From owner-chemistry@ccl.net Wed Jun 26 08:15:00 2013 From: "Simon Cross simon . moldiscovery.com" To: CCL Subject: CCL: PharmBench v1.0 Community Benchmarking Dataset - Web Service Message-Id: <-48856-130626035503-22405-Z9TJZpS2khAePrFFiXvhmg!A!server.ccl.net> X-Original-From: Simon Cross Content-Type: multipart/alternative; boundary="------------020206070202090403060600" Date: Wed, 26 Jun 2013 09:54:49 +0200 MIME-Version: 1.0 Sent to CCL by: Simon Cross [simon:_:moldiscovery.com] This is a multi-part message in MIME format. --------------020206070202090403060600 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Everyone, several months ago we announced the release of the PharmBench dataset for evaluating molecular alignment and pharmacophore elucidation approaches. We have now added a web service so that you can score alignments according to the three approaches described in the paper (dx.doi.org/10.1021/ci300154n): 1. To measure how well the bioactive conformation of each ligand has been reproduced (rmsd) 2. To measure the overall alignment quality by aligning the model to the gold standard using an iterative approach; the percentage of ligands that are correct (<2.0 A) is reported (50% is the objective measure of success reported in the paper) 3. To measure the pharmacophoric similarity of the model compared to the gold standard in terms of their FLAPpharm Pharmacophoric Interaction Field similarities. There are of course limitations with each objective measure (for example the pharmacophoric regions may be identified correctly but the molecules not aligned well as a whole), however we think its a good starting point. The dataset and web service are available at pharmbench.moldiscovery.com. Best regards, Simon On 05/10/12 12:54, Simon Cross wrote: > 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 > --------------020206070202090403060600 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Hi Everyone, several months ago we announced the release of the PharmBench dataset for evaluating molecular alignment and pharmacophore elucidation approaches. We have now added a web service so that you can score alignments according to the three approaches described in the paper (dx.doi.org/10.1021/ci300154n):

  1. To measure how well the bioactive conformation of each ligand has been reproduced (rmsd)
  2. To measure the overall alignment quality by aligning the model to the gold standard using an iterative approach; the percentage of ligands that are correct (<2.0 A) is reported (50% is the objective measure of success reported in the paper)
  3. To measure the pharmacophoric similarity of the model compared to the gold standard in terms of their FLAPpharm Pharmacophoric Interaction Field similarities.

There are of course limitations with each objective measure (for example the pharmacophoric regions may be identified correctly but the molecules not aligned well as a whole), however we think its a good starting point.

The dataset and web service are available at pharmbench.moldiscovery.com.

Best regards,

Simon



On 05/10/12 12:54, Simon Cross wrote:
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


--------------020206070202090403060600-- From owner-chemistry@ccl.net Wed Jun 26 09:43:00 2013 From: "Bin Sun sunbinxod##gmail.com" To: CCL Subject: CCL: syntax error in route section Message-Id: <-48857-130626094121-16908-4YR4YW9UlPUwRUyfMQEvGA : server.ccl.net> X-Original-From: Bin Sun Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 26 Jun 2013 21:41:15 +0800 MIME-Version: 1.0 Sent to CCL by: Bin Sun [sunbinxod{}gmail.com] Hi Everyone, I want to calculate the optical rotation of a molecule using TDDFT/GIAOs method . Part of my input file of Gaussisn09 reads as following : ----------------------------------------------------------------------------------------- %nproc=12 %mem=20GB # TD=(nstates=5) B3LYP/aug-cc-pVDZ Polar=optrot giao ------------------------------------------------------------------------------------------ But once I submitted the job , a error showed up with the message "A syntax error was detected in the input file" . Actually, I know that normally the GIAO keyword is used in the NMR calculation and I wonder how to combine the TDDFT and GIAOs together to perform Optical Rotation calculation ? What is the right form of route section in the input file ? -Sincerely SunBin From owner-chemistry@ccl.net Wed Jun 26 10:18:00 2013 From: "Pierre Archirel pierre.archirel]|[u-psud.fr" To: CCL Subject: CCL: DFT for iron Message-Id: <-48858-130626100015-2057-kt2YMBDyE0MtFOL8fZ67Ng||server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 26 Jun 2013 16:00:24 +0200 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel##u-psud.fr] Dear colleagues, I want to calculate complexes of Fe(II) with ligands like water and carboxylates with G09. Could you advise me about functional (pbe?) and basis set (sdd?) Thanks in advance, Pierre Archirel LCP, Universite d'Orsay, France pierre.archirel|u-psud.fr ______________________________________________________________ Pierre Archirel Groupe Théosim: Théorie et Simulation Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bât 349 Fax: 01 69 15 61 88 91405 Orsay Cédex France pierre.archirel|u-psud.fr ______________________________________________________________ From owner-chemistry@ccl.net Wed Jun 26 10:53:00 2013 From: "=?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= jurgen[*]chem.gu.se" To: CCL Subject: CCL: syntax error in route section Message-Id: <-48859-130626104732-1732-wtyylTaIwjENN9asqUvHDA..server.ccl.net> X-Original-From: =?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 26 Jun 2013 14:47:19 +0000 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?J=FCrgen_Gr=E4fenstein?= [jurgen[*]chem.gu.se] Dear SunBin, Just omit the GIAO keyword. GIAO's are relevant and implemented only for magnetic response properties, not for electric ones. Best regards, Jürgen Gräfenstein University of Gothenburg, Department of Chemistry and Molecular Biology SE-412 96 GÖTEBORG, SWEDEN Phone: +46-31-786 9016 e-mail: Jurgen.Grafenstein-#-chem.gu.se ________________________________________ > From: owner-chemistry+jurgen.grafenstein==chem.gu.se-#-ccl.net [owner-chemistry+jurgen.grafenstein==chem.gu.se-#-ccl.net] on behalf of Bin Sun sunbinxod##gmail.com [owner-chemistry-#-ccl.net] Sent: Wednesday, June 26, 2013 15:41 To: Gräfenstein, Jürgen Subject: CCL: syntax error in route section Sent to CCL by: Bin Sun [sunbinxod{}gmail.com] Hi Everyone, I want to calculate the optical rotation of a molecule using TDDFT/GIAOs method . Part of my input file of Gaussisn09 reads as following : ----------------------------------------------------------------------------------------- %nproc=12 %mem=20GB # TD=(nstates=5) B3LYP/aug-cc-pVDZ Polar=optrot giao ------------------------------------------------------------------------------------------ But once I submitted the job , a error showed up with the message "A syntax error was detected in the input file" . Actually, I know that normally the GIAO keyword is used in the NMR calculation and I wonder how to combine the TDDFT and GIAOs together to perform Optical Rotation calculation ? What is the right form of route section in the input file ? -Sincerely SunBinhttp://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 Wed Jun 26 12:34:00 2013 From: "Abrash, Sam sabrash^-^richmond.edu" To: CCL Subject: CCL: G09: CIS(D) Convergence Problem Message-Id: <-48860-130626123339-3962-bLh7h+6wlD4Roe020u5nzg+*+server.ccl.net> X-Original-From: "Abrash, Sam" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640F6AErinzlerrichmond_" Date: Wed, 26 Jun 2013 16:33:30 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Sam" [sabrash,richmond.edu] --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640F6AErinzlerrichmond_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Folks, I'm running a CIS(D) NStates=3D4 job on three distonic cations of pyrimidin= e. Two of the jobs completed successfully, but the third failed to converg= e the SCF. The input files were identical except for the input geometries. The input file for the failed job is: %chk=3Dpyrimidine+_1CISD.chk %mem=3D400mw %nproc=3D8 # CIS(D,NStates=3D4)/aug-cc-pVTZ Pop=3DReg pyrimidine cation init geom from pyrimidine+_2.log optimized final CCSD geo= metry 1 2 7 -1.196323 -0.596137 0.000000 7 0.000000 1.295173 0.000000 6 -1.206062 0.735602 0.000000 6 -0.078588 -1.322861 0.000000 6 1.193636 -0.724369 0.000000 6 1.175765 0.676881 0.000000 1 -2.127883 1.323031 0.000000 1 -0.208849 -2.413025 0.000000 1 2.124965 -1.297879 0.000000 1 2.077522 1.303099 0.000000 And the relevant part of the output is: Restarting incremental Fock formation. Rare condition: small coef for last iteration: 0.000D+00 Rare condition: small coef for last iteration: 0.000D+00 Rare condition: small coef for last iteration: 0.000D+00 Rare condition: small coef for last iteration: 0.000D+00 Rare condition: small coef for last iteration: 0.000D+00 Rare condition: small coef for last iteration: 0.000D+00 Rare condition: small coef for last iteration: 0.000D+00 Rare condition: small coef for last iteration: 0.000D+00 Rare condition: small coef for last iteration: 0.000D+00 >>>>>>>>>> Convergence criterion not met. SCF Done: E(UHF) =3D -262.443127698 A.U. after 129 cycles Convg =3D 0.6285D-04 -V/T =3D 2.0022 =3D 0.0000 =3D 0.0000 =3D 0.5000 =3D 0.9342 S=3D 0.5882 =3D 0.000000000000E+00 Annihilation of the first spin contaminant: S**2 before annihilation 0.9342, after 0.7759 Convergence failure -- run terminated. Error termination via Lnk1e in /usr/local/g09/l502.exe at Wed Jun 26 11:17:= 47 2013. Can anyone suggest a strategy I can use to try to get this job to successfu= lly converge? Thanks! Sam --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640F6AErinzlerrichmond_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Folks,

 

I’m running a CIS(D) NStates=3D4 job on three = distonic cations of pyrimidine.  Two of the jobs completed successfull= y, but the third failed to converge the SCF.

 

The input files were identical except for the input = geometries.

 

The input file for the failed job is:

 

%chk=3Dpyrimidine+_1CISD.chk

%mem=3D400mw

%nproc=3D8

# CIS(D,NStates=3D4)/aug-cc-pVTZ Pop=3DReg

 

pyrimidine cation init geom from pyrimidine+_2.l= og optimized final CCSD geometry

 

1  2

7    -1.196323   -0.596137&= nbsp;   0.000000

7     0.000000   = 1.295173    0.000000

6    -1.206062    0.73= 5602    0.000000

6    -0.078588   -1.322861&= nbsp;   0.000000

6     1.193636   -0.72= 4369    0.000000

6     1.175765   = 0.676881    0.000000

1    -2.127883    1.32= 3031    0.000000

1    -0.208849   -2.413025&= nbsp;   0.000000

1     2.124965   -1.29= 7879    0.000000

1     2.077522   = 1.303099    0.000000

 

And the relevant part of the output is:

 

Restarting incremental Fock formation.

Rare condition: small coef for last iteration: = 0.000D+00

Rare condition: small coef for last iteration: = 0.000D+00

Rare condition: small coef for last iteration: = 0.000D+00

Rare condition: small coef for last iteration: = 0.000D+00

Rare condition: small coef for last iteration: = 0.000D+00

Rare condition: small coef for last iteration: = 0.000D+00

Rare condition: small coef for last iteration: = 0.000D+00

Rare condition: small coef for last iteration: = 0.000D+00

Rare condition: small coef for last iteration: = 0.000D+00

>>>>>>>>>> Convergence= criterion not met.

SCF Done:  E(UHF) =3D  -262.443127698 = ;    A.U. after  129 cycles

        &nbs= p;    Convg  =3D    0.6285D-04 &nbs= p;           -V/T =3D&nbs= p; 2.0022

<Sx>=3D 0.0000 <Sy>=3D 0.0000 <Sz>= =3D 0.5000 <S**2>=3D 0.9342 S=3D 0.5882

<L.S>=3D 0.000000000000E+00

Annihilation of the first spin contaminant:

S**2 before annihilation     0.9= 342,   after     0.7759

Convergence failure -- run terminated.

Error termination via Lnk1e in /usr/local/g09/l502.e= xe at Wed Jun 26 11:17:47 2013.

 

 

Can anyone suggest a strategy I can use to try to ge= t this job to successfully converge?

 

Thanks!

Sam

--_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640F6AErinzlerrichmond_-- From owner-chemistry@ccl.net Wed Jun 26 13:37:00 2013 From: "Devang Sachdev dsachdev-.-nvidia.com" To: CCL Subject: CCL: Uncovering the Elusive HIV Capsid with Kepler GPUs Running NAMD & VMD Message-Id: <-48861-130626133439-3659-Lge8lSrXj4NA/Gnw9Ft6Vw(-)server.ccl.net> X-Original-From: "Devang Sachdev" Date: Wed, 26 Jun 2013 13:34:38 -0400 Sent to CCL by: "Devang Sachdev" [dsachdev]|[nvidia.com] Hi Join us for a webinar presented by Dr. Juan R. Perilla to learn how computational scientists at University of Illinois at Urbana Champaign resolved the elusive HIV capsid structure running NAMD and VMD on NVIDIA Kepler GPUs. Dr. Perilla will talk about how the researchers combined NMR structure analysis, electron microscopy and data-guided molecular dynamics simulations to obtain and characterize the HIV-1 capsid. You will also learn about how NAMD performs with the latest NVIDIA Kepler K20 GPUs and benefits of GPU computing for computational chemistry. The webinar is planned for July 11th 2013 at 9.00 AM Pacific Time. Register at: http://goo.gl/72WYO Thanks Devang Sachdev Sr. Product Manager - GPU Computing NVIDIA From owner-chemistry@ccl.net Wed Jun 26 14:11:00 2013 From: "kalyan onekalyan*yahoo.com" To: CCL Subject: CCL: DFT for iron Message-Id: <-48862-130626135213-16047-uyv6FEAPMCouETWAbvrL2Q#server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="-167995730-1019376183-1372269127=:73388" Date: Wed, 26 Jun 2013 10:52:07 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan%yahoo.com] ---167995730-1019376183-1372269127=:73388 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear =0APierre archirel =0A=0AFuctional use b3lyp .. it is quite good to fa= r . =0AFor metal use sdd basis set and for water and carboxylates use 6-311= +g(d,p) basis set =0A=0Aif not clear , then drop me a msg =0A=0ABest regard= s=0Akalyan =0A=0A=0A=0A=0A=0A=0A>________________________________=0A> From:= Pierre Archirel pierre.archirel]|[u-psud.fr =0A>T= o: "Dhar, Kalyan kumar " =0A>Sent: Wed= nesday, June 26, 2013 4:00 PM=0A>Subject: CCL: DFT for iron=0A> =0A>=0A>=0A= >Sent to CCL by: Pierre Archirel [pierre.archirel##u-psud.fr]=0A>Dear colle= agues,=0A>I want to calculate complexes of Fe(II) with ligands like water a= nd =0A>carboxylates with G09.=0A>Could you advise me about functional (pbe?= ) and basis set (sdd?)=0A>Thanks in advance,=0A>Pierre Archirel=0A>LCP, Uni= versite d'Orsay, France=0A>pierre.archirel*u-psud.fr=0A>=0A>=0A>___________= ___________________________________________________=0A>=0A>=A0 Pierre Archi= rel=0A>=A0 Groupe Th=E9osim: Th=E9orie et Simulation=0A>=A0 Laboratoire de = Chimie Physique=A0 =A0 =A0 Tel: 01 69 15 63 86=0A>=A0 B=E2t 349=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax: 01 69 15 61 88=0A>=A0 914= 05 Orsay C=E9dex=0A>=A0 France=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 pierre.a= rchirel*u-psud.fr=0A>______________________________________________________= ________=0A>=0A>=0A>=0A>-=3D This is automatically added to each message by= the mailing script =3D-=0A>To recover the email address of the author of t= he message, please change=0A>the strange characters on the top line to the = === sign. You can also=0A>look up the X-Original-From: line in the mail heade= r.=0A>=0A=0A>=A0 =A0 =A0 h= ttp://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A>=0A>E-mail to administrat= ors: CHEMISTRY-REQUEST===ccl.net or use=0A>=A0 =A0 =A0 http://www.ccl.net/cgi= -bin/ccl/send_ccl_message=0A>=0A=0A>=A0 =A0 =A0 htt= p://www.ccl.net/chemistry/sub_unsub.shtml=0A>=0A>Before posting, check wait= time at: http://www.ccl.net=0A>=0A=0A>Confer= ences: http://server.ccl.net/chemistry/announcements/conferences/=0A>=0A>Se= arch Messages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A>=0A>If= your mail bounces from CCL with 5.7.1 error, check:=0A>=A0 =A0 =A0 http://= www.ccl.net/spammers.txt=0A>=0A>RTFI: http://www.ccl.net/chemistry/aboutccl= /instructions/=0A>=0A>=0A>=0A>=0A>=0A> ---167995730-1019376183-1372269127=:73388 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear
= Pierre archirel

Fuctional use b3lyp .. it is quite good to far . For metal use sdd basis set and for water and carboxylates use 6-311+g(d,= p) basis set

if not clear , then drop me a msg

Best regards=
kalyan



From: Pierre Archirel pierre.archirel]|[u-psud= .fr <owner-chemistry===ccl.net>
To: "Dhar, Kalyan kumar " <kalyan.dhar===mail.p= olimi.it>
Sent: We= dnesday, June 26, 2013 4:00 PM
Su= bject: CCL: DFT for iron


Sent to CCL by: Pierre Archirel [pierre.archirel##u-psud= .fr]
Dear colleagues,
I want to calculate complexes of Fe(II) with li= gands like water and
carboxylates with G09.
Could you advise me abou= t functional (pbe?) and basis set (sdd?)
Thanks in advance,
Pierre Ar= chirel
LCP, Universite d'Orsay, France
pierre.archirel*u-psud.fr
<= br>
______________________________________________________________
  Pierre Archirel
  Groupe Th=E9osim: Th=E9orie et Simulatio= n
  Laboratoire de Chimie Physique      Tel: 01 69 1= 5 63 86
  B=E2t 349                            Fax: 01 69 15 61 88
&= nbsp; 91405 Orsay C=E9dex
  France         = ;         pierre.archirel*u-psud.fr
_______________= _______________________________________________



-=3D This is= automatically added to each message by the mailing script =3D-
To recov= er the email address of the author of the message, please change
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---167995730-1019376183-1372269127=:73388-- From owner-chemistry@ccl.net Wed Jun 26 21:33:00 2013 From: "Abrash, Sam sabrash[a]richmond.edu" To: CCL Subject: CCL: Question re excited state calculations Message-Id: <-48863-130626113509-13365-/jnGhlt/9Yox/Zi1nxF3Mw*_*server.ccl.net> X-Original-From: "Abrash, Sam" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640F4BFrinzlerrichmond_" Date: Wed, 26 Jun 2013 15:34:59 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Sam" [sabrash^richmond.edu] --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640F4BFrinzlerrichmond_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Folks, I'm currently studying distonic (hydrogen transfer) cations of pyrimidine. = I've gotten some anomalous results in which some of the hydrogen transfer = cations have lower energy than the pyrimidine cation itself for several, bu= t not all model chemistries. Oddly enough it is some of the more sophistic= ated theories, such as CCSD and MP2 which are producing this anomalous resu= lt. I suspect that the reason is that the radical cation has low-lying exc= ited states which are mixing with the ground state and driving its energy l= ower for the models which are producing the anomalous result. As a result I'd like to do some crude excited state calculations to get a s= ense of the excited state spacing. I'm already doing CIS(D), but I suspect= this will only be informative for my MP2 calculations (since the (D) repre= sents a second order perturbative correction. Am I correct that to get use= ful information for B3LYP and M062X excited states I should use TDDFT, and = for CCSD I should use EOM-CCSD to see the relevant excited states? Sam --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640F4BFrinzlerrichmond_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Folks,

 

I’m currently studying distonic (hydrogen tran= sfer) cations of pyrimidine.  I’ve gotten some anomalous results= in which some of the hydrogen transfer cations have lower energy than the = pyrimidine cation itself for several, but not all model chemistries.  Oddly enough it is some of the more sophisticated theor= ies, such as CCSD and MP2 which are producing this anomalous result.  = I suspect that the reason is that the radical cation has low-lying excited = states which are mixing with the ground state and driving its energy lower for the models which are producing the anomal= ous result. 

 

As a result I’d like to do some crude excited = state calculations to get a sense of the excited state spacing.  IR= 17;m already doing CIS(D), but I suspect this will only be informative for = my MP2 calculations (since the (D) represents a second order perturbative correction.  Am I correct that to get useful infor= mation for B3LYP and M062X excited states I should use TDDFT, and for CCSD = I should use EOM-CCSD to see the relevant excited states?

 

Sam

--_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640F4BFrinzlerrichmond_-- From owner-chemistry@ccl.net Wed Jun 26 22:08:00 2013 From: "Johannes Hachmann jh|*|chemistry.harvard.edu" To: CCL Subject: CCL: DFT for iron Message-Id: <-48864-130626153814-17194-bFQrZCGGMdMn51hbM5GiaQ__server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Language: en-us Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 26 Jun 2013 15:38:05 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh]|[chemistry.harvard.edu] Dear Pierre, Performing meaningful calculations on transition metal complexes using DFT is a challenging business and the choice of method very much depends on what kind of properties you are interested in. I would very much recommend Frank Neese's awesome article in Coord Chem Rev before you get started. http://www.sciencedirect.com/science/article/pii/S0010854508001197 There are a few more recent developments (in particular coming from the Grimme Group in Bonn) such as dispersion corrections or double hybrid functionals which you should consider as well. Best wishes Johannes ----------------------------------------------- Dr. Johannes Hachmann Research Associate Harvard University Department of Chemistry and Chemical Biology 12 Oxford St, Rm M104A Cambridge, MA 02138 ----------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh==chemistry.harvard.edu---ccl.net [mailto:owner- > chemistry+jh==chemistry.harvard.edu---ccl.net] On Behalf Of kalyan > onekalyan*yahoo.com > Sent: Wednesday, 26 June, 2013 13:52 > To: Hachmann, Johannes > Subject: CCL: DFT for iron > > Dear > Pierre archirel > > Fuctional use b3lyp .. it is quite good to far . > For metal use sdd basis set and for water and carboxylates use 6-311+g(d,p) > basis set > > if not clear , then drop me a msg > > Best regards > kalyan > > > > > > > ________________________________ > > From: Pierre Archirel pierre.archirel]|[u-psud.fr chemistry=ccl.net> > To: "Dhar, Kalyan kumar " > Sent: Wednesday, June 26, 2013 4:00 PM > Subject: CCL: DFT for iron > > > > Sent to CCL by: Pierre Archirel [pierre.archirel##u-psud.fr] > Dear colleagues, > I want to calculate complexes of Fe(II) with ligands like water and > carboxylates with G09. > Could you advise me about functional (pbe?) and basis set (sdd?) > Thanks in advance, > Pierre Archirel > LCP, Universite d'Orsay, France > pierre.archirel*u-psud.fr > > > __________________________________________________________ > ____ > > Pierre Archirel > Groupe Théosim: Théorie et Simulation > Laboratoire de Chimie Physique Tel: 01 69 15 63 86 > Bât 349 Fax: 01 69 15 61 88 > 91405 Orsay Cédex > France pierre.archirel*u-psud.fr > __________________________________________________________ > ____> To recover the email address of the author of the message, please > change > the strange characters on the top line to the = sign. You can also> > E-mail to subscribers: CHEMISTRY=ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST=ccl.net or use> > Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > > > From owner-chemistry@ccl.net Wed Jun 26 23:08:00 2013 From: "Joel Fried jfried1%%udayton.edu" To: CCL Subject: CCL:G: computational chemistry of molecules containing iodine Message-Id: <-48865-130626223204-32603-hI/I2hNdAzryP3ZBftFmIw_._server.ccl.net> X-Original-From: "Joel Fried" Date: Wed, 26 Jun 2013 22:32:01 -0400 Sent to CCL by: "Joel Fried" [jfried1 : udayton.edu] I am interested in determining the ESP charge distribution of 1,8-diiodooctane (DIO) using Gaussian. Can anyone suggest an appropriate level of theory and basis set or know of previously published studies of DIO? Joel Fried jfried1(a)udayton.edu University of Dayton