From owner-chemistry@ccl.net Sat Mar 6 00:40:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim _ compchem.net" To: CCL Subject: CCL: Hydrogen Bond Message-Id: <-41380-100306003250-17236-vSfTViHTDGzPM0xQU1lIRg() server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e6d99a7f62ec8f04811b28c8 Date: Sat, 6 Mar 2010 05:32:28 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim^compchem.net] --0016e6d99a7f62ec8f04811b28c8 Content-Type: text/plain; charset=ISO-8859-1 Dear S. Bill I believe you got confused between PM2 and MP2 levels. According to your enquiry, you have tested PM2 with 6-31+G** and aug-cc-pvdz basis set. Semi-empirical methods don't require a basis set at all. I believe you should have got an error at the beginning of your run. PM2 with aug-cc-pvdz will be enough. One study has been carried out on comparison between these two basis set, on geometry optimization. For more information, please check the following reference: Basis set effects on calculated geometries: 6-311++G** vs. aug-cc-pVDZ *DOI: 10.1002/jcc.20058 * * * *Sincerely;* *M. Ibrahim * On Fri, Mar 5, 2010 at 2:52 PM, Abrash, Sam sabrash.- -.richmond.edu < owner-chemistry- -ccl.net> wrote: > > Sent to CCL by: "Abrash, Sam" [sabrash[*]richmond.edu] > PM2 and other force field methods are not reliable for hydrogen bonds. > While there is controversy about the use of DFT methods to treat hydrogen > bonds, Truhlar did an extensive review several years ago indicating that > some of the functionals are able to treat them quite well. I strongly > recommend finding and referring to that review. Methods like the > Moller-Plesset perturbation theory and CCSD are extremely reliable, although > both are more computationally expensive (both CPU and hard disk). Your > basis sets are probably fine, although you should probably test them by > doing at least a test calculation with a larger basis set and making sure > that there are no significant changes. > > Be careful with the use of the correlation consistent basis sets for > hydrogen bonds. They are unusually compact, so the effect of augmentation > is not as large as in the case of the Pople basis sets. Sometimes > additional augmentation is required. > > Finally it is worthwhile to explore doing the counterpoise corrections for > your geometries and energies to account for basis set superposition error. > > I hope this is of some assistance. > > Samuel A. Abrash > Department of Chemistry > University of Richmond > Richmond, VA 23173 > Phone: 804-289-8248 > Fax: 804-287-1897 > E-mail: sabrash*richmond.edu > Web-page: http://oncampus.richmond.edu/~sabrash > > "In 1893 Charles Hinton left Japan to become a mathematics instructor at > Princeton University, where he invented a baseball-pitching machine that > used gunpowder to propel the balls, like a cannon. After several accidents, > the device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian > Steward and Jack Cohen, The Science of Diskworld III > > -----Original Message----- > > From: owner-chemistry+sabrash==richmond.edu*ccl.net [mailto: > owner-chemistry+sabrash ==richmond.edu*ccl.net] > On Behalf Of S Bill s_bill36#,#yahoo.co.uk > Sent: Thursday, March 04, 2010 11:31 PM > To: Abrash, Sam > Subject: CCL: Hydrogen Bond > > > Sent to CCL by: "S Bill" [s_bill36##yahoo.co.uk] > Dear CCL > I have two molecules forming hydrogen bond, I want to calculate energy of > that > bond. I calculated it using B3LYP and PM2 methods, and 6-311+G** and > aug-cc- > pVDZ diffuse as basis set. > In case, B3LYP and PM2 with 6-311+G** I got different values. In case, PM2 > with > aug-cc-pVDZ, the SCF convergence not completed even if I increase SCF > cycles to > more than 1000 cycle. Why it doesn't converge? And which method and basis > set > do you recommend. > Thanks in advance > S. BillJob: > http://www.ccl.net/jobs> > > - This is automatically added to each message by the mailing script -> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim- -compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016e6d99a7f62ec8f04811b28c8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear S. Bill
I believe you got confused between PM2 and MP2 levels.
According to your enquiry, you have tested PM2 with 6-31+G** and aug= -cc-pvdz basis set. Semi-empirical methods don't require a basis set at= all. I believe you=A0should=A0have got =A0an error at the=A0beginning=A0of= your run.
PM2 with aug-cc-pvdz will be enough. One study has been carried out on= =A0comparison=A0between these two basis set, on geometry optimization. For = more information, please check the following reference:
Basis set effects on calcu= lated geometries: 6-311++G** vs. aug-cc-pVDZ
DOI:=A0= 10.1002/jcc.20058=A0

= Sincerely;
M. Ibrahim

On Fri, Mar = 5, 2010 at 2:52 PM, Abrash, Sam sabrash.- -.r= ichmond.edu <owner-chemistry- -ccl.net> wrote:

Sent to CCL by: "Abrash, Sam" [sabrash[*]richmond.edu]
PM2 and other force field methods are not reliable for hydrogen bonds. =A0W= hile there is controversy about the use of DFT methods to treat hydrogen bo= nds, Truhlar did an extensive review several years ago indicating that some= of the functionals are able to treat them quite well. =A0I strongly recomm= end finding and referring to that review. =A0Methods like the Moller-Plesse= t perturbation theory and CCSD are extremely reliable, although both are mo= re computationally expensive (both CPU and hard disk). =A0Your basis sets a= re probably fine, although you should probably test them by doing at least = a test calculation with a larger basis set and making sure that there are n= o significant changes.

Be careful with the use of the correlation consistent basis sets for hydrog= en bonds. =A0They are unusually compact, so the effect of augmentation is n= ot as large as in the case of the Pople basis sets. =A0Sometimes additional= augmentation is required.

Finally it is worthwhile to explore doing the counterpoise corrections for = your geometries and energies to account for basis set superposition error.<= br>
I hope this is of some assistance.

Samuel A. Abrash
Department of Chemistry
University of Richmond
Richmond, VA 23173
Phone: =A0804-289-8248
Fax: =A0804-287-1897
E-mail: =A0sabrash*richmo= nd.edu
Web-page: =A0http://oncampus.richmond.edu/~sabrash

"In 1893 Charles Hinton left Japan to become a mathematics instructor = at Princeton University, where he invented a baseball-pitching machine that= used gunpowder to propel the balls, like a cannon. =A0After several accide= nts, the device was abandoned and Hinton lost his job ..." Terry Pratc= hett, Ian Steward and Jack Cohen, The Science of Diskworld III

-----Original Message-----
> From: owner-chemistry+sabrash=3D=3Drichmond.edu*ccl.net [mailto:owner-ch= emistry+sabrash=3D=3D= richmond.edu*ccl.net] = On Behalf Of S Bill s_bill36#,#yahoo.co.uk
Sent: Thursday, March 04, 2010 11:31 PM
To: Abrash, Sam
Subject: CCL: Hydrogen Bond


Sent to CCL by: "S =A0Bill" [s_bill36##yahoo.co.uk]
Dear CCL
I have two molecules forming hydrogen bond, I want to calculate energy of t= hat
bond. I calculated it using B3LYP and PM2 methods, and 6-311+G** and aug-cc= -
pVDZ diffuse as basis set.
In case, B3LYP and PM2 with 6-311+G** I got different values. In case, PM2 = with
aug-cc-pVDZ, the SCF convergence not completed even if I increase SCF cycle= s to
more than 1000 cycle. Why it doesn't converge? And which method and bas= is set
do you recommend.
Thanks in advance
S. Bill



-=3D This is automatically added to each message by the mailing scrip= t =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messa= geSubscribe/Unsubscribe: Job: http://www.ccl.net/jobs http://www.ccl.net/spammers.txt



--
=A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0= The University of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim- -compche= m.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623= 42601
--0016e6d99a7f62ec8f04811b28c8-- From owner-chemistry@ccl.net Sat Mar 6 01:15:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim^_^compchem.net" To: CCL Subject: CCL: Hydrogen Bond Message-Id: <-41381-100306004635-21054-zXWqMZCqrop8zFGpcckuFQ ~~ server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e6db2ae7c68a9004811b59af Date: Sat, 6 Mar 2010 05:46:17 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim__compchem.net] --0016e6db2ae7c68a9004811b59af Content-Type: text/plain; charset=ISO-8859-1 Sorry, I mistyped my answer :-) I mean MP2 with aug-cc-pvdz in my reply Dear S. Bill I believe you got confused between PM2 and MP2 levels. According to your enquiry, you have tested PM2 with 6-31+G** and aug-cc-pvdz basis set. Semi-empirical methods don't require a basis set at all. I believe you should have got an error at the beginning of your run. *MP2 with aug-cc-pvdz* will be enough. One study has been carried out on comparison between these two basis set, on geometry optimization. For more information, please check the following reference: Basis set effects on calculated geometries: 6-311++G** vs. aug-cc-pVDZ *DOI: 10.1002/jcc.20058 * * * *Sincerely;* *M. Ibrahim* On Sat, Mar 6, 2010 at 5:42 AM, Mahmoud A. A. Ibrahim < m.ibrahim-,-compchem.net> wrote: > Sorry; mistyping: > MP2 with aug-cc-pvdz > Sincerely; > M. Ibrahim > > > On Sat, Mar 6, 2010 at 5:32 AM, Mahmoud A. A. Ibrahim < > m.ibrahim-,-compchem.net> wrote: > >> Dear S. Bill >> I believe you got confused between PM2 and MP2 levels. >> According to your enquiry, you have tested PM2 with 6-31+G** and >> aug-cc-pvdz basis set. Semi-empirical methods don't require a basis set at >> all. I believe you should have got an error at the beginning of your run. >> PM2 with aug-cc-pvdz will be enough. One study has been carried out >> on comparison between these two basis set, on geometry optimization. For >> more information, please check the following reference: >> Basis set effects on calculated geometries: 6-311++G** vs. aug-cc-pVDZ >> *DOI: 10.1002/jcc.20058 * >> * >> * >> *Sincerely;* >> *M. Ibrahim >> * >> >> On Fri, Mar 5, 2010 at 2:52 PM, Abrash, Sam sabrash.-,-.richmond.edu < >> owner-chemistry-,-ccl.net> wrote: >> >>> >>> Sent to CCL by: "Abrash, Sam" [sabrash[*]richmond.edu] >>> PM2 and other force field methods are not reliable for hydrogen bonds. >>> While there is controversy about the use of DFT methods to treat hydrogen >>> bonds, Truhlar did an extensive review several years ago indicating that >>> some of the functionals are able to treat them quite well. I strongly >>> recommend finding and referring to that review. Methods like the >>> Moller-Plesset perturbation theory and CCSD are extremely reliable, although >>> both are more computationally expensive (both CPU and hard disk). Your >>> basis sets are probably fine, although you should probably test them by >>> doing at least a test calculation with a larger basis set and making sure >>> that there are no significant changes. >>> >>> Be careful with the use of the correlation consistent basis sets for >>> hydrogen bonds. They are unusually compact, so the effect of augmentation >>> is not as large as in the case of the Pople basis sets. Sometimes >>> additional augmentation is required. >>> >>> Finally it is worthwhile to explore doing the counterpoise corrections >>> for your geometries and energies to account for basis set superposition >>> error. >>> >>> I hope this is of some assistance. >>> >>> Samuel A. Abrash >>> Department of Chemistry >>> University of Richmond >>> Richmond, VA 23173 >>> Phone: 804-289-8248 >>> Fax: 804-287-1897 >>> E-mail: sabrash*richmond.edu >>> Web-page: http://oncampus.richmond.edu/~sabrash >>> >>> "In 1893 Charles Hinton left Japan to become a mathematics instructor at >>> Princeton University, where he invented a baseball-pitching machine that >>> used gunpowder to propel the balls, like a cannon. After several accidents, >>> the device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian >>> Steward and Jack Cohen, The Science of Diskworld III >>> >>> -----Original Message----- >>> > From: owner-chemistry+sabrash==richmond.edu*ccl.net [mailto: >>> owner-chemistry+sabrash ==richmond.edu* >>> ccl.net] On Behalf Of S Bill s_bill36#,#yahoo.co.uk >>> Sent: Thursday, March 04, 2010 11:31 PM >>> To: Abrash, Sam >>> Subject: CCL: Hydrogen Bond >>> >>> >>> Sent to CCL by: "S Bill" [s_bill36##yahoo.co.uk] >>> Dear CCL >>> I have two molecules forming hydrogen bond, I want to calculate energy of >>> that >>> bond. I calculated it using B3LYP and PM2 methods, and 6-311+G** and >>> aug-cc- >>> pVDZ diffuse as basis set. >>> In case, B3LYP and PM2 with 6-311+G** I got different values. In case, >>> PM2 with >>> aug-cc-pVDZ, the SCF convergence not completed even if I increase SCF >>> cycles to >>> more than 1000 cycle. Why it doesn't converge? And which method and basis >>> set >>> do you recommend. >>> Thanks in advance >>> S. Billhttp://www.ccl.net/spammers.txt >>> >>> >>> - This is automatically added to each message by the mailing script ->>> >>> >>> >> >> >> -- >> Mahmoud A. A. Ibrahim >> Current Address >> 7.05, School of Chemistry, >> The University of Manchester, >> Oxford Road, Manchester, M13 9PL, >> United Kingdom. >> >> Home Address >> Chemistry Department, >> Faculty of Science, >> Minia University, >> Minia 61519, >> Egypt. >> >> Contact Information >> Email: m.ibrahim-,-compchem.net >> Website: www.compchem.net >> Fax No.: +20862342601 >> > > > > -- > Mahmoud A. A. Ibrahim > Current Address > 7.05, School of Chemistry, > The University of Manchester, > Oxford Road, Manchester, M13 9PL, > United Kingdom. > > Home Address > Chemistry Department, > Faculty of Science, > Minia University, > Minia 61519, > Egypt. > > Contact Information > Email: m.ibrahim-,-compchem.net > Website: www.compchem.net > Fax No.: +20862342601 > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim-,-compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016e6db2ae7c68a9004811b59af Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Sorry, I mistyped my answer :-)=A0
I mean MP2 with aug-cc-pv= dz in my reply

Dear S. Bill
I believe you got = confused between PM2 and MP2 levels.
According to your enquiry, y= ou have tested PM2 with 6-31+G** and aug-cc-pvdz basis set. Semi-empirical = methods don't require a basis set at all. I believe you=A0should=A0have= got =A0an error at the=A0beginning=A0of your run.
MP2 with aug-cc-pvdz will be enough. One study has been carried= out on=A0comparison=A0between these two basis set, on geometry optimizatio= n. For more information, please check the following reference:
Basis set effects on calculated geometries: 6-311= ++G** vs. aug-cc-pVDZ
DOI:=A010.1002/jcc.= 20058=A0

Sincerely;
M.= Ibrahim

On Sat, Mar 6, 2010 at 5:42 AM, Mahmoud A. A. Ibrahim &= lt;m.ibrahim-,-compchem.net>= wrote:
Sorry;=A0mistyping:
MP2 with aug-cc-pvd= z
Sincerely;
M. Ibrahim


On Sat, Mar 6, 2010 at 5:32 AM, Mahmoud A. A= . Ibrahim <m.ibrahim-,-compchem.net> wrote:
Dear S. Bill
I believe you got confused = between PM2 and MP2 levels.
According to your enquiry, you have t= ested PM2 with 6-31+G** and aug-cc-pvdz basis set. Semi-empirical methods d= on't require a basis set at all. I believe you=A0should=A0have got =A0a= n error at the=A0beginning=A0of your run.
PM2 with aug-cc-pvdz will be enough. One study has been carried out on= =A0comparison=A0between these two basis set, on geometry optimization. For = more information, please check the following reference:
Basis set effects on calculated geometries: 6-311++G** vs. aug-= cc-pVDZ
DOI:=A010.1002/jcc.20058= =A0

Sincerely;
M. Ibra= him

On Fri, Mar 5, 2010 at 2:52 PM, Abrash, Sam sabrash.-,-.richmond.edu &l= t;owner-chemis= try-,-ccl.net> wrote:

Sent to CCL by: "Abrash, Sam" [sabrash[*]richmond.edu]
PM2 and other force field methods are not reliable for hydrogen bonds. =A0W= hile there is controversy about the use of DFT methods to treat hydrogen bo= nds, Truhlar did an extensive review several years ago indicating that some= of the functionals are able to treat them quite well. =A0I strongly recomm= end finding and referring to that review. =A0Methods like the Moller-Plesse= t perturbation theory and CCSD are extremely reliable, although both are mo= re computationally expensive (both CPU and hard disk). =A0Your basis sets a= re probably fine, although you should probably test them by doing at least = a test calculation with a larger basis set and making sure that there are n= o significant changes.

Be careful with the use of the correlation consistent basis sets for hydrog= en bonds. =A0They are unusually compact, so the effect of augmentation is n= ot as large as in the case of the Pople basis sets. =A0Sometimes additional= augmentation is required.

Finally it is worthwhile to explore doing the counterpoise corrections for = your geometries and energies to account for basis set superposition error.<= br>
I hope this is of some assistance.

Samuel A. Abrash
Department of Chemistry
University of Richmond
Richmond, VA 23173
Phone: =A0804-289-8248
Fax: =A0804-287-1897
E-mail: =A0sabrash*richmo= nd.edu
Web-page: =A0http://oncampus.richmond.edu/~sabrash

"In 1893 Charles Hinton left Japan to become a mathematics instructor = at Princeton University, where he invented a baseball-pitching machine that= used gunpowder to propel the balls, like a cannon. =A0After several accide= nts, the device was abandoned and Hinton lost his job ..." Terry Pratc= hett, Ian Steward and Jack Cohen, The Science of Diskworld III

-----Original Message-----
> From: owner-chemistry+sabrash=3D=3Drichmond.edu*ccl.net [mailto:owner-chemistry+sabrash=3D=3Drichmond.edu*ccl.net] On Behalf Of S Bill s_bill36#,#yahoo.co.uk
Sent: Thursday, March 04, 2010 11:31 PM
To: Abrash, Sam
Subject: CCL: Hydrogen Bond


Sent to CCL by: "S =A0Bill" [s_bill36##yahoo.co.uk]
Dear CCL
I have two molecules forming hydrogen bond, I want to calculate energy of t= hat
bond. I calculated it using B3LYP and PM2 methods, and 6-311+G** and aug-cc= -
pVDZ diffuse as basis set.
In case, B3LYP and PM2 with 6-311+G** I got different values. In case, PM2 = with
aug-cc-pVDZ, the SCF convergence not completed even if I increase SCF cycle= s to
more than 1000 cycle. Why it doesn't converge? And which method and bas= is set
do you recommend.
Thanks in advance
S. Bill



-=3D This is automatically added to each message by the mailing scrip= t =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messa= geSubscribe/Unsubscribe: Job: http://www.ccl.net/jobs http://www.ccl.net/spammers.txt



-- =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 = =A0 =A0 =A0The University of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim-,-compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: www.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 Fax No.: +20862342601



--
=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi= ty of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim-,-compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: www.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 Fax No.: +20862342601



--
=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi= ty of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim-,-compche= m.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623= 42601
--0016e6db2ae7c68a9004811b59af-- From owner-chemistry@ccl.net Sat Mar 6 11:40:01 2010 From: "may abdelghani may01dz##yahoo.fr" To: CCL Subject: CCL: interpretation the Natural Bond Orbitals (NBO) results Message-Id: <-41382-100306060908-28819-LcGpFIc45uGYSkfShCiqtw||server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-949396927-1267870135=:18813" Date: Sat, 6 Mar 2010 02:08:55 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz#yahoo.fr] --0-949396927-1267870135=:18813 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear CCL'ers1. What we mean by the world "antibond BD*" in the output of NB= O; or I have in my NBO output the flowing sentences:575. (0.66522) BD ( 1)R= u 3-Ru 4=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0(=C2=A0=C2=A04.= 23%)=C2=A0=C2=A0=C2=A00.2056*Ru 3 s( 76.43%)p 0.04(=C2=A0=C2=A02.89%)d 0.27= ( 20.69%)576. (0.47855) BD*( 1)Ru 3-Ru 4=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0( 95.77%)=C2=A0=C2=A0=C2=A00.9786*Ru 3 s( 76.43%)p 0.04(= =C2=A0=C2=A02.89%)d 0.27( 20.69%)The question is: I have a bond between the= atom Ru3 and Ru4 or not=E2=80=A6what is the bonding character of this bond= ? 2. There is any relationship between the =C2=ABcluster valence electron" co= ncept and the results of =C2=ABNatural Electron Configuration"? 4. In terms of single, double and triple bonds, where=C2=A0=C2=A0we classif= y that of=C2=A0=C2=A0non-Lewis-type NBOs=C2=A0=C2=A0: BD*, RY* and LP? 5. Can the version 3 of NBO software, NBO.3, give a=C2=A0credibility=C2=A0d= escription of metal-metal bond?thank a lot for all, =0A=0A=0A=0A=0A --0-949396927-1267870135=:18813 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

= Dear CCL'ers

1. What we m= ean by the world "antibond BD*" in the output of NBO; or I have in my NBO o= utput the flowing sentences:

575. (0.66522) BD (= 1)Ru 3-Ru 4=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0(=C2=A0=C2=A04.23%)=C2=A0=C2=A0=C2=A00.2056*Ru 3 s( 76.43%)p 0.04(=C2=A0=C2=A02.89%)d 0.27( 20.69%)

57= 6. (0.47855) BD*( 1)Ru 3-Ru 4=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0

=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0( 95.77%)=C2=A0=C2=A0=C2= =A00.9786*Ru 3 s( 76.43%)p 0.04(=C2= =A0=C2=A02.89%)d 0.27( 20.69%)

The question is: I have a bond b= etween the atom Ru3 and Ru4 or not=E2=80=A6what is the bonding character of= this bond?


2.= There is any relationship between the =C2=ABcluster valence electron" conc= ept and the results of =C2=ABNatural Electron Configuration"?


4. In terms of single, doubl= e and triple bonds, where=C2=A0=C2=A0= we classify that of=C2=A0=C2=A0=C2=A0=C2=A0: BD*, RY* and LP?


5. Can the version 3 of NBO = software, NBO.3, give a=C2=A0credibility=C2=A0description of met= al-metal bond?

thank a lot for all= ,


=0A
= =0A

=0A=0A=0A=0A=0A --0-949396927-1267870135=:18813-- From owner-chemistry@ccl.net Sat Mar 6 16:15:00 2010 From: "Soaring Bear soaringbear---yahoo.com" To: CCL Subject: CCL: Hydrogen Bond Message-Id: <-41383-100305153631-23891-Qi/15h0q537V5ifM5IZkKA^^^server.ccl.net> X-Original-From: Soaring Bear Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 5 Mar 2010 11:36:19 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Soaring Bear [soaringbear|-|yahoo.com] H bonds are so weak that protein structuralists continue to debate how much= contribution they make. So you must begin with the assumption that hydrog= en bonds are poorly parameterized by any computational methods. This is an= area ripe for further work and progress. =0A=0ASoaring Bear Ph.D. Pharmaco= logy soaringbear at yahoo.com=0Ahttp://soaringbear.com/nature/WeedsforNeed= s.html=0Ahttp://www.nlm.nih.gov/mesh/presentations/bear_2005_aug/index.htm= =0Aauthor of http://HerbMed.org & http://HerbInsight.com=0A=0A=0A--- On Thu= , 3/4/10, S Bill s_bill36#,#yahoo.co.uk wrote:=0A= =0A> Sent to CCL by: "S=A0 Bill" [s_bill36##yahoo.co.uk]=0A> I have two mol= ecules forming hydrogen bond, I want to=0A> calculate energy of that =0A> b= ond. I calculated it using B3LYP and PM2 methods, and=0A> 6-311+G** and aug= -cc-=0A> pVDZ diffuse as basis set.=0A> In case, B3LYP and PM2 with 6-311+G= ** I got different=0A> values. In case, PM2 with=A0 =0A> aug-cc-pVDZ, the S= CF convergence not completed even if I=0A> increase SCF cycles to =0A> more= than 1000 cycle. Why it doesn't converge? And which=0A> method and basis s= et =0A> do you recommend.=0A> Thanks in advance=0A> S. Bill=0A From owner-chemistry@ccl.net Sat Mar 6 21:43:01 2010 From: "Pablo Vitoria Garcia qibvigap]_[lg.ehu.es" To: CCL Subject: CCL: Cp-M-Cp bond angle Message-Id: <-41384-100306160212-5877-EsrbTOuQoObhzitdoXSUTg^server.ccl.net> X-Original-From: Pablo Vitoria Garcia Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sat, 6 Mar 2010 21:32:32 +0100 MIME-Version: 1.0 Sent to CCL by: Pablo Vitoria Garcia [qibvigap++lg.ehu.es] Hi, PLATON will indeed recognize all ferrocene-like fragments without user =20 input, and will calculate automatically the Cp ring centroids, =20 distances from the centroids to the metal, the angle =20 centroid1-M-centroid2, and much more. But I don't know if it accepts .xyz files as input, although you could =20 tranform them to pdb or another formats easily. Cheers Pablo "Radoslaw Kaminski rkaminski.rk,,gmail.com" =20 ha escrito: > Hi, > > I'm a crystallographer but programs like Diamond, PLATON or maybe Mercury > can do it very easily. I use Diamond 3 and it can read different types of > files like e.g. XYZ ones so it can be used also with theoretical data. > Mercury also. I'm sure there are lots of such programs. Is this answer yo= ur > question at least partially? I don't know programs which could recognize = Cp > rings automatically and calculate appropriate angles, unfortunately. > > Cheers, > > Radek > > > 2010/3/5 keetch keetch keeetch^^yahoo.com > >> Dear CCL members, >> >> I have calculated the centroids and got the angle. I have sent the p= ost >> to know whether it is possible to get the Cg-M-Cg angle directly from an= y >> programmes, which can calculate the centroids automatically. I am sorry = for >> the inconvenience. >> >> Krishna >> >> >> --- On *Fri, 5/3/10, Radoslaw Kaminski rkaminski.rk(!)gmail.com >> * wrote: >> >> >> From: Radoslaw Kaminski rkaminski.rk(!)gmail.com > > >> Subject: CCL: Cp-M-Cp bond angle >> To: "Bellie, Krishnamoorthy Sundaram " >> Date: Friday, 5 March, 2010, 8:22 PM >> >> Hi, >> >> What does it mean to view? You can calculate the centroids and than the >> angle. I don't understand the problem to be honest... >> >> Cheers, >> >> Radek >> >> 2010/3/5 Krishna B S bskimo*|*gmail.com =20 >> >> > >> >>> >>> Sent to CCL by: "Krishna B S" [bskimo_._gmail.com] >>> Dear CCL Members, >>> >>> Can anyone tell me, how to view the Cp(centroid)-M-Cp(centroide) Bond >>> Angle from the optimized geometry?... >>> >>> Thanks in advance... >>> >>> krishna>> >>> E-mail to subscribers: =20 >>> CHEMISTRY++ccl.netor =20 >>> use:>> >>> E-mail to administrators: =20 >>> CHEMISTRY-REQUEST++ccl.netor =20 >>> use>> >>> >>> >> >> ------------------------------ >> The INTERNET now has a personality. YOURS! See your Yahoo! =20 >> Homepage >> . > --=20 ******************************** Pablo Vitoria Garcia Servicios Generales de Rayos X Universidad del Pa=EDs Vasco (UPV/EHU) Fac. Ciencia y Tecnolog=EDa, Edificio CD3 c/ Barrio Sarriena s/n, 48940 Leioa (Bizkaia) Tfno. +34 946015334 Fax +34 946013500 ********************************