362.<br></blockquote></div>




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--


Christopher J. Cramer

University of Minnesota

Department of Chemistry

207 Pleasant St. = SE

Minneapolis, MN 55455-0431

--------------------------

=

Phone:=A0 (612) 624-0859 || FAX:=A0 (612) 626-2006

Mobile: (952) = 297-2575

cramer-,-pollux.chem.umn.edu<= /FONT>

http://pollux.chem.umn.edu/~cr= amer

(website = includes information about the textbook "Essentials

=A0 =A0 of Computational = Chemistry:=A0 Theories and = Models, 2nd Edition")


=

= --Apple-Mail-1--313972720--