From owner-chemistry@ccl.net Thu Nov 13 02:38:00 2008 From: "Stan van Gisbergen vangisbergen{=}scm.com" To: CCL Subject: CCL: DOS Density of States ?? Message-Id: <-38092-081113022953-24097-4RlLy+AQbCub5wbwZT6Myw]~[server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-14--853918395 Date: Thu, 13 Nov 2008 08:29:44 +0100 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Stan van Gisbergen [vangisbergen]_[scm.com] --Apple-Mail-14--853918395 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Dr. Ramzan Saeed, Thank you for your message. You may send follow up questions to our support E-mail address or the ADF forum on our website. For periodic LCAO DFT calculations you can use the BANDdos GUI utility of our BAND program: For the simplest example see: http://www.scm.com/Doc/Doc2008.01/ BANDGUI/BANDGUI_tutorial/page15.html You can use it to show also partial density of states, for example only d-functions of selected atoms. For ADF itself, you can use the DOS program, which produces text output at the moment: http://www.scm.com/Doc/Doc2008.01/ADF/Analysis/page26.html It also has several unique features, including support for ADF's fragment orbitals. The following options are available for computations by dos: TDOS: Total Density of States GPDOS: Gross Population Density of States OPDOS: Overlap Population Density of States PDOS: Projected Density of States An example input is given here (see also $ADFHOME/examples/adf in your ADF directory): http://www.scm.com/Doc/Doc2008.01/ADF/Examples/page110.html Best regards, Stan van Gisbergen SCM On Nov 10, 2008, at 6:09 PM, Janjua Ramzan Saeed janjua]^[nenu.edu.cn wrote: Sent to CCL by: "Janjua Ramzan Saeed" [janjua()nenu.edu.cn] Hi ! I want to know that how can we calculate DOS (density of states) by using ADF software? Janjua PhD Scholar Northeast Normal University, Changchun, CHINA --Apple-Mail-14--853918395 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1

Dear Dr. = Ramzan Saeed,=A0

Thank you for your message.=A0

You may send follow up questions to our support E-mail = address or the ADF forum on our website.=A0

For = periodic LCAO DFT calculations you can use the BANDdos GUI utility of = our BAND program:=A0

For the = simplest example see: http://www.scm.com/Doc/Doc2008.01/BANDGUI/BANDGUI_tutorial/pag= e15.html

You can = use it to show also partial density of states, for example only = d-functions of selected atoms.=A0

For ADF itself, you can use = the DOS program, which produces text output at the = moment:=A0

htt= p://www.scm.com/Doc/Doc2008.01/ADF/Analysis/page26.html

It also has several unique features, including support = for ADF's fragment orbitals.=A0

The following options are available for = computations by dos:

TDOS: Total Density of States
GPDOS: Gross = Population Density of States
OPDOS: Overlap Population Density of = States
PDOS: Projected Density of States

An example input is given here (see also = $ADFHOME/examples/adf in your ADF directory):

ht= tp://www.scm.com/Doc/Doc2008.01/ADF/Examples/page110.html

Best regards,

Stan van = Gisbergen

SCM=A0

On Nov 10, 2008, at 6:09 PM, Janjua Ramzan Saeed = janjua]^[nenu.edu.cn wrote:

Sent to CCL by: "Janjua=A0 Ramzan Saeed" = [janjua()nenu.edu.cn]

Hi !

I want to know that how can we calculate DOS = (density of states) by using

ADF software?

Janjua PhD = Scholar

Northeast Normal University, Changchun, = CHINA

= --Apple-Mail-14--853918395-- From owner-chemistry@ccl.net Thu Nov 13 06:36:00 2008 From: "Ramon Crehuet rcsqtc||iiqab.csic.es" To: CCL Subject: CCL: ORCA and MPI Message-Id: <-38093-081113063314-30837-YFhVYmupf9miDiQXlN/oKA%server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 13 Nov 2008 12:32:59 +0100 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc^iiqab.csic.es] Hi again... I am trying to use Orca in parallel. I have a running version of MPI but the program dies with: mpirun: cannot start orca/orca_scf_mpi on n0 (o): No such file or directory An error has occured in the SCF module CALLING COMMAND: mpirun -np 4 orca/orca_scf_mpi Fuca-orca-mpi.gbw b RETURN CODE : 512 ABORTING THE RUN ABORTING THE RUN Probably because orca_scf_mpi is not in the orca directory. It is located in: /usuaris/progs/programes/orca_amd64_exe/ This directory is in the path. Should I rename it? Or how can I indicate to Orca where the MPI executables are? Thanks again, Ramon From owner-chemistry@ccl.net Thu Nov 13 07:40:00 2008 From: "John McKelvey jmmckel===gmail.com" To: CCL Subject: CCL: ORCA and MPI Message-Id: <-38094-081113073804-27261-J6a86/9Zlre9zqGUS4Gmrg%%server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_28477_26432172.1226579870747" Date: Thu, 13 Nov 2008 07:37:50 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel . gmail.com] ------=_Part_28477_26432172.1226579870747 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline According to the ORCA group it is necessary to fully specify the path to the executables when running in parallel. This might help. Cheers! John McKelvey On Thu, Nov 13, 2008 at 6:32 AM, Ramon Crehuet rcsqtc||iiqab.csic.es < owner-chemistry.:.ccl.net> wrote: > > Sent to CCL by: Ramon Crehuet [rcsqtc^iiqab.csic.es] > Hi again... > I am trying to use Orca in parallel. I have a running version of MPI but > the program dies with: > > > mpirun: cannot start orca/orca_scf_mpi on n0 (o): No such file or directory > > An error has occured in the SCF module > CALLING COMMAND: mpirun -np 4 orca/orca_scf_mpi Fuca-orca-mpi.gbw b > RETURN CODE : 512 > ABORTING THE RUN > ABORTING THE RUN > > > Probably because orca_scf_mpi is not in the orca directory. It is > located in: > /usuaris/progs/programes/orca_amd64_exe/ > This directory is in the path. > Should I rename it? Or how can I indicate to Orca where the MPI > executables are? > Thanks again, > Ramon> > > ------=_Part_28477_26432172.1226579870747 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline According to the ORCA group it is necessary to fully specify the path to the executables when running in parallel. This might help.

Cheers!

John McKelvey

On Thu, Nov 13, 2008 at 6:32 AM, Ramon Crehuet rcsqtc||iiqab.csic.es <owner-chemistry.:.ccl.net> wrote:

Sent to CCL by: Ramon Crehuet [rcsqtc^iiqab.csic.es]
Hi again...
I am trying to use Orca in parallel. I have a running version of MPI but
the program dies with:

mpirun: cannot start orca/orca_scf_mpi on n0 (o): No such file or directory

An error has occured in the SCF module
CALLING COMMAND: mpirun -np 4 orca/orca_scf_mpi Fuca-orca-mpi.gbw b
RETURN CODE : 512
ABORTING THE RUN
ABORTING THE RUN

Probably because orca_scf_mpi is not in the orca directory. It is
located in:
/usuaris/progs/programes/orca_amd64_exe/
This directory is in the path.
Should I rename it? Or how can I indicate to Orca where the MPI
executables are?
Thanks again,
Ramon

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------=_Part_28477_26432172.1226579870747-- From owner-chemistry@ccl.net Thu Nov 13 08:42:00 2008 From: "Mihaly Mezei Mihaly.Mezei%%mssm.edu" To: CCL Subject: CCL: Zn2+ - CYS covalent bond parameters Message-Id: <-38095-081112133428-8334-gK1ftkuwBwW0CU+N/IJaxg%%server.ccl.net> X-Original-From: "Mihaly Mezei" Date: Wed, 12 Nov 2008 13:34:23 -0500 Sent to CCL by: "Mihaly Mezei" [Mihaly.Mezei]|[mssm.edu] Greetings, I came across the Charmm patch to form covalent bonds between ZN2+ and its surrouning cage of CYS and/or HIS residues written by Jason Wan (version 010906), but nowhere did I find the corresponding additional parameters that Charmm would need to run. Could someone cpint me to where these parameters exist? Thanks in advance. From owner-chemistry@ccl.net Thu Nov 13 09:16:00 2008 From: "Mikko Vainio mikko.vainio_-_abo.fi" To: CCL Subject: CCL: MPI Message-Id: <-38096-081112102039-19123-+B9LyJaL94XpOt5f2i/kcQ,server.ccl.net> X-Original-From: Mikko Vainio Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 12 Nov 2008 16:32:10 +0200 MIME-Version: 1.0 Sent to CCL by: Mikko Vainio [mikko.vainio%a%abo.fi] John McKelvey jmmckel:+:gmail.com wrote: > > Folks, > > I am a newbie as to running parallel under linux, and need to install > MPI under RHEL4/AMD-64bit. > > Simple question: Where to start? > > All suggestions gratefully appreciated! > > Best regards! > > John McKelvey > Try running (as root) yum list *mpi* in order to see which mpi implementations come packaged with the OS. Alternatively, go to http://www.open-mpi.org/ and see for instructions how to compile MPI from source. Rgds, Mikko From owner-chemistry@ccl.net Thu Nov 13 09:51:01 2008 From: "Mehdi Davari mehdi.davari#%#gmail.com" To: CCL Subject: CCL: Self Consistent Field (SCF) method before Hartree Message-Id: <-38097-081112151416-446-KVM7MxgReXgtTkuM2+zVAg . server.ccl.net> X-Original-From: "Mehdi Davari" Content-Type: multipart/alternative; boundary="----=_Part_8215_15514423.1226520845603" Date: Wed, 12 Nov 2008 23:44:05 +0330 MIME-Version: 1.0 Sent to CCL by: "Mehdi Davari" [mehdi.davari{:}gmail.com] ------=_Part_8215_15514423.1226520845603 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All, Does any body knows any references for using Self Consistent Field (SCF) method and algorithmin in physics, mathematics, or... before Doglus Hartree in 1920s. Thank you in advance. Regards Mehdi ------=_Part_8215_15514423.1226520845603 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All,
Does any body knows any references for using Self Consistent Field (SCF) method and algorithmin in physics, mathematics, or... before Doglus Hartree in 1920s.
Thank you in advance.
Regards
Mehdi
------=_Part_8215_15514423.1226520845603-- From owner-chemistry@ccl.net Thu Nov 13 10:29:01 2008 From: "John McKelvey jmmckel(!)gmail.com" To: CCL Subject: CCL: MPI Message-Id: <-38098-081113100354-17194-OAAuWJa7i64P8XImzL1jkA=server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_31359_17048633.1226588622193" Date: Thu, 13 Nov 2008 10:03:42 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel-.-gmail.com] ------=_Part_31359_17048633.1226588622193 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Re: MPI Many thanks to all the suggestions I have received. In the end it turns out that I can not use openmpi or mpich2, but have to have mpich-1.2.7 which seems more difficult to build. I have downloaded it from ArgonneNationalLabs and built it, but things aren't going correctly. Even more suggestions are welcome... Many thanks! John McKelvey On Wed, Nov 12, 2008 at 9:32 AM, Mikko Vainio mikko.vainio_-_abo.fi < owner-chemistry{=}ccl.net> wrote: > > Sent to CCL by: Mikko Vainio [mikko.vainio%a%abo.fi] > John McKelvey jmmckel:+:gmail.com wrote: > >> >> Folks, >> >> I am a newbie as to running parallel under linux, and need to install MPI >> under RHEL4/AMD-64bit. >> >> Simple question: Where to start? >> >> All suggestions gratefully appreciated! >> >> Best regards! >> >> John McKelvey >> >> Try running (as root) > yum list *mpi* > in order to see which mpi implementations come packaged with the OS. > Alternatively, go to http://www.open-mpi.org/ and see for instructions how > to compile MPI from source. > > Rgds, > Mikkohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_31359_17048633.1226588622193 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Re: MPI

Many thanks to all the suggestions I have received. In the end it turns out that I can not use openmpi or mpich2, but have to have mpich-1.2.7 which seems more difficult to build. I have downloaded it from ArgonneNationalLabs and built it, but things aren't going correctly.

Even more suggestions are welcome...

Many thanks!

John McKelvey

On Wed, Nov 12, 2008 at 9:32 AM, Mikko Vainio mikko.vainio_-_abo.fi <owner-chemistry{=}ccl.net> wrote:

Sent to CCL by: Mikko Vainio [mikko.vainio%a%abo.fi]

John McKelvey jmmckel:+:gmail.com wrote:

Folks,

I am a newbie as to running parallel under linux, and need to install MPI under RHEL4/AMD-64bit.

Simple question: Where to start?

All suggestions gratefully appreciated!

Best regards!

John McKelvey

Try running (as root)
yum list *mpi*
in order to see which mpi implementations come packaged with the OS.
Alternatively, go to http://www.open-mpi.org/ and see for instructions how to compile MPI from source.

Rgds,
Mikko

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------=_Part_31359_17048633.1226588622193-- From owner-chemistry@ccl.net Thu Nov 13 11:00:01 2008 From: "Ramon Crehuet rcsqtc=-=iiqab.csic.es" To: CCL Subject: CCL: Orca and float/double Message-Id: <-38099-081113073239-25933-FZMx+Dlyw4Wie/JMqjjZWw%server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 13 Nov 2008 13:32:27 +0100 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc{}iiqab.csic.es] Hi CCLers, I have yet another question with the ORCA input. I see no difference in the timing or output from compressed double and float calculations (I am working with 64 AMD machines). These are the first lines of my input: #Test a DFT calculation with cdouble ! RKS Quick-DFT cdouble *xyz 1 1 #Test a DFT calculation with cfloat ! RKS Quick-DFT cfloat *xyz 1 1 Is this the correct syntax (the program does not complain). I have also tried the alternative input: %SCF VALFORMAT COMPRESSION CFLOAT end But this gives an error. Thanks again for your help. I have tried to contact the orca team but they have not answered... Regards, Ramon From owner-chemistry@ccl.net Thu Nov 13 12:41:00 2008 From: "John McKelvey jmmckel._+_.gmail.com" To: CCL Subject: CCL: Running ORCA in parallel Message-Id: <-38100-081113123904-3657-w4tUXVfBNyCTL+PbHV8l4A_+_server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_34272_20841479.1226597931637" Date: Thu, 13 Nov 2008 12:38:51 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel-*-gmail.com] ------=_Part_34272_20841479.1226597931637 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello! Is anyone currently running ORCA in SMP parallel? What file system are you using? I have tried openmpi and mpich2, but have been told that mpich-1.2.x is what's required. Have built 1.2.7-p1, but that seems to have problems.. Am using dual-dual 64bit AMD box.. This is an open invitation to tell me where to go (to solve the problem, that is) and what to do.. :-) John McKelvey ------=_Part_34272_20841479.1226597931637 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello!

Is anyone currently running ORCA in SMP parallel? What file system are you using? I have tried openmpi and mpich2, but have been told that mpich-1.2.x is what's required. Have built 1.2.7-p1, but that seems to have problems.. Am using dual-dual 64bit AMD box..

This is an open invitation to tell me where to go (to solve the problem, that is) and what to do.. :-)

John McKelvey
------=_Part_34272_20841479.1226597931637-- From owner-chemistry@ccl.net Thu Nov 13 13:15:00 2008 From: "Peter Bladon cbas25:_:strath.ac.uk" To: CCL Subject: CCL: Windows command for selecting a processor Message-Id: <-38101-081113130021-12537-Dg3LNOHK+IFLRCrSp3G7HQ%%server.ccl.net> X-Original-From: "Peter Bladon" Date: Thu, 13 Nov 2008 13:00:18 -0500 Sent to CCL by: "Peter Bladon" [cbas25 .. strath.ac.uk] My apologies if this request is outside the usual scope of ccl postings, but then ccl people have wide experience. I know that in Linux, there is a tool, that when entered on the command line, will select one or more processors on a multi-core system thus: taskset -c 0,4-6 command [optional arguments] will cause the command to use processors 0,4,5,and 6. The question is is there a similar facility in Windows? Any help would be welcome Thanks Peter Bladon Interprobe Chemical Services Gallowhill HOuse Larch Avenue Lenzie, Kirkintilloch Glasgow G66 4HX Scotland. UK cbas25{:}strath.ac.uk Phone +44-(0)-141-578-1109 From owner-chemistry@ccl.net Thu Nov 13 14:01:00 2008 From: "Rick Venable venabler!^!nhlbi.nih.gov" To: CCL Subject: CCL: Zn2+ - CYS covalent bond parameters Message-Id: <-38102-081113134710-12269-Gb3mptse5GVVRLlIGA81nA::server.ccl.net> X-Original-From: Rick Venable Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Thu, 13 Nov 2008 13:46:26 -0500 Mime-version: 1.0 Sent to CCL by: Rick Venable [venabler]-[nhlbi.nih.gov] You may wish to try posting your question on the "Parameters" forum at www.charmm.org -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. > Sent to CCL by: "Mihaly Mezei" [Mihaly.Mezei]|[mssm.edu] > Greetings, > > I came across the Charmm patch to form covalent bonds between ZN2+ and its > surrouning cage of CYS and/or HIS residues written by Jason Wan (version > 010906), but nowhere did I find the corresponding additional parameters that > Charmm would need to run. Could someone cpint me to where these parameters > exist? From owner-chemistry@ccl.net Thu Nov 13 15:09:00 2008 From: "Ol Ga eurisco1 _ pochta.ru" To: CCL Subject: CCL: Running ORCA in parallel: not an answer, but reasonable advice Message-Id: <-38103-081113150748-6069-fGTBnrz9EEJ11ICOb15S0g_+_server.ccl.net> X-Original-From: "Ol Ga" Date: Thu, 13 Nov 2008 15:07:44 -0500 Sent to CCL by: "Ol Ga" [eurisco1**pochta.ru] Dear John McKelvey, I suggest you to send your question direct to ORCA developers e-mail theochem_at_thch.uni-bonn.de. They answer fast and give concrete advices. _Good_ support and _free_ (for academic use) software! But I hope also that on CCL are people who have positive experience in ORCA (what revision?) parallel execution and who are able to provide instructions not for *nix-programmers but for quantum chemists. Sincerely, Ol Ga From owner-chemistry@ccl.net Thu Nov 13 15:43:00 2008 From: "Daniel Jana dfjana|,|gmail.com" To: CCL Subject: CCL: ORCA and MPI Message-Id: <-38104-081113152957-16953-gynGQ2pnIlbCNIfo+Slqlw!=!server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 13 Nov 2008 21:29:41 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana(!)gmail.com] Hello Ramon, Ramon Crehuet rcsqtc||iiqab.csic.es wrote: > Probably because orca_scf_mpi is not in the orca directory. It is > located in: > /usuaris/progs/programes/orca_amd64_exe/ > This directory is in the path. > Should I rename it? Or how can I indicate to Orca where the MPI > executables are The easiest way to indicate where the binaries are (and that's what is mentioned once in a while in ORCA's mailing list) is simply creating a soft link from the real place to the folder where you are working. Something like: ln -s /path/to/orca_folder/orca orca I've never tried it, though... Daniel From owner-chemistry@ccl.net Thu Nov 13 16:19:01 2008 From: "Frank Neese neese-.-thch.uni-bonn.de" To: CCL Subject: CCL: Orca and float/double Message-Id: <-38105-081113152713-15553-n+Ozm/18DBLnSHt+qIhqcg%x%server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 13 Nov 2008 20:26:38 +0100 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese#,#thch.uni-bonn.de] > I have yet another question with the ORCA input. I see no difference in > the timing or output from compressed double and float calculations (I am > working with 64 AMD machines). > These are the first lines of my input: > #Test a DFT calculation with cdouble > ! RKS Quick-DFT cdouble > *xyz 1 1 > > > #Test a DFT calculation with cfloat > ! RKS Quick-DFT cfloat > *xyz 1 1 > > Is this the correct syntax (the program does not complain). I have also > tried the alternative input: > %SCF VALFORMAT COMPRESSION CFLOAT > end > But this gives an error. > Thanks again for your help. I have tried to contact the orca team but > they have not answered... > Regards, > Ramon > that is the correct result: in SCF calculation it does not matter since floats are never used (it would be deadly). It is MP2 where you see the difference. Best regards, FN PS: the syntax is not correct. You would have to use COMPRESSED and FLOAT as keywords in the simple input line and otherwise specifically assign the correct variables. -- --------------------------------------------------------------- Prof. Dr. Frank Neese Lehrstuhl fuer Theoretische Chemie Universitaet Bonn Wegelerstr. 12 D-53115 Bonn, Germany neese(-)thch.uni-bonn.de Phone: +49-228-732351 FAX: +49-(0)228-739064 --------------------------------------------------------------- From owner-chemistry@ccl.net Thu Nov 13 16:54:01 2008 From: "Oleg Trott trott^-^scripps.edu" To: CCL Subject: CCL: Video Tutorial: Docking using Vina with AutoDock Tools and PyMOL Message-Id: <-38106-081113164657-12140-96WeYYwiG8S+wmNZyZnczw|a|server.ccl.net> X-Original-From: "Oleg Trott" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 13 Nov 2008 13:46:45 -0800 MIME-Version: 1.0 Sent to CCL by: "Oleg Trott" [trott:_:scripps.edu] This video tutorial demonstrates molecular docking of imatinib using Vina with AutoDock Tools and PyMOL: http://vina.scripps.edu/tutorial/ (flash-capable browser is required) -- Oleg Trott, Ph.D. (Columbia University) http://olegtrott.com From owner-chemistry@ccl.net Thu Nov 13 22:52:00 2008 From: "Mr Shabbir shabbir^^^nenu.edu.cn" To: CCL Subject: CCL: NMR shielding Effects Message-Id: <-38107-081113225051-10427-PO8CTpabol4ulIBys8l2QA]=[server.ccl.net> X-Original-From: "Mr Shabbir" Date: Thu, 13 Nov 2008 22:50:47 -0500 Sent to CCL by: "Mr Shabbir" [shabbir * nenu.edu.cn] Hello CCL users This Q is second time but still reply is missing.... I am in bit confusion and need some comments to clarify it. I have calculated the NMR spectra of complex system consist of an alkali metal atom with a complexant. During the formation of complex, alkali metal transfer its s electron to the electron deficient complexant and all the atoms of complexant shows a downfield shift (lower chemical shift value) while two atoms and their Hydrogens in that complexant shows upfield (higher chemical shift value). When I looked at the HOMO Orbital of that alkali MetalComplex, there is no electron density on these two atoms and their Hydrogen. So Can I present this HOMO diagram to support the higher chemical shift value of these only atoms and say that these became deshielded during the formation of MetalComplex? And one thing more Can my downfield shieldings (lower chemical shift value) of all other atoms rationalize the formation of charge metalcomplex..? 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