From owner-chemistry@ccl.net Tue Jun 24 09:03:01 2008 From: "Marcelo Puiatti marcelo.puiatti__gmail.com" To: CCL Subject: CCL: C-H+ deprotonation energy barrier Message-Id: <-37243-080623184612-30194-pYhTgfGoItD5b5LZiOwvhQ]|[server.ccl.net> X-Original-From: "Marcelo Puiatti" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 23 Jun 2008 18:51:10 -0300 MIME-Version: 1.0 Sent to CCL by: "Marcelo Puiatti" [marcelo.puiatti++gmail.com] Dear CCL, I need to calculate the activation energy barriers of two reactions: a C-C fragmentation reaction, and a C-H+ deprotonation in acetonitrile. As far as I know the C-H+ deprotonation activation barriers are usually overestimated. Could anyone give me guidance or point me in the right direction for references about the treatment of C-H+ deprotonation energy barriers. Thanks in advance, Marcelo Puiatti From owner-chemistry@ccl.net Tue Jun 24 09:36:01 2008 From: "Alberto Sergio Garay sgaray(_)fbcb.unl.edu.ar" To: CCL Subject: CCL: Problem compiling tinker binaries.... Message-Id: <-37244-080624090157-7064-6EjN11qAwBmu2aob/t292A*server.ccl.net> X-Original-From: Alberto Sergio Garay Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 24 Jun 2008 09:06:34 -0300 MIME-Version: 1.0 Sent to CCL by: Alberto Sergio Garay [sgaray~~fbcb.unl.edu.ar] Hi My name is Sergio Garay and I've been trying to compile the tinkers binaries without success. I'm working in a linux system (redhat 9.0) with ifort compiler. I run firstly the script debug.make in order to find some trouble and I got many errors like these: (Am I doing something wrong? fortcom: Error: analyze.f, line 1581: This name does not have a type, and must have an explicit type. [RSOLV] write (iout,480) k,i,rsolv(i),asolv(i) .....................................^ fortcom: Error: analyze.f, line 1581: This name does not have a type, and must have an explicit type. [ASOLV] write (iout,480) k,i,rsolv(i),asolv(i) ..............................................^ compilation aborted for analyze.f (code 1) fortcom: Error: born.f, line 74: This name does not have a type, and must have an explicit type. [RSOLV] roff(i) =3D rsolv(i) + doffset ...................^ fortcom: Error: born.f, line 74: This name does not have a type, and must have an explicit type. [DOFFSET] roff(i) =3D rsolv(i) + doffset ..............................^ fortcom: Error: born.f, line 79: This name does not have a type, and must have an explicit type. [SOLVTYP] if (solvtyp .eq. 'ONION') then ..........^ fortcom: Error: born.f, line 104: This name has not been declared as an array or a function. [RBORN] rborn(i) =3D 1.0d0 / total ............^ fortcom: Error: born.f, line 115: This name does not have a type, and must have an explicit type. [P5] p5inv =3D 1.0d0 / p5 .........................^ Any help will be appreciated. --=20 Dr. Sergio Garay Facultad de Bioquimica y Cs. Biol=F3gicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 From owner-chemistry@ccl.net Tue Jun 24 16:05:00 2008 From: "Qiang Fu qfu!^!kth.se" To: CCL Subject: CCL:G: How to calculate overlap of two total wavefunctions Message-Id: <-37245-080624160200-1151-8CYoqGM3wqANpczOnkKPNA-x-server.ccl.net> X-Original-From: "Qiang Fu" Date: Tue, 24 Jun 2008 16:01:57 -0400 Sent to CCL by: "Qiang Fu" [qfu*kth.se] Dear All, I am doing a project concerning the stucture changes of an organic moleucle. The calculations are performed using Gaussian 03. In the analysis, an overlap of the total wavefunctions (Slater determinant not single molecular orbital) between the initial structure and the structure of the molecule which has been changed is needed. As the configurations are not the same in the two total wavefunctions, Slater integral rules may not be used as the sites of the atoms (the center of the gaussian basis set) are changed. Could you please give me some advice about hwo to calculate this overlap. Besides, the calculations can also be performed in VASP using a plane wave basis set, if it is difficult to calculate the overlap using Gaussian 03. I am most appreciative of your generous help. Best Regards! Sincerely yours, Qiang Fu From owner-chemistry@ccl.net Tue Jun 24 16:39:00 2008 From: "Cenk Selcuki cselcuki^yahoo.com" To: CCL Subject: CCL:G: NBO Error in G03 Message-Id: <-37246-080624163303-15431-jUeM7HpEtDb3J95ldP4UaQ-x-server.ccl.net> X-Original-From: "Cenk Selcuki" Date: Tue, 24 Jun 2008 16:32:59 -0400 Sent to CCL by: "Cenk Selcuki" [cselcuki^^yahoo.com] Dear All, One of my collegues have performed an NBO analysis with G03 on a formerly optimized geometry and faced an error as Sorting of NBOs: 294 169 167 172 274 422 151 205 117 255 Sorting of NBOs: 395 222 378 100 409 326 345 360 238 434 Sorting of NBOs: 429 425 277 270 272 131 310 182 168 275 Sorting of NBOs: 426 NBStor is confused about NOcc. Error termination via Lnk1e in C:\G03W\l607.exe at Tue Jun 10 21:12:37 2008. Job cpu time: 0 days 2 hours 39 minutes 2.0 seconds. File lengths (MBytes): RWF= 144 Int= 0 D2E= 0 Chk= 7 Scr= 1 Could you please inform me about the possible reasons? Thanks a lot in advance. Cheers, Cenk Selcuki cselcuki .. yahoo.com Ege University Izmir/Turkey From owner-chemistry@ccl.net Tue Jun 24 17:17:00 2008 From: "Don Steiger sd00_2002===yahoo.com" To: CCL Subject: CCL: Problem compiling tinker binaries.... Message-Id: <-37247-080624163152-14917-oFUubBI8b8HYIDholY4Ciw---server.ccl.net> X-Original-From: Don Steiger Content-Type: multipart/alternative; boundary="0-765506286-1214335897=:80854" Date: Tue, 24 Jun 2008 12:31:37 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Don Steiger [sd00_2002 ~~ yahoo.com] --0-765506286-1214335897=:80854 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable It sounds like a problem with a ".i" file.=A0 Use grep (or egrep) to find w= here these variable are defined and allocated.=A0 E.g. egrep "variable name= " *.i --- On Tue, 6/24/08, Alberto Sergio Garay sgaray(_)fbcb.unl.edu.ar wrote: > From: Alberto Sergio Garay sgaray(_)fbcb.unl.edu.ar Subject: CCL: Problem compiling tinker binaries.... To: "Steiger, Don " Date: Tuesday, June 24, 2008, 5:06 AM Sent to CCL by: Alberto Sergio Garay [sgaray~~fbcb.unl.edu.ar] Hi My name is Sergio Garay and I've been trying to compile the tinkers binaries without success. I'm working in a linux system (redhat 9.0) with ifort compiler. I run firstly the script debug.make in order to find some trouble and I got many errors like these: (Am I doing something wrong? fortcom: Error: analyze.f, line 1581: This name does not have a type, and must have an explicit type. [RSOLV] write (iout,480) k,i,rsolv(i),asolv(i) .....................................^ fortcom: Error: analyze.f, line 1581: This name does not have a type, and must have an explicit type. [ASOLV] write (iout,480) k,i,rsolv(i),asolv(i) ..............................................^ compilation aborted for analyze.f (code 1) fortcom: Error: born.f, line 74: This name does not have a type, and must have an explicit type. [RSOLV] roff(i) =3D rsolv(i) + doffset ...................^ fortcom: Error: born.f, line 74: This name does not have a type, and must have an explicit type. [DOFFSET] roff(i) =3D rsolv(i) + doffset ..............................^ fortcom: Error: born.f, line 79: This name does not have a type, and must have an explicit type. [SOLVTYP] if (solvtyp .eq. 'ONION') then ..........^ fortcom: Error: born.f, line 104: This name has not been declared as an array or a function. [RBORN] rborn(i) =3D 1.0d0 / total ............^ fortcom: Error: born.f, line 115: This name does not have a type, and must have an explicit type. [P5] p5inv =3D 1.0d0 / p5 .........................^ Any help will be appreciated. --=20 Dr. Sergio Garay Facultad de Bioquimica y Cs. Biol=F3gicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt=0A=0A=0A --0-765506286-1214335897=:80854 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
It sounds like a problem with a ".i" file.&nb= sp; Use grep (or egrep) to find where these variable are defined and alloca= ted.  E.g. egrep "variable name" *.i

--- On Tue, 6/24/08, Al= berto Sergio Garay sgaray(_)fbcb.unl.edu.ar <owner-chemi= stry:-:ccl.net> wrote:
From: Alberto S= ergio Garay sgaray(_)fbcb.unl.edu.ar <owner-chemistry:-:ccl.net>
Sub= ject: CCL: Problem compiling tinker binaries....
To: "Steiger, Don -id#4= cn-" <dsteiger:-:bioeng.ucsd.edu>
Date: Tuesday, June 24, 2008, 5:06= AM

Sent to CCL by: Alberto Sergio Garay [sgaray~~fbcb.unl.edu.=
ar]
Hi

My name is Sergio Garay and I've been trying to compile th=
e tinkers
binaries without success. I'm working in a linux system (redha=
t
 9.0)
with ifort compiler. I run firstly the script debug.make in order =
to
find some trouble and I got many errors like these: (Am I doing
so=
mething wrong?


fortcom: Error: analyze.f, line 1581: This name d=
oes not have a type,
and must have an explicit type.   [RSOLV]
      =
           write (iout,480)  k,i,rsolv(i),asolv(i)
.....................=
................^
fortcom: Error: analyze.f, line 1581: This name does n=
ot have a type,
and must have an explicit type.   [ASOLV]
           =
      write (iout,480)  k,i,rsolv(i),asolv(i)
..........................=
....................^
compilation aborted for analyze.f (code 1)
fort=
com: Error: born.f, line 74: This name does not have a type, and
must ha=
ve an explicit type.   [RSOLV]
           roff(i) =3D rsolv(i) + doffset=

...................^
fortcom: Error: born.f, line 74: This name does=
 not have a type, and
must have an explicit type.   [DOFFSET]
 =20
         roff(i) =3D rsolv(i) + doffset
..............................^<=
br>fortcom: Error: born.f, line 79: This name does not have a type, and
=
must have an explicit type.   [SOLVTYP]
        if (solvtyp .eq. 'ONION'=
) then
..........^
fortcom: Error: born.f, line 104: This name has no=
t been declared as
an array or a function.   [RBORN]
              rb=
orn(i) =3D 1.0d0 / total
............^
fortcom: Error: born.f, line 1=
15: This name does not have a type, and
must have an explicit type.   [P=
5]
           p5inv =3D 1.0d0 / p5
.........................^

=
Any help will be appreciated.


-- 
Dr. Sergio Garay
Faculta=
d de Bioquimica y Cs. Biol=F3gicas
Universidad Nacional del Litoral
S=
anta Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
A=
rgentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221


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=0A=0A --0-765506286-1214335897=:80854-- From owner-chemistry@ccl.net Tue Jun 24 17:49:01 2008 From: "Alcides Simao alsimao(_)gmail.com" To: CCL Subject: CCL: Shape of absorpion bands Message-Id: <-37248-080624170214-5015-WTQQpNJ4JzBSzJn1pLO+xA=server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_5891_26932334.1214341320539" Date: Tue, 24 Jun 2008 22:02:00 +0100 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao^gmail.com] ------=_Part_5891_26932334.1214341320539 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline We would appreciate recommending a source (reference to a book or an original paper, if possible with the entire document in an electronic format) explaining the shape of absorption bands in the vibrational (infrared) spectra of solid films of different composition (unordered solid - glass, or amorphous film as well as crystal) as a function of temperature or other factors. In particular, factors responsible for the symmetric or asymmetric shape of band contours are interesting. The solids in question consist of simple organic molecules without hydrogen bonds. ------=_Part_5891_26932334.1214341320539 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline We would appreciate recommending a source
(reference to a book or an original paper,
if possible with the entire document in an electronic format)
explaining the shape of absorption bands in the
vibrational (infrared) spectra of solid films of different composition
(unordered solid - glass, or amorphous film as well as crystal)
as a function of temperature or other factors.
In particular, factors responsible for the symmetric or
asymmetric shape of band contours are interesting.
The solids in question consist of simple organic molecules
without hydrogen bonds. ------=_Part_5891_26932334.1214341320539--