From owner-chemistry@ccl.net Thu Mar 24 00:02:00 2011 From: "guo ya juan garlic007{:}126.com" To: CCL Subject: CCL:G: thanks for you time Message-Id: <-44197-110323232406-6860-9hPHMW+QA8/i/01J/WeMKw*|*server.ccl.net> X-Original-From: "guo ya juan" Date: Wed, 23 Mar 2011 23:24:04 -0400 Sent to CCL by: "guo ya juan" [garlic007**126.com] ear CCL memebers: I am doing an PM3 optimization calculation on the Gaussian program. there is always an error in the job end, it is said that " unable to achieve self-consistence" at L402, but when i used the keyword "iop(4/43=10)", the job can be complated. it is truth that i do not know why. i really hope you can give some suggestion. there is the error out job : It=299 PL= 1.20D-02 DiagD=TT ESCF= 67322.227111 Diff= 1.21D+04 RMSDP= 1.23D-02. It=299 PL= 1.20D-02 DiagD=TT ESCF= 20119.965002 Diff= 1.21D+04 RMSDP= 1.23D-02. It=300 PL= 1.20D-02 DiagD=TT ESCF= 172092.026142 Diff= 2.08D+02 RMSDP= 1.23D-02. """""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE DELTAE= 0.4796E+04 DELTAP= 0.1198E-01 Error termination via Lnk1e in e:\G03W\l402.exe at Mon Mar 21 17:33:00 2011. thanks very much for you hope. From owner-chemistry@ccl.net Thu Mar 24 00:37:00 2011 From: "david.anick..rcn.com" To: CCL Subject: CCL: Correctly drawing aromatic compounds Message-Id: <-44198-110323211533-8495-HeHgdGz0wQpta+b9wjWuIQ]~[server.ccl.net> X-Original-From: Content-Type: multipart/alternative; boundary="-----10282b64034ffb488619ba25d7428f27" Date: Wed, 23 Mar 2011 21:15:20 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: [david.anick^^rcn.com] -------10282b64034ffb488619ba25d7428f27 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: base64 RGVhciBBYXJvbiwKSWYgSSBhbSB1bmRlcnN0YW5kaW5nIHlvdSBjb3JyZWN0bHksIHlvdSBo YXZlIGEKY29ubmVjdGl2aXR5IHBhdHRlcm4gb3IgZ3JhcGggKGluIHRoZSBtYXRoZW1hdGlj YWwKc2Vuc2UpIHJlcHJlc2VudGluZyB3aGljaCBhdG9tcyBhcmUgYm9uZGVkIHRvIHdoaWNo CmluIGFuIG9yZ2FuaWMgbW9sZWN1bGUsIGFuZCB5b3Ugd2FudCB0byBrbm93IGhvdwptYW55 IG9mIHRoZSBib25kcyBhcmUgZG91YmxlIGJvbmRzPwpJdCdzIGVhc3kuICBJIHdpbGwgYXNz dW1lIHlvdXIgbW9sZWN1bGUgY29uc2lzdHMgb2YKQywgTiwgTywgSCBvbmx5LiAgWW91IGhh 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<-44199-110323185842-21390-363K16slFY08/Y/ryawORQ]-[server.ccl.net> X-Original-From: Jonathan Brecher Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 23 Mar 2011 18:54:51 -0400 Mime-Version: 1.0 Sent to CCL by: Jonathan Brecher [jsb!^!cambridgesoft.com] >Sent to CCL by: "Deskins, N Aaron" [nadeskins---WPI.EDU] >But a more fundamental question is how do you predict the number of >double bonds? I don't want to have to assume that a particular >program is drawing the structure right, unless absolutely necessary. >Much better is to determine the number of C=C bonds myself (as >mentioned in my first email, I want to run some isodesmic reactions >on these). Coronene and other small aromatics are easy because there >are plenty of references on these structures. But I'd like to look >at other large compounds for which there is likely little data >available. Someone must have some theory/method to determining the >ideal number of double bonds in an aromatic structure. This is a surprisingly difficult problem. For all-carbon systems, there is a straightforward answer: You want every carbon atom to have a double bond. Every double bond connects two carbon atoms. Therefore, numDB = numC / 2. Unfortunately, the straightforward answer is wrong. Consider a "pyramid" of three fused six-membered rings: c1(c23)cccc3cccc2ccc1. That system has an odd number of carbon atoms, so there has to be a carbon atom lacking a double bond. OK, so you can modify the straightforward answer to say that numDB = numC / 2 when there is an even number of carbon atoms, while numDB = (numC - 1) / 2 when there is an odd number. That is also wrong. Consider a "pyramid" of six six-membered rings, with three rings fused in a row, then two fused above those, and one fused at the very top: c1(c2c(c34)c56)cccc2cc6cccc5cc4cccc3c1. That system indeed has an even number of carbon atoms, but numDB = (numC - 2) / 2. No matter how you position the double bonds, there will always be two carbon atoms "left over". There is no way to get those final two carbon atoms "next to each other" so that they can accept the final double bond that "should" be there. I have never seen a simple way of accurately identifying the number of double bonds that can be supported in a given fused ring system. The only non-simple ways that I've seen involve some seriously high level mathematics that make my head hurt! ...and that only touches on all-carbon cases. Try coming up with a way to predict that n1sncnsnc1 has four double bonds -- and how to position them to produce the correct formula, which has only two hydrogen atoms! Jonathan Brecher CambridgeSoft Corporation jsb,cambridgesoft.com From owner-chemistry@ccl.net Thu Mar 24 01:47:01 2011 From: "Radoslaw Kaminski rkaminski.rk]=[gmail.com" To: CCL Subject: CCL: Correctly drawing aromatic compounds Message-Id: <-44200-110323185509-19463-xhdP57q31p9kbvtldzQ46Q!=!server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=0016e64bb9640c921d049f2e4069 Date: Wed, 23 Mar 2011 23:54:58 +0100 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk|gmail.com] --0016e64bb9640c921d049f2e4069 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi, For such thing (single/double bonds assignments) it would be useful to go into graph theory I presume. However, I don't really get why do you need such a description? Distinguishing single and double bonds in aromatic compounds it not so much useful. Actually in such compounds there are no single neither double bonds present. All you can say it's that some bonds are shorter or longer (in the sense of distances between different nuclei). I may be wrong but from the chemical point of view you don't need to think in terms of chemical bonds t= o run and analyze energies of so-called isodesmic reactions. I presume you need to optimize such geometries anyway? Radek 2011/3/23 Deskins, N Aaron nadeskins]-[WPI.EDU > > Sent to CCL by: "Deskins, N Aaron" [nadeskins---WPI.EDU] > Thank you all for your suggestions. I=92m looking into other software > (ChemDraw) that may do a better job drawing some of these aromatics. > > But a more fundamental question is how do you predict the number of doubl= e > bonds? I don=92t want to have to assume that a particular program is draw= ing > the structure right, unless absolutely necessary. Much better is to > determine the number of C=3DC bonds myself (as mentioned in my first emai= l, I > want to run some isodesmic reactions on these). Coronene and other small > aromatics are easy because there are plenty of references on these > structures. But I=92d like to look at other large compounds for which the= re is > likely little data available. Someone must have some theory/method to > determining the ideal number of double bonds in an aromatic structure. > > Any more ideas? > > N. Aaron Deskins > Assistant Professor > Chemical Engineering Department > Worcester Polytechnic Institute > http://users.wpi.edu/~nadeskins > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Radoslaw Kaminski, M.Sc. Eng. Ph.D. Student Crystallochemistry Laboratory Department of Chemistry University of Warsaw Pasteura 1, 02-093 Warszawa, Poland http://www.chem.uw.edu.pl/people/RKaminski/ --0016e64bb9640c921d049f2e4069 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi,

For such thing (single/double bonds assignments) it would be use= ful to go into graph theory I presume.

However, I don't really g= et why do you need such a description? Distinguishing single and double bon= ds in aromatic compounds it not so much useful. Actually in such compounds = there are no single neither double bonds present. All you can say it's = that some bonds are shorter or longer (in the sense of distances between di= fferent nuclei). I may be wrong but from the chemical point of view you don= 't need to think in terms of chemical bonds to run and analyze energies= of so-called isodesmic reactions. I presume you need to optimize such geom= etries anyway?

Radek


2011/3/23 Deskins, N Aaron = nadeskins]-[WPI.EDU <owner-chemistry^_^ccl.net>

Sent to CCL by: "Deskins, N Aaron" [nadeskins---WPI.EDU]
Thank you all for your suggestions. I=92m looking into other software (Chem= Draw) that may do a better job drawing some of these aromatics.

But a more fundamental question is how do you predict the number of double = bonds? I don=92t want to have to assume that a particular program is drawin= g the structure right, unless absolutely necessary. Much better is to deter= mine the number of C=3DC bonds myself (as mentioned in my first email, I wa= nt to run some isodesmic reactions on these). Coronene and other small arom= atics are easy because there are plenty of references on these structures. = But I=92d like to look at other large compounds for which there is likely l= ittle data available. Someone must have some theory/method to determining t= he ideal number of double bonds in an aromatic structure.

Any more ideas?

N. Aaron Deskins
Assistant Professor
Chemical Engineering Department
Worcester Polytechnic Institute
http://user= s.wpi.edu/~nadeskins






--
Radoslaw Ka= minski, M.Sc. Eng.
Ph.D. Student
Crystallochemistry Laboratory
Dep= artment of Chemistry
University of Warsaw
Pasteura 1, 02-093 Warszawa= , Poland
h= ttp://www.chem.uw.edu.pl/people/RKaminski/
--0016e64bb9640c921d049f2e4069-- From owner-chemistry@ccl.net Thu Mar 24 02:22:00 2011 From: "Arun Manna arun.manna17]*[gmail.com" To: CCL Subject: CCL: Fermi energy for a periodic calculation Message-Id: <-44201-110324013804-6475-MnPY/Jhf2STiXIsAFjJ1Hg|*|server.ccl.net> X-Original-From: Arun Manna Content-Type: multipart/alternative; boundary=bcaec517a9a0380501049f33e154 Date: Thu, 24 Mar 2011 11:07:57 +0530 MIME-Version: 1.0 Sent to CCL by: Arun Manna [arun.manna17,,gmail.com] --bcaec517a9a0380501049f33e154 Content-Type: text/plain; charset=ISO-8859-1 Dear All, Could anyone please tell me how do I obtain the Fermi energy of semi-conducting system for a periodic calculation using g09? Does the program print the Fermi energy for a periodic calculation? Is there any IOP index to print the Fermi energy for this calculation? Waiting for some comments/suggestions. Thank in advance Arun -- Arun K Manna PhD Student, TSU, JNCASR, Bangalore - 560064, India --bcaec517a9a0380501049f33e154 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
=A0 Dear All,

=A0 Could anyone please tell me how do I obtain th= e Fermi energy
=A0 of semi-conducting system for a periodic calculation = using g09?
=A0
=A0 Does the program print the Fermi energy for a per= iodic calculation?
=A0 Is there any IOP index to print the Fermi energy for this calculation?<= br>
=A0=A0 Waiting for some comments/suggestions.

=A0 Thank in ad= vance
=A0=A0 Arun
=A0

--
Arun K Manna
Ph= D Student, TSU, JNCASR,
Bangalore - 560064, India

--bcaec517a9a0380501049f33e154-- From owner-chemistry@ccl.net Thu Mar 24 03:16:00 2011 From: "Joannis Apostolakis apostola]=[bio.ifi.lmu.de" To: CCL Subject: CCL: Chil2 Platform freely available Message-Id: <-44202-110324030422-30177-T79+31KDHsUPoTN12efp0w-,-server.ccl.net> X-Original-From: "Joannis Apostolakis" Date: Thu, 24 Mar 2011 03:04:20 -0400 Sent to CCL by: "Joannis Apostolakis" [apostola**bio.ifi.lmu.de] The Chil2 Cheminformatics and modelling platform has been made freely available for general educational and research purposes. Chil2 contains the docking program GlamDock the molecular superposition tools GMA and HomDock and a feature graph based molecular similarity method called FUZZEE. Chil2 now has a perpetual license and can be used for proprietary as well as academic research. We ask however that you cite the corresponding papers, and that you do not distribute the software to others researchers, and point them instead to the original site www.chil2.de where the software can be obtained. Should there be sufficient interest from the community the authors will consider making the source available under an open source license. On behalf of Chil2's authors: Jannis Apostolakis For general feedback or specific questions (which will not necessarily be answered) please use the contact specifics at www.chil2.de From owner-chemistry@ccl.net Thu Mar 24 05:41:00 2011 From: "Radoslaw Kaminski rkaminski.rk(!)gmail.com" To: CCL Subject: CCL: d-orbital populations for a transition metal Message-Id: <-44203-110324053846-31320-Wb9BgJc06ZG7Ob9JBWct2Q__server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=0016e64bb964fe9291049f373d3d Date: Thu, 24 Mar 2011 10:38:38 +0100 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk{:}gmail.com] --0016e64bb964fe9291049f373d3d Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, If so where exactly I could find this information and what analysis is that= ? What about specific choice of the coordinate system used for the descriptio= n of d-orbitals orientations? Question rather trivial but I'm not a theoretician:) My point is to get such information not as a populations of the basis-set functions but rather like orbital model fitted into the theoretical data. Does it sound reasonable? Radek 2011/3/23 Nuno A. G. Bandeira nuno.bandeira()ist.utl.pt < owner-chemistry||ccl.net> > > Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira###ist.utl.pt] > > On 23-03-2011 18:59, Radoslaw Kaminski rkaminski.rk*gmail.com wrote: > >> Is it possible somehow to extract information of d-orbital populations >> from calculations? I was thinking that it could be related to Mulliken >> population scheme or NPA. How it would be related to my chosen coordinat= e >> system? >> > > I don't understand your problem. You can extract d orbital populations > >> from any ADF calculation. >> > > > -- > Nuno A. G. Bandeira, AMRSC > Departamento de Qu=EDmica F=EDsica i Inorg=E1nica > Despatx 207, N4 - Universitat Rovira i Virgili > Campus Sescelades, Carrer Marcel.l=ED Domingo > 43007 Tarragona - SPAIN > -- > > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --=20 Radoslaw Kaminski, M.Sc. Eng. Ph.D. Student Crystallochemistry Laboratory Department of Chemistry University of Warsaw Pasteura 1, 02-093 Warszawa, Poland http://www.chem.uw.edu.pl/people/RKaminski/ --0016e64bb964fe9291049f373d3d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

If so where exactly I could find this information and what analy= sis is that? What about specific choice of the coordinate system used for t= he description of d-orbitals orientations? Question rather trivial but I= 9;m not a theoretician:) My point is to get such information not as a popul= ations of the basis-set functions but rather like orbital model fitted into= the theoretical data. Does it sound reasonable?

Radek


2011/3/23 Nuno A. G. Bandei= ra nuno.bandeira()ist.utl.pt <owner-chemistry||ccl.ne= t>

Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira###ist.utl.pt]

On 23-03-2011 18:59, Radoslaw Kaminski rkaminski.rk*gmail.com wrote:
Is it possible somehow to extract information of d-orbital populations from= calculations? I was thinking that it could be related to Mulliken populati= on scheme or NPA. How it would be related to my chosen coordinate system?

I don't understand your problem. You can extract d orbital populations =
> from any ADF calculation.


--
Nuno A. G. Bandeira, AMRSC
Departamento de Qu=EDmica F=EDsica i Inorg=E1nica
Despatx 207, N4 - Universitat Rovira i Virgili
Campus Sescelades, Carrer Marcel.l=ED Domingo
43007 Tarragona - SPAIN
--




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--
Radoslaw Ka= minski, M.Sc. Eng.
Ph.D. Student
Crystallochemistry Laboratory
Dep= artment of Chemistry
University of Warsaw
Pasteura 1, 02-093 Warszawa= , Poland
h= ttp://www.chem.uw.edu.pl/people/RKaminski/
--0016e64bb964fe9291049f373d3d-- From owner-chemistry@ccl.net Thu Mar 24 08:13:00 2011 From: "Nuno A. G. Bandeira nuno.bandeira[-]ist.utl.pt" To: CCL Subject: CCL: d-orbital populations for a transition metal Message-Id: <-44204-110324080550-32672-xnyTqYcuyvqZRbD1FLJbRw!^!server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 24 Mar 2011 13:05:24 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[]ist.utl.pt] On 24-03-2011 10:38, Radoslaw Kaminski rkaminski.rk(!)gmail.com wrote: > Hi, > > If so where exactly I could find this information and what analysis is > that? What about specific choice of the coordinate system used for the > description of d-orbitals orientations? Question rather trivial but > I'm not a theoretician:) My point is to get such information not as a > populations of the basis-set functions but rather like orbital model > fitted into the theoretical data. Does it sound reasonable? Well if you want to do theory you have to start reading program manuals, look carefully at your output files as well as reading some textbooks. Look for the following in your ADF output: M U L L I K E N P O P U L A T I O N S ======================================= The survey below gives for each atom: a) the total charge (Z minus electrons) b) the net spin polarization (nr of electrons spin-A minus spin-B) c) for each spin the atomic electron valence density (integrated) per L-value. Atom Charge Spin density S P D F ---- ------ ------------ ------ ------ ------ ------ -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN -- From owner-chemistry@ccl.net Thu Mar 24 08:48:01 2011 From: "Marcel Swart marcel.swart[]icrea.cat" To: CCL Subject: CCL: d-orbital populations for a transition metal Message-Id: <-44205-110324083653-27450-gccLWVHxExQ0RrOUIeEBBw|a|server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-8-540455664 Date: Thu, 24 Mar 2011 13:36:42 +0100 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Marcel Swart [marcel.swart**icrea.cat] --Apple-Mail-8-540455664 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Please have a look at the output, in particular the following part: List of all MOs, ordered by energy, with the most significant SFO gross = populations = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D =20 Each percentage contribution in the table below corresponds to the = indicated SFO. In general, a SFO may be a linear combination of several Fragment = Orbitals on the same, or on symmetry-related Fragments. Only the first 'member' of such a = combination is specified here. A full definition of all SFOs is given in an earlier = part of the output. The numbering of the SFOs in this table does NOT include the Core = Orbitals, and starts from one for each symmetry representation, as in the SFO definition = list earlier. as an example, the partial output for an iron-complex: -5.262 1.00 42 A.g 34.26% 1 D:xz -7.900 = 1.20 1 FE 24.11% 1 D:xy -7.900 = 1.20 1 FE 15.25% 2 P:x -8.644 = 1.67 2 CL 10.74% 1 D:yz -7.900 = 1.20 1 FE 6.05% 1 D:x2-y2 -7.900 = 1.20 1 FE 4.66% 1 D:z2 -7.900 = 1.20 1 FE This indicates how much each of the d-orbitals of Fe contribute to this = MO. You can sum these contributions, and then get an idea of the how the = different d-orbitals of iron are occupied. In this particular case for instance: OCCUPATIONS (total) A.g 46.0 // 42.0 A.u 44.0 // 44.0 Total 90.0 86.0 FE occupations 1 D:z2 A.g 97.1600 12.4400 1 D:x2-y2 A.g 96.2900 14.3600 1 D:xy A.g 94.4900 15.6700 1 D:xz A.g 96.5300 53.9100 1 D:yz A.g 95.4400 26.6400 2 D:yz A.g 1.3400 0.0000 Marcel On Mar 24, 2011, at 10:38 AM, Radoslaw Kaminski rkaminski.rk(!)gmail.com = wrote: > Hi, >=20 > If so where exactly I could find this information and what analysis is = that? What about specific choice of the coordinate system used for the = description of d-orbitals orientations? Question rather trivial but I'm = not a theoretician:) My point is to get such information not as a = populations of the basis-set functions but rather like orbital model = fitted into the theoretical data. Does it sound reasonable? >=20 > Radek =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Facultat de Ci=E8ncies Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart::icrea.cat marcel.swart::udg.edu web http://www.marcelswart.eu =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail-8-540455664 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1  List of all MOs, ordered by energy, with the = most significant SFO gross = populations
 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
<= font class=3D"Apple-style-span" face=3D"'Andale Mono'">       =                     =         
 Each percentage = contribution in the table below corresponds to the indicated = SFO.
 In general, a SFO may be a linear combination of = several Fragment Orbitals on the same,
 or on = symmetry-related Fragments. Only the first 'member' of such a = combination is
 specified here. A full definition of all SFOs is = given in an earlier part of the output.
 The numbering of the = SFOs in this table does NOT include the Core Orbitals, and = starts
 from one for each symmetry representation, as in = the SFO definition list = earlier.

as an example, the = partial output for an iron-complex:

      -5.262  1.00    42 = A.g       34.26%     1 D:xz     =       -7.900  1.20     1 = FE
               =                     = 24.11%     1 D:xy           -7.900 =  1.20     1 FE
       =                     =         15.25%     2 P:x     =        -8.644  1.67     2 = CL
               =                     = 10.74%     1 D:yz           -7.900 =  1.20     1 FE
       =                     =          6.05%     1 D:x2-y2   =      -7.900  1.20     1 = FE
               =                     =  4.66%     1 D:z2           = -7.900  1.20     1 = FE

This indicates how much = each of the d-orbitals of Fe contribute to this MO.
You can = sum these contributions, and then get an idea of the how the different = d-orbitals
of iron are occupied. In this particular case for = instance:

OCCUPATIONS = (total)
       A.g       =    46.0     //     = 42.0
       A.u       =    44.0     //     = 44.0

     Total     =      90.0           =  86.0

FE occupations
 1 = D:z2               A.g     =   97.1600       12.4400
 1 D:x2-y2 =            A.g       = 96.2900       14.3600
 1 D:xy   =             A.g       = 94.4900       15.6700
 1 D:xz   =             A.g       = 96.5300       53.9100
 1 D:yz   =             A.g       = 95.4400       26.6400
 2 D:yz   =             A.g       =  1.3400       =  0.0000

Marcel
=
On Mar 24, 2011, at 10:38 AM, Radoslaw Kaminski = rkaminski.rk(!)gmail.com = wrote:

Hi,

If so where exactly I could find this = information and what analysis is that? What about specific choice of the = coordinate system used for the description of d-orbitals orientations? = Question rather trivial but I'm not a theoretician:) My point is to get = such information not as a populations of the basis-set functions but = rather like orbital model fitted into the theoretical data. Does it = sound reasonable?

Radek

17071 = Girona
Catalunya = (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mailmarcel.swart::icrea.cat
marce= l.swart::udg.edu
web
http://www.marcelswart.eu
=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D

= --Apple-Mail-8-540455664-- From owner-chemistry@ccl.net Thu Mar 24 09:23:00 2011 From: "Tamas Gunda tgunda2 ~~ puma.unideb.hu" To: CCL Subject: CCL:G: Mol2mol 5.6.3 available Message-Id: <-44206-110323101059-7942-vOmPpP6GxNqDAzwcAwuqhw---server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-2"; reply-type=original Date: Wed, 23 Mar 2011 15:10:46 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2{=}puma.unideb.hu] Dear Colleagues, 21.03.2011 The 5.6.3 version of the molecule file manipulating and converting program Mol2mol is available. This is small upgrade, it contains mainly refinements and bug fixes. * New file format: Gaussian input file (gjf) in Cartesian format (read in manual mode and write) * Every now and then endless cycle during the automatic rearrangement of Sybyl files - fixed * Crash when creating folder libraries - fixed * Several other small fixes, corrections (mainly in POV-Ray and MDL formats) More about Mol2Mol at its homepage: http://www.gunda.hu/mol2mol May I remember you that Mol2mol is capable to input and output coordinates from ASCII files in practically every formats by supplying a simple format string. For example, the coordinates 1 C 1.2340 5.6678 4.4444 pcharge 0.0112 2 O 2.3456 7.8911 5.5555 pcharge -0.3456 ... can be inputted if the format string is: d e x y z d p or in words: dummy(=skip this column), elemental symbol, x, y, z, dummy, partial charges This works in the case of Z matrices or when the data are copy/pasted via the Windows clipboard (for example, from an email). The coordinates can be set to Angstroms or nanometers, even polar coordinates can be used. More datails can be found in the Mol2mol Help file. The output format can also be controlled by using a format string, it is similar to the formatting used in C/C++ language. There are no limits for experimentation, for example, you can export the coordinates to several general 3D modelling applications. - - - - - - - - - I would be very indebted if you could send me any feedback about your experiences with Mol2mol. Any wishes are also welcome. As you know, Mol2mol was created about 20 years ago as a toolset for manipulating molecule files, to solve conversion problems, to edit corrupted files, to extract info etc. It never tried to compete with real modelling applications. Instead it has features which are usually not or only seldom available in other applications. Kind regards Dr. Tamas E. Gunda From owner-chemistry@ccl.net Thu Mar 24 09:58:00 2011 From: "Dr David N Haney haney _ edusoft-lc.com" To: CCL Subject: CCL: Correctly drawing aromatic compounds Message-Id: <-44207-110324014032-8523-2/seb8LrI7I1vdV4ipGQNQ!=!server.ccl.net> X-Original-From: Dr David N Haney Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 23 Mar 2011 22:39:51 -0700 Mime-Version: 1.0 Sent to CCL by: Dr David N Haney [haney]![edusoft-lc.com] As I mentioned previously, alkene double bonds are very different both chemically and physically than aromatic bonds. Both of these "descriptors" (double bonds and aromatic bonds) can be evaluated with many different Kier-Hall descriptor programs like Molconn-Z from www.edusoft-lc.com. On Wed, Mar 23, 2011 at 05:37:34PM +0100, Wolf Ihlenfeldt wdi++xemistry.com wrote: > Why don't you just merge cyclohexane rings and then later change the bond > orders if your drawing software cannot figure it out on its own? > > Or you retrieve the compound data in some format without Kekule bond orders, > and use a chemistry toolkit which can resolve it for your operations. > > In Cactvs - www.xemistry.com, free for academic users) you can easily do > something like > > cactvs>ens create c2c7c1c6c5c4c3c1c(c2)ccc3ccc4ccc5ccc6cc7 > ens0 > cactvs>ens bonds ens0 {arobond doublebond} count > 12 > cactvs> > > > > > > On Wed, Mar 23, 2011 at 1:58 PM, Deskins, N Aaron nadeskins,WPI.EDU < > owner-chemistry ~~ ccl.net> wrote: > > > > > Sent to CCL by: "Deskins, N Aaron" [nadeskins*o*WPI.EDU] > > Hello all, > > > > I'm trying to draw (2-D) some aromatic compounds but can't seem to get > > them right. For instance, all the pictures of coronene I've seen show 12 C=C > > bonds (see for example en.wikipedia.org/wiki/File:Coronene_structure.png). > > But I tried making coronene in ChemSketch but it puts draws a structure with > > 10-11 C=C bonds depending on the order I put the benzene rings together. > > Same problem with pyrene. My drawings show 7 C=C bonds, while I believe it > > should have 8. > > > > More importantly, I'd like to figure out how many C=C bonds different > > large aromatic compounds have for a series of isodesmic reactions I'm > > interested in. > > > > Any ideas? > > > > Thank you, > > > > N. Aaron Deskins > > Assistant Professor > > Chemical Engineering Department > > Worcester Polytechnic Institute > > http://users.wpi.edu/~nadeskins> > > > > > > > -- > Wolf-D. Ihlenfeldt, Xemistry GmbH > www.xemistry.com -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney###edusoft-lc.com # ################# ##################### From owner-chemistry@ccl.net Thu Mar 24 10:33:00 2011 From: "Cem Burak YILDIZ cemburakyildiz(a)bau.edu.tr" To: CCL Subject: CCL: NICS calculation Geometrical Point Message-Id: <-44208-110324051612-12997-E5tY7DZ828U7hiJNIq1vMQ++server.ccl.net> X-Original-From: "Cem Burak YILDIZ" Date: Thu, 24 Mar 2011 05:16:10 -0400 Sent to CCL by: "Cem Burak YILDIZ" [cemburakyildiz#,#bau.edu.tr] I have a problem with NICS calculation. If you help me, I'm glad. I'm trying to calculate NICS values of some molecules. Howeover, I have trouble with determine geometrical pouint for non-plane or 3D-molecules. Now, this calculation type is easy for benzene or cyclohexane, because the molecules are symetrical. Howeover, I have a problem molecules which are non-plane. For instance, I could not find geometrical point of furan or pyrrole or these typesmolecules exactly. so, i obtained a bit different values of shielding of Bq in these molecules. For instance, Acoording to Schlayer et al, NICS value of Bq of pyrrole is 15.1 ppm at Hf/6-31+g* theory of level, but obtained value by me for this molecule is 14.85 ppm at the same level of theory. How can i fix this mistake? How can i determine geometrical point correctly? Can you help me about this topic? If it is possible, can you send me input file of furan or a molecules is not plane. From owner-chemistry@ccl.net Thu Mar 24 11:07:00 2011 From: "Deskins, N Aaron nadeskins/./WPI.EDU" To: CCL Subject: CCL: Correctly drawing aromatic compounds Message-Id: <-44209-110324084905-4334-SefO8uG02nctn2nc0ImAFQ[*]server.ccl.net> X-Original-From: "Deskins, N Aaron" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 24 Mar 2011 08:47:53 -0400 MIME-Version: 1.0 Sent to CCL by: "Deskins, N Aaron" [nadeskins{:}WPI.EDU] Thank you David. That is exactly what I was looking for. I must have learned this many years ago in general chemistry, but forgotten it. Thank you again. ________________________________________ > From: david.anick(~)rcn.com [david.anick(~)rcn.com] Sent: Wednesday, March 23, 2011 9:15 PM To: CCL Subscribers Cc: Deskins, N Aaron Subject: CCL: Correctly drawing aromatic compounds Dear Aaron, If I am understanding you correctly, you have a connectivity pattern or graph (in the mathematical sense) representing which atoms are bonded to which in an organic molecule, and you want to know how many of the bonds are double bonds? It's easy. I will assume your molecule consists of C, N, O, H only. You have two equations. Let E be the number of valence electrons that are involved in bonding. Then: E = 4C + 3N + 2O + H + (net charge). Because every single bond uses two valence electrons and every double bond uses four, E = 2 * (single bonds) + 4 * (double bonds). Put these together and divide by 2 to get Equation (1): Eq. (1) (single bonds) + 2 * (double bonds) = [4C + 3N + 2O + H + (net charge) ] / 2. Next, just count the total number of bonds in your drawing. Obviously, Eq. (2) (single bonds) + (double bonds) = (total # of bonds). Your unknowns here are (single bonds) and (double bonds). Everything else is known from the drawing. You have two equations in two unknowns. Subtract Eq. (2) from Eq. (1) to get the # of double bonds. I think the derivation and the two equations is clearest, but if you want me to do it for you, your final answer is: (double bonds) = [4C + 3N + 2O + H + (net charge) ] / 2 - (total # of bonds). Example: Anthracene is C14H10 and has 16 CC bonds and 10 CH bonds, giving (total bonds) = 26. The formula gives (double bonds) = [4*14 + 10]/2 - (26) = 33 - 26 = 7. There are several possible "resonance structures" for anthracene but all of them use exactly 7 C=C double bonds. Obviously the formula will break down if there are unfilled shells, and it would have to be modified if there are triple bonds or 3rd row atoms. I suppose if you have halogen atoms they are the same as "H" for the purposes of this calculation. I hope this is helpful! David Anick PhD MD Harvard Medical School From owner-chemistry@ccl.net Thu Mar 24 11:43:01 2011 From: "Radoslaw Kaminski rkaminski.rk++gmail.com" To: CCL Subject: CCL: d-orbital populations for a transition metal Message-Id: <-44210-110324093831-26278-rd8ELvMq2lQkuN0FHuevVQ[#]server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=20cf30363f0f5f2a25049f3a970a Date: Thu, 24 Mar 2011 14:38:23 +0100 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk++gmail.com] --20cf30363f0f5f2a25049f3a970a Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, This I found out I did not write onto CCL before checking it:) For example = I have: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D M U L L I K E N P O P U L A T I O N S =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D The survey below gives for each atom: a) the total charge (Z minus electrons) b) the net spin polarization (nr of electrons spin-A minus spin-B) c) for each spin the atomic electron valence density (integrated) per L-value. Atom Charge Spin density S P D F ---- ------ ------------ ------ ------ ------ ------ 1 O -0.5014 3.8430 4.6062 0.0523 0.0000 As I'm not very much familiar with those population schemes my question is how to interpret this table in terms of local atomic coordinate systems. In manual it's not much written in details about. Thanks for helping:) Radek 2011/3/24 Nuno A. G. Bandeira nuno.bandeira[-]ist.utl.pt < owner-chemistry++ccl.net> > > Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[]ist.utl.pt] > On 24-03-2011 10:38, Radoslaw Kaminski rkaminski.rk(!)gmail.com wrote: > >> Hi, >> >> If so where exactly I could find this information and what analysis is >> that? What about specific choice of the coordinate system used for the >> description of d-orbitals orientations? Question rather trivial but I'm = not >> a theoretician:) My point is to get such information not as a population= s of >> the basis-set functions but rather like orbital model fitted into the >> theoretical data. Does it sound reasonable? >> > > Well if you want to do theory you have to start reading program manuals, > look carefully at your output files as well as reading some textbooks. > > Look for the following in your ADF output: > > M U L L I K E N P O P U L A T I O N S > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > The survey below gives for each atom: > a) the total charge (Z minus electrons) > b) the net spin polarization (nr of electrons spin-A minus spin-B) > c) for each spin the atomic electron valence density (integrated) per > L-value. > > Atom Charge Spin density S P D > F > ---- ------ ------------ ------ ------ -----= - > ------ > > > > > -- > Nuno A. G. Bandeira, AMRSC > Departamento de Qu=EDmica F=EDsica i Inorg=E1nica > Despatx 207, N4 - Universitat Rovira i Virgili > Campus Sescelades, Carrer Marcel.l=ED Domingo > 43007 Tarragona - SPAIN > -- > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --=20 Radoslaw Kaminski, M.Sc. Eng. Ph.D. Student Crystallochemistry Laboratory Department of Chemistry University of Warsaw Pasteura 1, 02-093 Warszawa, Poland http://www.chem.uw.edu.pl/people/RKaminski/ --20cf30363f0f5f2a25049f3a970a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

This I found out I did not write onto CCL before checking it:) F= or example I have:

=A0=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
=A0M U L L I K E N=A0= =A0 P O P U L A T I O N S
=A0=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
=A0
=A0The survey below gives for each atom:
=A0a) the total charge = (Z minus electrons)
=A0b) the net spin pol= arization (nr of electrons spin-A minus spin-B)
=A0c) for each spin the= atomic electron valence density (integrated) per L-value.

=A0Atom=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 Charge=A0=A0=A0 Spin density=A0=A0=A0=A0=A0=A0=A0= =A0=A0 S=A0=A0=A0=A0=A0=A0=A0=A0 P=A0=A0=A0=A0=A0=A0=A0=A0 D=A0=A0=A0=A0=A0= =A0=A0=A0 F
=A0----=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0 ------=A0=A0=A0 ------------=A0=A0=A0=A0=A0=A0 ------=A0= =A0=A0 ------=A0=A0=A0 ------=A0=A0=A0 ------
=A01 O=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 -0.5014=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 3.8430=A0=A0=A0 4.6062=A0=A0=A0 0.0523=A0=A0=A0 0.= 0000

As I'm not very much familiar with those population = schemes my question is how to interpret this table in terms of local atomic= coordinate systems. In manual it's not much written in details about.<= br>
Thanks for helping:)

Radek


2011/3/24 Nuno A. G. Bandeira nuno.bandeira[-]ist.utl.pt <owner-chemistry++ccl.net>

Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[]ist.utl.pt]
On 24-03-2011 10:38, Radoslaw Kaminski rkaminski.rk(!)gmail.com wrote:
Hi,

If so where exactly I could find this information and what analysis is that= ? What about specific choice of the coordinate system used for the descript= ion of d-orbitals orientations? Question rather trivial but I'm not a t= heoretician:) My point is to get such information not as a populations of t= he basis-set functions but rather like orbital model fitted into the theore= tical data. Does it sound reasonable?

Well if you want to do theory you have to start reading program manuals, lo= ok carefully at your output files as well as reading some textbooks.

Look for the following in your ADF output:

=A0M U L L I K E N =A0 P O P U L A T I O N S
=A0=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

=A0The survey below gives for each atom:
=A0a) the total charge (Z minus electrons)
=A0b) the net spin polarization (nr of electrons spin-A minus spin-B)
=A0c) for each spin the atomic electron valence density (integrated) per L-= value.

=A0Atom =A0 =A0 =A0 =A0 =A0 =A0 =A0Charge =A0 =A0Spin density =A0 =A0 =A0 = =A0 =A0S =A0 =A0 =A0 =A0 P =A0 =A0 =A0 =A0 D =A0 =A0 =A0 =A0 F
=A0---- =A0 =A0 =A0 =A0 =A0 =A0 =A0------ =A0 =A0------------ =A0 =A0 =A0 -= ----- =A0 =A0------ =A0 =A0------ =A0 =A0------




--
Nuno A. G. Bandeira, AMRSC
Departamento de Qu=EDmica F=EDsica i Inorg=E1nica
Despatx 207, N4 - Universitat Rovira i Virgili
Campus Sescelades, Carrer Marcel.l=ED Domingo
43007 Tarragona - SPAIN
--



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--
Radoslaw Ka= minski, M.Sc. Eng.
Ph.D. Student
Crystallochemistry Laboratory
Dep= artment of Chemistry
University of Warsaw
Pasteura 1, 02-093 Warszawa= , Poland
h= ttp://www.chem.uw.edu.pl/people/RKaminski/
--20cf30363f0f5f2a25049f3a970a-- From owner-chemistry@ccl.net Thu Mar 24 12:18:00 2011 From: "Renier Dreyer renier.dreyer : crunchyard.com" To: CCL Subject: CCL: All CP2K simulations using 4 CPU's run free of charge Message-Id: <-44211-110324103321-14865-q7bE1r+KtjrN1hYXltcRvg.@.server.ccl.net> X-Original-From: "Renier Dreyer" Date: Thu, 24 Mar 2011 10:33:19 -0400 Sent to CCL by: "Renier Dreyer" [renier.dreyer---crunchyard.com] CrunchYard would like to announce that ALL simulations (Including CP2K) that uses 4 CPUs or less running under 1 hour are now free. This will allow users to fine tune their simulations before using more resources. This offer includes all commercial and open source packages. Other packages such as GAMESS to follow soon. Registering for an account on CrunchYard is free. ------------------------------------------------------------ Dr. Renier Dreyer CEO CrunchYard BSc (Elec) Eng, PhD Website: www.crunchyard.com ------------------------------------------------------------ From owner-chemistry@ccl.net Thu Mar 24 12:52:00 2011 From: "E.J. Baerends e.j.baerends^^^vu.nl" To: CCL Subject: CCL: d-orbital populations for a transition metal Message-Id: <-44212-110324101317-28182-OFUNW9gYltZiQct4YWPq3A*_*server.ccl.net> X-Original-From: "E.J. Baerends" Content-Type: multipart/alternative; boundary="Apple-Mail-37-546234308" Date: Thu, 24 Mar 2011 15:13:01 +0100 MIME-Version: 1.0 (Apple Message framework v936) Sent to CCL by: "E.J. Baerends" [e.j.baerends{=}vu.nl] --Apple-Mail-37-546234308 Content-Type: text/plain; charset="ISO-8859-1"; format=flowed; delsp=yes Content-Transfer-Encoding: quoted-printable In view of your question: "how would it be related to my chosen =20 coordinate system": Note that by default the local coordinate system on each atom is the =20 same as your overall coordinate system. So the local z axis with respect to which e.g. the dz2 orbital for =20 which you see the population is defined, is just the overall z axis. Sometimes it is convenient to reorient the local axes. For instance =20 when you discern an approximate local square planar coordination, but =20= the plane is not parallel to the xy plane but tilted. Then you can do =20= a calculation with the local coordinate system rotated, in your =20 preferred direction, and the atomic orbitals for which you see the =20 populations are then defined in that new system. See http://www.scm.com/Doc/Doc2010/ADF/ADFUsersGuide/page56.html Evert Jan Baerends On Mar 24, 2011, at 1:36 PM, Marcel Swart marcel.swart[]icrea.cat wrote: > Please have a look at the output, in particular the following part: > > List of all MOs, ordered by energy, with the most significant SFO =20 > gross populations > =20 > =3D=20 > =3D=20 > =3D=20 > =3D=20 > =3D=20 > =3D=20 > =3D=20 > =3D=20 > =3D=20 > =3D=20 > =3D=20 > =3D=20 > =3D=20 > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > Each percentage contribution in the table below corresponds to the =20= > indicated SFO. > In general, a SFO may be a linear combination of several Fragment =20 > Orbitals on the same, > or on symmetry-related Fragments. Only the first 'member' of such a =20= > combination is > specified here. A full definition of all SFOs is given in an =20 > earlier part of the output. > The numbering of the SFOs in this table does NOT include the Core =20 > Orbitals, and starts > from one for each symmetry representation, as in the SFO definition =20= > list earlier. > > as an example, the partial output for an iron-complex: > > -5.262 1.00 42 A.g 34.26% 1 D:xz =20 > -7.900 1.20 1 FE > 24.11% 1 D:xy =20 > -7.900 1.20 1 FE > 15.25% 2 P:x =20 > -8.644 1.67 2 CL > 10.74% 1 D:yz =20 > -7.900 1.20 1 FE > 6.05% 1 D:x2-y2 =20 > -7.900 1.20 1 FE > 4.66% 1 D:z2 =20 > -7.900 1.20 1 FE > > This indicates how much each of the d-orbitals of Fe contribute to =20 > this MO. > You can sum these contributions, and then get an idea of the how the =20= > different d-orbitals > of iron are occupied. In this particular case for instance: > > OCCUPATIONS (total) > A.g 46.0 // 42.0 > A.u 44.0 // 44.0 > > Total 90.0 86.0 > > FE occupations > 1 D:z2 A.g 97.1600 12.4400 > 1 D:x2-y2 A.g 96.2900 14.3600 > 1 D:xy A.g 94.4900 15.6700 > 1 D:xz A.g 96.5300 53.9100 > 1 D:yz A.g 95.4400 26.6400 > 2 D:yz A.g 1.3400 0.0000 > > Marcel > > On Mar 24, 2011, at 10:38 AM, Radoslaw Kaminski =20 > rkaminski.rk(!)gmail.com wrote: > >> Hi, >> >> If so where exactly I could find this information and what analysis =20= >> is that? What about specific choice of the coordinate system used =20 >> for the description of d-orbitals orientations? Question rather =20 >> trivial but I'm not a theoretician:) My point is to get such =20 >> information not as a populations of the basis-set functions but =20 >> rather like orbital model fitted into the theoretical data. Does it =20= >> sound reasonable? >> >> Radek > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > dr. Marcel Swart > > ICREA Research Professor at > Institut de Qu=EDmica Computacional > Universitat de Girona > > Facultat de Ci=E8ncies > Campus Montilivi > 17071 Girona > Catalunya (Spain) > > tel > +34-972-418861 > fax > +34-972-418356 > e-mail > marcel.swart|*|icrea.cat > marcel.swart|*|udg.edu > web > http://www.marcelswart.eu > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > Prof. E. J. Baerends World Class University program at Dep. of Chemistry Pohang University of Science and Technology San 31, Hyojadong, Namgu Pohang 790-784, Korea email: e.j.baerends_-_vu.nl Tel +82-54-279-5230 Secr. +82-54-279-8133 or 8681 Fax +82-54-279-8137 and VU University FEW / Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam email: e.j.baerends_-_vu.nl tel. +31-20-5987623 secr. +31-20-5987519 fax: +31-20-5987629 --Apple-Mail-37-546234308 Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable In view of your question: "how = would it be related to my chosen coordinate = system":


Note that by default the = local coordinate system on each atom is the same as your overall = coordinate system. 
So the local z axis with respect to = which e.g. the dz2 orbital for which you see the population is defined, = is just the overall z axis.

Sometimes it is = convenient to reorient the local axes. For instance when you discern an = approximate local square planar coordination, but the plane is not = parallel to the xy plane but tilted. Then you can do a calculation with = the local coordinate system rotated, in your preferred direction, and = the atomic orbitals for which you see the populations are then defined = in that new system.

= Evert Jan = Baerends



On = Mar 24, 2011, at 1:36 PM, Marcel Swart marcel.swart[]icrea.cat = wrote:

Please have a look at = the output, in particular the following = part:

 List of all MOs, ordered by energy, with the = most significant SFO gross = populations
 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
<= font class=3D"Apple-style-span" face=3D"'Andale Mono'">       =                     =         
 Each percentage = contribution in the table below corresponds to the indicated = SFO.
 In general, a SFO may be a linear combination of = several Fragment Orbitals on the same,
 or on = symmetry-related Fragments. Only the first 'member' of such a = combination is
 specified here. A full definition of all SFOs is = given in an earlier part of the output.
 The numbering of the = SFOs in this table does NOT include the Core Orbitals, and = starts
 from one for each symmetry representation, as in = the SFO definition list = earlier.

as an example, the = partial output for an iron-complex:

      -5.262  1.00    42 = A.g       34.26%     1 D:xz     =       -7.900  1.20     1 = FE
               =                     = 24.11%     1 D:xy           -7.900 =  1.20     1 FE
       =                     =         15.25%     2 P:x     =        -8.644  1.67     2 = CL
               =                     = 10.74%     1 D:yz           -7.900 =  1.20     1 FE
       =                     =          6.05%     1 D:x2-y2   =      -7.900  1.20     1 = FE
               =                     =  4.66%     1 D:z2           = -7.900  1.20     1 = FE

This indicates how much = each of the d-orbitals of Fe contribute to this MO.
You can = sum these contributions, and then get an idea of the how the different = d-orbitals
of iron are occupied. In this particular case for = instance:

OCCUPATIONS = (total)
       A.g       =    46.0     //     = 42.0
       A.u       =    44.0     //     = 44.0

     Total     =      90.0           =  86.0

FE occupations
 1 = D:z2               A.g     =   97.1600       12.4400
 1 D:x2-y2 =            A.g       = 96.2900       14.3600
 1 D:xy   =             A.g       = 94.4900       15.6700
 1 D:xz   =             A.g       = 96.5300       53.9100
 1 D:yz   =             A.g       = 95.4400       26.6400
 2 D:yz   =             A.g       =  1.3400       =  0.0000

Marcel
=
On Mar 24, 2011, at 10:38 AM, Radoslaw Kaminski = rkaminski.rk(!)gmail.com = wrote:

Hi,

If so where exactly I could find this = information and what analysis is that? What about specific choice of the = coordinate system used for the description of d-orbitals orientations? = Question rather trivial but I'm not a theoretician:) My point is to get = such information not as a populations of the basis-set functions but = rather like orbital model fitted into the theoretical data. Does it = sound reasonable?

Radek

17071 = Girona
Catalunya = (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mailmarcel.swart|*|icrea.cat
m= arcel.swart|*|udg.edu
web
http://www.marcelswart.eu
=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D
=

Prof. E. J. = Baerends
World Class University program at Dep. of = Chemistry
Pohang University of Science and Technology
San 31, = Hyojadong, Namgu
Pohang 790-784, Korea
email: e.j.baerends_-_vu.nl
Tel = +82-54-279-5230
Secr. +82-54-279-8133 or 8681
Fax = +82-54-279-8137

and
VU University
FEW / Theoretical = Chemistry
De Boelelaan 1083
1081 HV Amsterdam
email: e.j.baerends_-_vu.nl
tel. = +31-20-5987623
secr. +31-20-5987519
fax: = +31-20-5987629
 =

= --Apple-Mail-37-546234308-- From owner-chemistry@ccl.net Thu Mar 24 13:28:01 2011 From: "Joaquin Calbo HimPhoenixCCL/./gmail.com" To: CCL Subject: CCL: Absorption spectrum with TDDFT Message-Id: <-44213-110324113633-12005-VbnhnGc0j8wzZqoCpsrDvA%%server.ccl.net> X-Original-From: "Joaquin Calbo" Date: Thu, 24 Mar 2011 11:36:31 -0400 Sent to CCL by: "Joaquin Calbo" [HimPhoenixCCL^-^gmail.com] Hi! I have some problems to reproduce experimental UV-Vis spectra with TDDFT calculations. I'm working with big systems with charge transfer and the difference between theoretical and experimental peaks is more than 0.5 eV. Is there any way to obtain better results? I'm using g09 and B3LYP/6-31G** level. Thanks in advance From owner-chemistry@ccl.net Thu Mar 24 14:03:01 2011 From: "Daniel Jana dfjana ~~ gmail.com" To: CCL Subject: CCL: NICS calculation Geometrical Point Message-Id: <-44214-110324115513-30748-I0K0chKeLNzqgwms3dArRQ]|[server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 24 Mar 2011 16:55:06 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana^_^gmail.com] Hello, If you take a look at the original paper by Schleyer et al (JACS, 1996, 118, 6317) they state that the position for the ring center is the "nonweighted mean of the heavy atom coordinates". You just get the coordinates of all the heavy atoms, average them out and that's your point. Keep in mind the sign of the NICS should be reversed (the value for pyrrole is -15.1 ppm). Hope this helps, Daniel On 24 March 2011 10:16, Cem Burak YILDIZ cemburakyildiz(a)bau.edu.tr wrote: > > Sent to CCL by: "Cem Burak YILDIZ" [cemburakyildiz#,#bau.edu.tr] > I have a problem with NICS calculation. If you help me, I'm glad. > > I'm trying to calculate NICS values of some molecules. Howeover, I have > > trouble with determine geometrical pouint for non-plane or 3D-molecules. > > Now, this calculation type is easy for benzene or cyclohexane, because > > the molecules are symetrical. > > Howeover, I have a problem molecules which are non-plane. > > For instance, I could not find geometrical point of furan or pyrrole or > > these typesmolecules exactly. > > so, i obtained a bit different values of shielding of Bq in these molecules. > > For instance, > > Acoording to Schlayer et al, NICS value of Bq of pyrrole is 15.1 ppm at > > Hf/6-31+g* theory of level, but obtained value by me for this molecule > > is 14.85 ppm at the same level of theory. > > How can i fix this mistake? > > How can i determine geometrical point correctly? > > Can you help me about this topic? > > If it is possible, can you send me input file of furan or a molecules is not plane.>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Mar 24 14:38:00 2011 From: "Mikael Johansson mikael.johansson::iki.fi" To: CCL Subject: CCL: d-orbital populations for a transition metal Message-Id: <-44215-110324122548-28780-CtUua5fsnQ+ygFhnBWkBAg%%server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 24 Mar 2011 18:25:38 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson:iki.fi] Hello Radek and All! The most straightforward way of analyzing these would, in my opinion, be to have a look at the actual orbitals. ADFview can do this quickly for you, the d-orbitals should be fairly easy to find at the top of the occupied spectrum. This as an addition, and corroboration of the populations analyses that have been suggested. A possible problem with the automatically generated numbers is related to your question of the orientation of your molecule. I wouldn't for example trust that the computed d_xz/d_yz designations correspond to your (experimental) d_pi designations, without a double check. A possible problem with the direct visualisation approach would be that in some cases, a single orbital is not really fully of d-character. If you have several TM centres, the DFT d-orbitals can also be delocalised over several metals. If you have a simple one-metal complex, I suspect you'll be lucky and avoid these caveats. Have fun, Mikael J. http://www.iki.fi/~mpjohans/ On Thu, 24 Mar 2011, Radoslaw Kaminski rkaminski.rk(!)gmail.com wrote: > If so where exactly I could find this information and what analysis is > that? What about specific choice of the coordinate system used for the > description of d-orbitals orientations? Question rather trivial but I'm > not a theoretician:) My point is to get such information not as a > populations of the basis-set functions but rather like orbital model > fitted into the theoretical data. Does it sound reasonable? From owner-chemistry@ccl.net Thu Mar 24 16:01:01 2011 From: "Farhan Pasha pashafa*yahoo.co.in" To: CCL Subject: CCL:G: thanks for you time Message-Id: <-44216-110324155535-21244-jUeM7HpEtDb3J95ldP4UaQ~!~server.ccl.net> X-Original-From: Farhan Pasha Content-Type: multipart/alternative; boundary="0-140148871-1300996524=:94210" Date: Fri, 25 Mar 2011 01:25:24 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Farhan Pasha [pashafa**yahoo.co.in] --0-140148871-1300996524=:94210 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Your Error is related to default number of SCF cycle=20 Please use SCFcyc=3D500 or more or similarly Maxcycle=3D500 or morefor opt =A0iop(4/43=3D10) means you are using=A0=0Aself-consistent solvent charges = which is not corect solution to your problem i guess. hope it will work otherwise you can post again to me. Best F A Pasha Correspondence Address =0ADr. Syed Farhan Ahmad Pasha --- On Thu, 24/3/11, guo ya juan garlic007{:}126.com wrote: > From: guo ya juan garlic007{:}126.com Subject: CCL:G: thanks for you time To: "Pasha, Frahan Ahmad " Date: Thursday, 24 March, 2011, 8:54 AM Sent to CCL by: "guo ya juan" [garlic007**126.com] ear CCL memebers: I am doing an PM3 optimization calculation=A0 on the Gaussian program. ther= e is always an error in the job end,=20 it is said that " unable to achieve self-consistence" at L402, but when i u= sed the keyword "iop(4/43=3D10)", the job can be complated. it is truth that i do not know why. i really hop= e you can give some suggestion.=20 there is the error out job : It=3D299 PL=3D 1.20D-02 DiagD=3DTT ESCF=3D=A0 67322.227111 Diff=3D 1.21D+0= 4 RMSDP=3D 1.23D-02. It=3D299 PL=3D 1.20D-02 DiagD=3DTT ESCF=3D=A0 20119.965002 Diff=3D 1.21D+0= 4 RMSDP=3D 1.23D-02. It=3D300 PL=3D 1.20D-02 DiagD=3DTT ESCF=3D 172092.026142 Diff=3D 2.08D+02 = RMSDP=3D 1.23D-02. =A0 =A0 =A0 =A0 =A0 """""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE =A0 =A0 =A0 =A0 =A0 DELTAE=3D=A0=A0=A00.4796E+04=A0 =A0=A0=A0DELTAP=3D=A0= =A0=A00.1198E-01 Error termination via Lnk1e in e:\G03W\l402.exe at Mon Mar 21 17:33:00 201= 1. thanks very much for you hope. -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A --0-140148871-1300996524=:94210 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi
Your Error is related to default number= of SCF cycle
Please use SCFcyc=3D500 or more or similarly Maxcycle=3D5= 00 or morefor opt
 iop(4/43=3D10) means you are using =0Aself-= consistent solvent charges which is not corect solution to your problem i g= uess.
hope it will work otherwise you can post again to me.
Best
F= A Pasha

Correspondence Address
=0ADr. Syed Farhan Ahmad Pasha
--- On Thu, 24/3/11, guo ya juan garlic007{:}126.com <owner-c= hemistry|a|ccl.net> wrote:

From: g= uo ya juan garlic007{:}126.com <owner-chemistry|a|ccl.net>
Subject: = CCL:G: thanks for you time
To: "Pasha, Frahan Ahmad " <pashaf= a|a|yahoo.co.in>
Date: Thursday, 24 March, 2011, 8:54 AM


Sent to CCL by: "guo ya juan" [garlic007**126.com]ear CCL memebers:

I am doing an PM3 optimization calculation  = on the Gaussian program. there is always an error in the job end,
it is= said that " unable to achieve self-consistence" at L402, but when i used t= he keyword "iop(4/43=3D10)",
the job can be complated. it is truth that= i do not know why. i really hope you can give some suggestion.
there i= s the error out job :

It=3D299 PL=3D 1.20D-02 DiagD=3DTT ESCF=3D  67322.227111 Diff=3D 1.21D+04 RMSDP=3D 1= .23D-02.
It=3D299 PL=3D 1.20D-02 DiagD=3DTT ESCF=3D  20119.965002 = Diff=3D 1.21D+04 RMSDP=3D 1.23D-02.
It=3D300 PL=3D 1.20D-02 DiagD=3DTT = ESCF=3D 172092.026142 Diff=3D 2.08D+02 RMSDP=3D 1.23D-02.
    =       """""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE

          DELTAE=3D   0.4796E+= 04     DELTAP=3D   0.1198E-01


Error termination via Lnk1e in e:\G03W\l402.exe at Mon Mar 21 17:33:0= 0 2011.
thanks very much for you hope.



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--0-140148871-1300996524=:94210-- From owner-chemistry@ccl.net Thu Mar 24 16:35:00 2011 From: "Nuno A. G. Bandeira nuno.bandeira-.-ist.utl.pt" To: CCL Subject: CCL: d-orbital populations for a transition metal Message-Id: <-44217-110324141327-3113-WwyaGV/ahFohug0Mzf94xw{=}server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 24 Mar 2011 19:13:20 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira- -ist.utl.pt] On 24-03-2011 14:38, Radoslaw Kaminski rkaminski.rk++gmail.com wrote: > > As I'm not very much familiar with those population schemes my > question is how to interpret this table in terms of local atomic > coordinate systems. In manual it's not much written in details about. > > Thanks for helping:) Mulliken population analyses are the primary and most used population analysis schemes used in computational chemistry. The original reference is J. Chem. Phys. 1955, 23, 1833. If you're interested in a certain atom and want to associate an orbital with any particular axis all you need to do is to translate your coordinate centre to that atom and adjust the axes accordingly. Symmetry helps symplify your problem too. Best wishes, Nuno -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN -- From owner-chemistry@ccl.net Thu Mar 24 19:34:01 2011 From: "John Free johnfree198|-|gmail.com" To: CCL Subject: CCL: TS inquiry Message-Id: <-44218-110324192457-22721-Xon7r69pDpi2ERfdZnr/yg.@.server.ccl.net> X-Original-From: "John Free" Date: Thu, 24 Mar 2011 19:24:55 -0400 Sent to CCL by: "John Free" [johnfree198 ~~ gmail.com] Dear all, What is the suggested transition state for the following reaction? [LZn](2+) + CH3OH >>> LZnOCH3 where L is macrocycle lignad My suggestion of TS structure include long bond formation (Zn...OCH3) and bond breaking (H...OCH3). Please let me know your opinion and the suitable lengths of these bonds in the initial structure. Thanks, John From owner-chemistry@ccl.net Thu Mar 24 20:14:00 2011 From: "Hanneke Jansen johanna.jansen|,|novartis.com" To: CCL Subject: CCL: ACS Anaheim: COMP Mentor lunches Message-Id: <-44219-110324175123-22287-lYDZr3o/cwEl91QUN2Cxdw:_:server.ccl.net> X-Original-From: "Hanneke Jansen" Date: Thu, 24 Mar 2011 17:51:22 -0400 Sent to CCL by: "Hanneke Jansen" [johanna.jansen],[novartis.com] Graduate students and post-docs in computational chemistry are invited to the COMP Mentor Lunches ! Please join us at the ACS national meeting in Anaheim, where we will offer an academic mentor lunch and an industrial mentor lunch on Tuesday, March 29 at noon. The goal is to allow for networking in an open, relaxed setting and to promote discussions about possible career paths in academia and industry. All are welcome. Groups will meet outside the COMP symposia and then depart for lunch at a local restaurant. You can register for this event through the COMP Together network. If you already signed up for the network, you can register for the lunch here: http://www.acscomp.org/COMP_Together/meeting_signup.php?event_id=3 and add in the comments field whether youre signing up for the industrial or academic lunch. If you have not yet signed up for the network, please do that first, using this link http://www.acscomp.org/COMP_Together/reg_form.php and then register for the lunch with the link above. As a reminder, the COMP Together initiative includes tools and a network of local champions to facilitate COMP members getting together on a local and informal level (seminars, networking events, mentoring lunches). You can select the local area where you live & work as well as the national meeting when you register on the network. In the future, you will then be notified of upcoming events in all of the areas that you registered for. We look forward to seeing you at one of our events ! Hanneke Jansen, on behalf of the COMP Together Team