You may tr= y "Chemcraft". Go to www.chemcraftprog.com and download this nice viewer. I= n the "Coord" part of the program you can convert Angstroms to Bohrs if you= enter the Cartesian coordinate of your system.

<= span>

Cina Foroutan-Nejad,

School of Chemistry,

College of Science, Universi= ty of Tehran

From: Bradley K Welch bwelch5(-)slu.edu <owner-chemistry()ccl= .net>
To: "Foroutan-= Nejad, Cina " <canyslopus()yahoo.co.uk>
Sent: Tuesday, 1 November 2011, 7:35
Subject: CCL: Coordinate conversion p= rogram

Sent to CCL by: "Bradley K Welch" [bwelch5|a= |slu.edu]
CCL readers,

Does anyone know of a program that will co= nvert bohr coordinates to angstroms
and vice versa? Is openbabel capabl= e of it?

Bradley Welch
Saint Louis University
Room 21= 8

-=3D This is automatically added to each message by the ma= iling script =3D-
To recover the email address of the author of the mess= age, please change
the strange characters on the top line to the () sign.= You can also<= br>E-mail to subscribers: CHEMISTRY()ccl.net or use:
&nb= sp; http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to ad= ministrators: CHEMISTRY-REQUEST()ccl.net or use
= http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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If your mail bounces from CCL with 5.7.1 error, che= ck:
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---213401403-1852225984-1320124846=:88809-- From owner-chemistry@ccl.net Tue Nov 1 02:07:00 2011 From: "Tapas Kar tapas.kar~~usu.edu" To: CCL Subject: CCL: o-hydroquinone to o-quinone reaction mechanism Message-Id: <-45794-111101020505-30764-8MzMIlREH3k/lgHp7S+nCA]~[server.ccl.net> X-Original-From: Tapas Kar Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 1 Nov 2011 06:04:56 +0000 MIME-Version: 1.0 Sent to CCL by: Tapas Kar [tapas.kar===usu.edu] Hello Kalju and Bruce, Thanks for your helpful suggestions. Best wishes, Tapas -----Original Message----- > From: owner-chemistry+tapas.kar==usu.edu ~~ ccl.net [mailto:owner-chemistry+tapas.kar==usu.edu ~~ ccl.net] On Behalf Of Kalju Kahn kalju+*+chem.ucsb.edu Sent: Tuesday, October 25, 2011 6:45 PM To: Tapas Kar Subject: CCL: o-hydroquinone to o-quinone reaction mechanism Sent to CCL by: "Kalju Kahn" [kalju+/-chem.ucsb.edu] Kar, Bruce's reply reminded me of an old theoretical work where I looked how triplet O2 may react with urate (hydroquinone in disguise) to yield something called dehydroisourate (quinone in disguise). Reactivity in this system was a strong function of the ionic form (as one would guess, anion was better e-donor than acid) and solvent (radical-ion pair stabilized by polar solvent). The work was published in Bioorganic Chemistry, 27(5), 351-362, 1999. There are couple of newer studies of the same reaction, that explore some of alternative mechanisms. Other systems with similar chemistry (but with possibly more stable radicals) are tetrahydropterin and the reduced flavin. Best wishes, Kalju > Generally, O2 (a triplet) reacts with singlet organics by an initial > single-electron transfer, forming a solvent-caged superoxide-organic > radical pair. Depending on relative rates of the possible processes, > a second electron transfer, coupled to proton transfer (s) could > occur, giving the oxidized organic and H2O2. Or, the radical > intermediate could couple, forming a peroxide which is protonated to the hydroperoxide. > Depending on the organic moiety (like an o-quinone), that could > eliminate > H2O2 leaving the unsaturated organic. Or, the radical pair could > separate by diffusion, and these radicals could oxidize the reduced > organic (SET > again) in a chain reaction. Another link in a chain reaction could be > the the reaction of oxidized and reduced organic to form to radicals - > especially possible with quinones. I don't know if the specifics of > what actually occurs have been addressed for o-quinones; the relative > rates of these possible reactions are likely to depend on the > reduction potentials (which will vary with substituents) and solvent. > > ciao, > Bruce > > Bruce A. Palfey > Associate Professor of Biological Chemistry & Associate Director, > Program in Chemical Biology Department of Biological Chemistry > University of Michigan Medical School 5220E MSRB III > 1150 W. Medical Center Drive > Ann Arbor, MI 48109-0606 > (734) 615-2452 > brupalf^^umich.edu > > http://www.biochem.med.umich.edu/?q=palfey > http://www.chembio.umich.edu/people/palfey.html > > > On Oct 25, 2011, at 5:15 PM, Tapas Kar tapas.kar||usu.edu wrote: > >> >> Sent to CCL by: "Tapas Kar" [tapas.kar()usu.edu] Hello, >> >> I am looking for o-hydroquinone to o-quinone reaction mechanism in >> O2/H2O. I checked literature but could not found any paper describing >> step-by-step reaction mechanism and kinetics. Is there any >> theoretical/computation study reported on this reaction? I am >> interested to know how this reaction takes place I guess some oxygen >> based radical is involved but what kind? Is singlet O2 or triplet O2 >> facilitated the reaction? >> >> >> Thanks >> >> TK>> To recover the email address of the author of the message, >> TK>> please >> change>> > > > >> >> >> > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Nov 1 02:41:00 2011 From: "Berger Raphael berger/./chem.helsinki.fi" To: CCL Subject: CCL: Coordinate conversion program Message-Id: <-45795-111101022158-29195-P8QXhCfBbiO9EnZx88pY0A[*]server.ccl.net> X-Original-From: Berger Raphael Content-Type: MULTIPART/MIXED; BOUNDARY="-696203250-360032900-1320128499=:18234" Date: Tue, 1 Nov 2011 08:21:39 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Berger Raphael [berger(a)chem.helsinki.fi] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---696203250-360032900-1320128499=:18234 Content-Type: TEXT/PLAIN; charset=iso-8859-1; format=flowed Content-Transfer-Encoding: 8BIT Hi, babel -i xyz aangstroems.xyz -o tmol bohr.coord f. i. does the job, in the tmol format however you have an additional $coord and $end line , and the element symbol is in the last column. On Tue, 1 Nov 2011, cina foroutan canyslopus!=!yahoo.co.uk wrote: > You may try "Chemcraft". Go to www.chemcraftprog.com and download this nice viewer. In the "Coord" part of the program you can convert Angstroms to Bohrs if you enter the Cartesian coordinate of your system. > > > Cina Foroutan-Nejad, > > School of Chemistry, > College of Science, University of Tehran > > > > ________________________________ > From: Bradley K Welch bwelch5(-)slu.edu > To: "Foroutan-Nejad, Cina " > Sent: Tuesday, 1 November 2011, 7:35 > Subject: CCL: Coordinate conversion program > > > Sent to CCL by: "Bradley K Welch" [bwelch5|a|slu.edu] > CCL readers, > > Does anyone know of a program that will convert bohr coordinates to angstroms > and vice versa? Is openbabel capable of it? > > > > Bradley Welch > Saint Louis University > Room 218> the strange characters on the top line to the %x% sign. You can also> > > > > E-mail to administrators: CHEMISTRY-REQUEST%x%ccl.net or use > > > > > > > ---213401403-1852225984-1320124846=:88809 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: quoted-printable > >

mes new roman, new york, times, serif;font-size:12pt">

You may tr= > y "Chemcraft". Go to www.chemcraftprog.com and download this nice viewer. I= > n the "Coord" part of the program you can convert Angstroms to Bohrs if you= > enter the Cartesian coordinate of your system.

<= > span>

Cina Foroutan-Nejad,

an>School of Chemistry,

College of Science, Universi= > ty of Tehran

es new roman, new york, times, serif; font-size: 12pt;">

family: times new roman, new york, times, serif; font-size: 12pt;"> ce=3D"Arial" size=3D"2">

> From: Bradley K Welch bwelch5(-)slu.edu <owner-chemistry%x%ccl= > .net>
To: "Foroutan-= > Nejad, > Cina " <canyslopus%x%yahoo.co.uk>
ight: bold;">Sent: Tuesday, 1 November 2011, 7:35
yle=3D"font-weight: bold;">Subject: CCL: Coordinate conversion p= > rogram

Sent to CCL by: "Bradley K Welch" [bwelch5|a= > |slu.edu]
CCL readers,

Does anyone know of a program that will co= > nvert bohr coordinates to angstroms
and vice versa? Is openbabel capabl= > e of it?

Bradley Welch
Saint Louis University
Room 21= > 8

-=3D This is automatically added to each message by the ma= > iling script =3D-
To recover the email address of the author of the mess= > age, please change
the strange characters on the top line to the %x% sign.= > You can also<= > br>E-mail to subscribers: ailto:CHEMISTRY%x%ccl.net">CHEMISTRY%x%ccl.net or use:
&nb= > sp; > nk">http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to ad= > ministrators: o:CHEMISTRY-REQUEST%x%ccl.net">CHEMISTRY-REQUEST%x%ccl.net or use
= > target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message
r
.net/chemistry/sub_unsub.shtml" target=3D"_blank">http://www.ccl.net/chemis= > try/sub_unsub.shtml

Before posting, check wait time at: =3D"http://www.ccl.net" target=3D"_blank">http://www.ccl.net

Job= > : http://www.ccl.net/= > jobs
Conferences: cements/conferences/" > target=3D"_blank">http://server.ccl.net/chemistry/announcements/conference= > s/

Search Messages: chccl/index.shtml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl= > /index.shtml

If your mail bounces from CCL with 5.7.1 error, che= > ck:
get=3D"_blank">http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/" target=3D"_blank">http= > ://www.ccl.net/chemistry/aboutccl/instructions/

v>

---696203250-360032900-1320128499=:18234-- From owner-chemistry@ccl.net Tue Nov 1 05:34:01 2011 From: "Dan Maftei dan.maftei=uaic.ro" To: CCL Subject: CCL: Coordinate conversion program Message-Id: <-45796-111101051231-14479-hhg/LpP1uYezM/GSZ91fcg**server.ccl.net> X-Original-From: Dan Maftei Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 01 Nov 2011 11:12:19 +0200 MIME-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei+/-uaic.ro] Hi, Assuming you have a xyz file (symbol x y z), to convert from angstroms to bohr you may use the following command-line construct: cat angstrom.xyz | awk '{print $1 " " $2/0.52918 " " $3/0.52918 " " $4/0.52918}' > bohr.xyz To do the reverse, the command will look like: cat bohr.xyz | awk '{print $1 " " $2*0.52918 " " $3*0.52918 " " $4*0.52918}' > angstroms.xyz For a prettier look, a printf awk command will to the trick: cat angstrom.xyz | awk '{printf("%2s %10.6f %10.6f %10.6f\n", $1, $2/0.52918, $3/0.52918, $4/0.52918 ) }' > borh.xyz You may need to check your file headers after the conversion (number of atoms, title and so on) Regards, Dan. On 11/01/2011 06:05 AM, Bradley K Welch bwelch5(-)slu.edu wrote: > Sent to CCL by: "Bradley K Welch" [bwelch5|a|slu.edu] > CCL readers, > > Does anyone know of a program that will convert bohr coordinates to angstroms > and vice versa? Is openbabel capable of it? > > > > Bradley Welch > Saint Louis University > Room 218> > -- Dan Maftei, Assistant Professor, Faculty of Chemistry/Department of Chemistry University Alexandru Ioan Cuza Iasi Bd. Carol 1, Nr. 11, 700506 Iasi, Romania Tel: +40 232 201307 E-mail(s): dan.maftei=chem.uaic.ro dan.maftei=uaic.ro From owner-chemistry@ccl.net Tue Nov 1 08:19:01 2011 From: "=?ISO-8859-1?Q?Markus_Sch=FCtz?= schuhtib!^!physik.tu-berlin.de" To: CCL Subject: CCL:G: excited state TDDFT Message-Id: <-45797-111101054723-3593-MnBHrtrGKrx3ioJ2o5B+3Q#server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Markus_Sch=FCtz?= Content-Type: multipart/alternative; boundary="------------040800050504080806000201" Date: Tue, 01 Nov 2011 10:46:58 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Markus_Sch=FCtz?= [schuhtib]~[physik.tu-berlin.de] This is a multi-part message in MIME format. --------------040800050504080806000201 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Hello, at the moment I can't say much about the S1 state, it's still calculating at the moment without any problems :-) While optimization both states changed from C3v to C1 (Omega: Change in point group or standard orientation.) Markus Am 31.10.2011 14:43, schrieb John McKelvey jmmckel!A!gmail.com: > Markus, > > I'm clearly not an expert on this... When you do the TDDFT or CIS > without optimizing any particular state are S1 and S2 close in > energy? of the same symmetry? It may be the case there could be a > problem optimizing S2 when it is the same symmetry of S1. Is there a > problem optimizing S1? > > My $0.02.. > > John McKelvey > > > On Mon, Oct 31, 2011 at 4:48 AM, Markus Schütz > schuhtib=-=physik.tu-berlin.de > > wrote: > > > Sent to CCL by: =?ISO-8859-15?Q?Markus_Sch=FCtz?= [schuhtib * > physik.tu-berlin.de ] > Am 27.10.2011 19:05, schrieb Markus Schütz > schuhtib!A!physik.tu-berlin.de : > > > Sent to CCL by: =?ISO-8859-15?Q?Markus_Sch=FCtz?= > [schuhtib::physik.tu-berlin.de ] > Hello, > > I tried to calculate the second excited state of adamantane > cation (opt and freq) in TDDFT ( # TD(root=2,NStates=40) > b3lyp/cc-pvtz opt sym=loose). Unfortunately the calculation > ended with > > 'You need to solve for more vectors in order to follow this > state.' > > So I set the keyword for NStates first to 10 then to 25 and > finally also to 40, but the message is the same. > I tried another way: From a cis calculation I wanted to get > the force contants using them for the TDDFT calculation. But > the cis calculation also ended with the message above > (NStates=25). Is it useful to set NStates much higher or is > there another way to do the TDDFT calculation? > > By the way, I also tried a cis calculation (# CIS=(Root=2, > NStates=40) hf/cc-pvtz opt(calcFC) freq sym=loose). This > delivers the message > > 'Tx not orthogonal to T.' > > I couldn't find any solution for this problem. > > Regards, > Markus > > Sorry, > > forgot to say I'm using Gaussian09. > > -- > Markus Schütz > Institut für Optik und Atomare Physik > AG Dopfer > Sekretariat EW 3-1 > Technische Universität Berlin > Hardenbergstraße 36 > 10623 Berlin > > Tel +49 (0)30 314 29808 > > Raum EW 337 > > > > -= This is automatically added to each message by the mailing > script =- > > > > E-mail to subscribers: CHEMISTRY*o*ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST*o*ccl.net > or useConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > > > > > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel*o*gmail.com -- Markus Schütz Institut für Optik und Atomare Physik AG Dopfer Sekretariat EW 3-1 Technische Universität Berlin Hardenbergstraße 36 10623 Berlin Tel +49 (0)30 314 29808 Raum EW 337 --------------040800050504080806000201 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello,

at the moment I can't say much about the S1 state, it's still calculating at the moment without any problems :-)
While optimization both states changed from C3v to C1 (Omega: Change in point group or standard orientation.)

Markus

Am 31.10.2011 14:43, schrieb John McKelvey jmmckel!A!gmail.com:

Markus,

I'm clearly not an expert on this... When you do the TDDFT or CIS without optimizing any particular state are S1 and S2 close in energy? of the same symmetry? It may be the case there could be a problem optimizing S2 when it is the same symmetry of S1. Is there a problem optimizing S1?

My $0.02..

John McKelvey

On Mon, Oct 31, 2011 at 4:48 AM, Markus Schütz schuhtib=-=physik.tu-berlin.de <owner-chemistry*o*ccl.net> wrote:

Sent to CCL by: =?ISO-8859-15?Q?Markus_Sch=FCtz?= [schuhtib * physik.tu-berlin.de]
Am 27.10.2011 19:05, schrieb Markus Schütz schuhtib!A!physik.tu-berlin.de:

Sent to CCL by: =?ISO-8859-15?Q?Markus_Sch=FCtz?= [schuhtib::physik.tu-berlin.de]
Hello,

I tried to calculate the second excited state of adamantane cation (opt and freq) in TDDFT ( # TD(root=2,NStates=40) b3lyp/cc-pvtz opt sym=loose). Unfortunately the calculation ended with

'You need to solve for more vectors in order to follow this state.'

So I set the keyword for NStates first to 10 then to 25 and finally also to 40, but the message is the same.
I tried another way: From a cis calculation I wanted to get the force contants using them for the TDDFT calculation. But the cis calculation also ended with the message above (NStates=25). Is it useful to set NStates much higher or is there another way to do the TDDFT calculation?

By the way, I also tried a cis calculation (# CIS=(Root=2, NStates=40) hf/cc-pvtz opt(calcFC) freq sym=loose). This delivers the message

'Tx not orthogonal to T.'

I couldn't find any solution for this problem.

Regards,
Markus

Sorry,

forgot to say I'm using Gaussian09.

--
Markus Schütz
Institut für Optik und Atomare Physik
AG Dopfer
Sekretariat EW 3-1
Technische Universität Berlin
Hardenbergstraße 36
10623 Berlin

Tel +49 (0)30 314 29808

Raum EW 337

E-mail to subscribers: CHEMISTRY*o*ccl.net or use:
http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST*o*ccl.net or use
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel*o*gmail.com

-- 
Markus Schütz
Institut für Optik und Atomare Physik
AG Dopfer
Sekretariat EW 3-1
Technische Universität Berlin
Hardenbergstraße 36
10623 Berlin

Tel +49 (0)30 314 29808

Raum EW 337

--------------040800050504080806000201-- From owner-chemistry@ccl.net Tue Nov 1 08:54:01 2011 From: "=?ISO-8859-1?Q?Markus_Sch=FCtz?= schuhtib+/-physik.tu-berlin.de" To: CCL Subject: CCL:G: excited state TDDFT Message-Id: <-45798-111101054319-22325-5UfS8OGDz212o8si79JLbA:+:server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Markus_Sch=FCtz?= Content-Type: multipart/alternative; boundary="------------060606030808040608030804" Date: Tue, 01 Nov 2011 10:42:53 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Markus_Sch=FCtz?= [schuhtib : physik.tu-berlin.de] This is a multi-part message in MIME format. --------------060606030808040608030804 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Hello, 1) Two steps were done before the error occured. The excited state energies are Excited State 1: 2.003-A 0.9648 eV 1285.03 nm f=0.0008 =0.753 35B -> 38B 0.13386 37B -> 38B 0.98970 Excited State 2: 2.004-A 5.5833 eV 222.06 nm f=0.0116 =0.754 22B -> 38B -0.53401 24B -> 38B -0.83903 This state for optimization and/or second-order correction. Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 3: 2.003-A 1.8148 eV 683.17 nm f=0.0269 =0.753 35B -> 38B 0.98621 37B -> 38B -0.12945 Excited State 4: 2.003-A 2.0116 eV 616.33 nm f=0.0314 =0.753 34B -> 38B -0.94699 36B -> 38B 0.31257 Excited State 5: 2.003-A 2.2788 eV 544.07 nm f=0.0020 =0.753 33B -> 38B -0.99091 Excited State 6: 2.003-A 2.5539 eV 485.47 nm f=0.0002 =0.753 32B -> 38B -0.99616 Excited State 7: 2.003-A 2.6189 eV 473.43 nm f=0.0018 =0.753 31B -> 38B 0.99456 Excited State 8: 2.004-A 3.9509 eV 313.82 nm f=0.0099 =0.754 29B -> 38B -0.99350 Excited State 9: 2.003-A 4.0173 eV 308.63 nm f=0.0260 =0.753 28B -> 38B -0.81958 30B -> 38B -0.55717 Excited State 10: 2.003-A 4.0601 eV 305.37 nm f=0.0542 =0.753 28B -> 38B -0.55290 30B -> 38B 0.81828 Excited State 11: 2.004-A 4.4433 eV 279.04 nm f=0.0008 =0.754 25B -> 38B 0.10556 27B -> 38B 0.98314 Excited State 12: 2.004-A 4.4851 eV 276.43 nm f=0.0009 =0.754 26B -> 38B -0.98298 28B -> 38B 0.12858 Excited State 13: 2.004-A 4.6138 eV 268.73 nm f=0.0003 =0.754 25B -> 38B -0.99330 27B -> 38B 0.10367 Excited State 14: 2.003-A 1.4227 eV 871.47 nm f=0.0018 =0.753 34B -> 38B -0.31570 36B -> 38B -0.94634 Excited State 15: 2.005-A 5.6244 eV 220.44 nm f=0.0013 =0.755 23B -> 38B -0.99394 Excited State 16: 2.005-A 5.7259 eV 216.53 nm f=0.0309 =0.755 21B -> 38B 0.21361 22B -> 38B 0.82038 24B -> 38B -0.51616 Excited State 17: 2.004-A 5.8980 eV 210.21 nm f=0.0312 =0.754 21B -> 38B 0.97248 22B -> 38B -0.16506 24B -> 38B 0.12690 Excited State 18: 2.022-A 7.6293 eV 162.51 nm f=0.0001 =0.772 38A -> 39A -0.96056 20B -> 38B -0.24178 Excited State 19: 2.008-A 7.7433 eV 160.12 nm f=0.0042 =0.758 38A -> 39A 0.23583 20B -> 38B -0.96440 Excited State 20: 3.455-A 8.0459 eV 154.10 nm f=0.0000 =2.734 37A -> 39A 0.66558 37B -> 39B -0.72556 Excited State 21: 2.039-A 8.2416 eV 150.44 nm f=0.0020 =0.790 37A -> 39A 0.73092 37B -> 39B 0.67468 Excited State 22: 3.415-A 8.4890 eV 146.05 nm f=0.0000 =2.666 36A -> 39A 0.59200 36B -> 39B 0.78048 Excited State 23: 3.100-A 8.6100 eV 144.00 nm f=0.0005 =2.152 35A -> 39A -0.22508 38A -> 42A 0.13425 35B -> 39B 0.94599 Excited State 24: 2.306-A 8.6781 eV 142.87 nm f=0.0011 =1.079 36A -> 39A 0.76067 34B -> 39B 0.21867 36B -> 39B -0.59306 Excited State 25: 2.046-A 8.6959 eV 142.58 nm f=0.0581 =0.797 38A -> 40A -0.97539 Excited State 26: 2.931-A 8.8246 eV 140.50 nm f=0.0001 =1.897 34A -> 39A 0.28513 36A -> 39A -0.16571 38A -> 41A 0.37487 34B -> 39B 0.83787 36B -> 39B 0.13429 Excited State 27: 2.186-A 8.9049 eV 139.23 nm f=0.0061 =0.945 35A -> 39A 0.66957 38A -> 42A -0.67289 35B -> 39B 0.26698 Excited State 28: 2.044-A 8.9651 eV 138.30 nm f=0.0157 =0.795 34A -> 39A 0.28953 36A -> 39A 0.12371 38A -> 41A 0.82060 34B -> 39B -0.44211 Excited State 29: 2.059-A 8.9955 eV 137.83 nm f=0.0419 =0.810 38A -> 40A -0.10093 38A -> 43A -0.93985 19B -> 38B -0.23970 Excited State 30: 2.013-A 9.0310 eV 137.29 nm f=0.0016 =0.763 38A -> 43A -0.24754 19B -> 38B 0.94870 Excited State 31: 2.402-A 9.0715 eV 136.67 nm f=0.0049 =1.192 33A -> 39A 0.11714 35A -> 39A 0.51872 37A -> 40A 0.26874 38A -> 42A 0.60550 38A -> 44A 0.45523 35B -> 39B 0.10381 37B -> 40B -0.15144 Excited State 32: 2.778-A 9.1431 eV 135.60 nm f=0.0001 =1.679 33A -> 39A -0.21806 35A -> 39A -0.12068 37A -> 40A -0.45091 38A -> 44A 0.70427 18B -> 38B -0.13321 33B -> 39B 0.19155 37B -> 40B 0.35730 Excited State 33: 2.151-A 9.1831 eV 135.01 nm f=0.0014 =0.907 34A -> 39A -0.49500 38A -> 41A 0.21184 38A -> 45A -0.79827 17B -> 38B 0.12297 34B -> 39B 0.14647 Excited State 34: 2.925-A 9.2364 eV 134.23 nm f=0.0009 =1.889 33A -> 39A -0.23112 35A -> 39A 0.38314 37A -> 40A -0.22231 37A -> 41A -0.15865 38A -> 42A 0.32733 38A -> 44A -0.43797 33B -> 39B 0.30788 37B -> 40B 0.49995 37B -> 41B 0.20700 Excited State 35: 3.142-A 9.2651 eV 133.82 nm f=0.0013 =2.217 34A -> 39A 0.44645 37A -> 42A 0.49409 37A -> 44A -0.12113 38A -> 41A -0.14607 38A -> 45A -0.31704 37B -> 42B -0.56897 37B -> 44B 0.13839 Excited State 36: 3.386-A 9.2747 eV 133.68 nm f=0.0006 =2.617 32A -> 39A -0.13283 33A -> 39A 0.30256 37A -> 40A -0.24142 37A -> 41A 0.43285 37A -> 43A -0.17761 38A -> 42A 0.13933 38A -> 44A -0.10509 18B -> 38B 0.15408 32B -> 39B 0.15236 33B -> 39B -0.27891 37B -> 40B 0.28228 37B -> 41B -0.53128 37B -> 43B 0.14745 Excited State 37: 2.837-A 9.2904 eV 133.45 nm f=0.0004 =1.762 31A -> 39A 0.11133 34A -> 39A -0.57541 36A -> 40A -0.10845 37A -> 42A 0.32198 38A -> 41A 0.28753 38A -> 45A 0.44283 31B -> 39B -0.10182 37B -> 42B -0.43343 Excited State 38: 2.081-A 9.3046 eV 133.25 nm f=0.0018 =0.833 37A -> 40A -0.22476 38A -> 44A 0.13151 18B -> 38B 0.90012 37B -> 40B -0.22910 37B -> 41B 0.10153 Excited State 39: 2.128-A 9.3159 eV 133.09 nm f=0.0097 =0.883 33A -> 39A 0.17420 35A -> 39A -0.16068 37A -> 40A 0.63369 37A -> 43A 0.22447 38A -> 44A 0.14606 18B -> 38B 0.31566 33B -> 39B 0.16236 37B -> 40B 0.55470 Excited State 40: 2.042-A 9.3756 eV 132.24 nm f=0.0000 =0.792 38A -> 45A 0.11905 38A -> 48A -0.10673 17B -> 38B 0.96711 Starting geometry was C3v but changed to C1 (Omega: Change in point group or standard orientation.) 2) I optimized the molecule in S0 state using the same functional and basis set (B3LYP/cc-pVTZ). Markus Am 31.10.2011 14:48, schrieb Soren Eustis soreneustis#gmail.com: > Sent to CCL by: Soren Eustis [soreneustis{:}gmail.com] > Marcus, > > I have seen this before. Unfortunately, it is generally not a good > sign. Often this means that your excited state is not stable (i.e. bond > dissociation), or your molecule is crossing to a lower potential energy > surface. > > Two questions: 1) what are the few lowest excited state energies > output by gaussian before it fails? 2) did you fully optimize this in the > S0 state with the same functional and basis set? If not, that could be > your issue. > > Soren > > > > Soren N. Eustis, Ph.D. > ETH Zürich > Institute for Biogeochemistry and Pollutant Dynamics > CHN F33 > Universitätstrasse 16 > 8092 Zürich > Switzerland > > +41 44 632 9348 (Office) > +41 44 632 1438(Fax) > > soren-#-env.ethz.ch > > > > > > > On 10/31/11 10:48 , "Markus Schütz schuhtib=-=physik.tu-berlin.de" > wrote: > >> Sent to CCL by: =?ISO-8859-15?Q?Markus_Sch=FCtz?= [schuhtib * >> physik.tu-berlin.de] >> Am 27.10.2011 19:05, schrieb Markus Schütz schuhtib!A!physik.tu-berlin.de: >>> Sent to CCL by: =?ISO-8859-15?Q?Markus_Sch=FCtz?= >>> [schuhtib::physik.tu-berlin.de] >>> Hello, >>> >>> I tried to calculate the second excited state of adamantane cation >>> (opt and freq) in TDDFT ( # TD(root=2,NStates=40) b3lyp/cc-pvtz opt >>> sym=loose). Unfortunately the calculation ended with >>> >>> 'You need to solve for more vectors in order to follow this state.' >>> >>> So I set the keyword for NStates first to 10 then to 25 and finally >>> also to 40, but the message is the same. >>> I tried another way: From a cis calculation I wanted to get the force >>> contants using them for the TDDFT calculation. But the cis calculation >>> also ended with the message above (NStates=25). Is it useful to set >>> NStates much higher or is there another way to do the TDDFT calculation? >>> >>> By the way, I also tried a cis calculation (# CIS=(Root=2, NStates=40) >>> hf/cc-pvtz opt(calcFC) freq sym=loose). This delivers the message >>> >>> 'Tx not orthogonal to T.' >>> >>> I couldn't find any solution for this problem. >>> >>> Regards, >>> Markus >>> >> Sorry, >> >> forgot to say I'm using Gaussian09. >> >> -- >> Markus Schütz >> Institut für Optik und Atomare Physik >> AG Dopfer >> Sekretariat EW 3-1 >> Technische Universität Berlin >> Hardenbergstraße 36 >> 10623 Berlin >> >> Tel +49 (0)30 314 29808 >> >> Raum EW 337> > -- Markus Schütz Institut für Optik und Atomare Physik AG Dopfer Sekretariat EW 3-1 Technische Universität Berlin Hardenbergstraße 36 10623 Berlin Tel +49 (0)30 314 29808 Raum EW 337 --------------060606030808040608030804 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello,

1) Two steps were done before the error occured. The excited state energies are

Excited State   1: 2.003-A      0.9648 eV 1285.03 nm f=0.0008 <S**2>=0.753
     35B -> 38B        0.13386
     37B -> 38B        0.98970

Excited State   2: 2.004-A      5.5833 eV 222.06 nm f=0.0116 <S**2>=0.754
     22B -> 38B       -0.53401
     24B -> 38B       -0.83903
This state for optimization and/or second-order correction.
Copying the excited state density for this state as the 1-particle RhoCI density.

Excited State   3: 2.003-A      1.8148 eV 683.17 nm f=0.0269 <S**2>=0.753
     35B -> 38B        0.98621
     37B -> 38B       -0.12945

Excited State   4: 2.003-A      2.0116 eV 616.33 nm f=0.0314 <S**2>=0.753
     34B -> 38B       -0.94699
     36B -> 38B        0.31257

Excited State   5: 2.003-A      2.2788 eV 544.07 nm f=0.0020 <S**2>=0.753
     33B -> 38B       -0.99091

Excited State   6: 2.003-A      2.5539 eV 485.47 nm f=0.0002 <S**2>=0.753
     32B -> 38B       -0.99616

Excited State   7: 2.003-A      2.6189 eV 473.43 nm f=0.0018 <S**2>=0.753
     31B -> 38B        0.99456

Excited State   8: 2.004-A      3.9509 eV 313.82 nm f=0.0099 <S**2>=0.754
     29B -> 38B       -0.99350

Excited State   9: 2.003-A      4.0173 eV 308.63 nm f=0.0260 <S**2>=0.753
     28B -> 38B       -0.81958
     30B -> 38B       -0.55717

Excited State 10: 2.003-A      4.0601 eV 305.37 nm f=0.0542 <S**2>=0.753
     28B -> 38B       -0.55290
     30B -> 38B        0.81828

Excited State 11: 2.004-A      4.4433 eV 279.04 nm f=0.0008 <S**2>=0.754
     25B -> 38B        0.10556
     27B -> 38B        0.98314

Excited State 12: 2.004-A      4.4851 eV 276.43 nm f=0.0009 <S**2>=0.754
     26B -> 38B       -0.98298
     28B -> 38B        0.12858

Excited State 13: 2.004-A      4.6138 eV 268.73 nm f=0.0003 <S**2>=0.754
     25B -> 38B       -0.99330
     27B -> 38B        0.10367

Excited State 14: 2.003-A      1.4227 eV 871.47 nm f=0.0018 <S**2>=0.753
     34B -> 38B       -0.31570
     36B -> 38B       -0.94634

Excited State 15: 2.005-A      5.6244 eV 220.44 nm f=0.0013 <S**2>=0.755
     23B -> 38B       -0.99394

Excited State 16: 2.005-A      5.7259 eV 216.53 nm f=0.0309 <S**2>=0.755
     21B -> 38B        0.21361
     22B -> 38B        0.82038
     24B -> 38B       -0.51616

Excited State 17: 2.004-A      5.8980 eV 210.21 nm f=0.0312 <S**2>=0.754
     21B -> 38B        0.97248
     22B -> 38B       -0.16506
     24B -> 38B        0.12690

Excited State 18: 2.022-A      7.6293 eV 162.51 nm f=0.0001 <S**2>=0.772
     38A -> 39A       -0.96056
     20B -> 38B       -0.24178

Excited State 19: 2.008-A      7.7433 eV 160.12 nm f=0.0042 <S**2>=0.758
     38A -> 39A        0.23583
     20B -> 38B       -0.96440

Excited State 20: 3.455-A      8.0459 eV 154.10 nm f=0.0000 <S**2>=2.734
     37A -> 39A        0.66558
     37B -> 39B       -0.72556

Excited State 21: 2.039-A      8.2416 eV 150.44 nm f=0.0020 <S**2>=0.790
     37A -> 39A        0.73092
     37B -> 39B        0.67468

Excited State 22: 3.415-A      8.4890 eV 146.05 nm f=0.0000 <S**2>=2.666
     36A -> 39A        0.59200
     36B -> 39B        0.78048

Excited State 23: 3.100-A      8.6100 eV 144.00 nm f=0.0005 <S**2>=2.152
     35A -> 39A       -0.22508
     38A -> 42A        0.13425
     35B -> 39B        0.94599

Excited State 24: 2.306-A      8.6781 eV 142.87 nm f=0.0011 <S**2>=1.079
     36A -> 39A        0.76067
     34B -> 39B        0.21867
     36B -> 39B       -0.59306

Excited State 25: 2.046-A      8.6959 eV 142.58 nm f=0.0581 <S**2>=0.797
     38A -> 40A       -0.97539

Excited State 26: 2.931-A      8.8246 eV 140.50 nm f=0.0001 <S**2>=1.897
     34A -> 39A        0.28513
     36A -> 39A       -0.16571
     38A -> 41A        0.37487
     34B -> 39B        0.83787
     36B -> 39B        0.13429

Excited State 27: 2.186-A      8.9049 eV 139.23 nm f=0.0061 <S**2>=0.945
     35A -> 39A        0.66957
     38A -> 42A       -0.67289
     35B -> 39B        0.26698

Excited State 28: 2.044-A      8.9651 eV 138.30 nm f=0.0157 <S**2>=0.795
     34A -> 39A        0.28953
     36A -> 39A        0.12371
     38A -> 41A        0.82060
     34B -> 39B       -0.44211

Excited State 29: 2.059-A      8.9955 eV 137.83 nm f=0.0419 <S**2>=0.810
     38A -> 40A       -0.10093
     38A -> 43A       -0.93985
     19B -> 38B       -0.23970

Excited State 30: 2.013-A      9.0310 eV 137.29 nm f=0.0016 <S**2>=0.763
     38A -> 43A       -0.24754
     19B -> 38B        0.94870

Excited State 31: 2.402-A      9.0715 eV 136.67 nm f=0.0049 <S**2>=1.192
     33A -> 39A        0.11714
     35A -> 39A        0.51872
     37A -> 40A        0.26874
     38A -> 42A        0.60550
     38A -> 44A        0.45523
     35B -> 39B        0.10381
     37B -> 40B       -0.15144

Excited State 32: 2.778-A      9.1431 eV 135.60 nm f=0.0001 <S**2>=1.679
     33A -> 39A       -0.21806
     35A -> 39A       -0.12068
     37A -> 40A       -0.45091
     38A -> 44A        0.70427
     18B -> 38B       -0.13321
     33B -> 39B        0.19155
     37B -> 40B        0.35730

Excited State 33: 2.151-A      9.1831 eV 135.01 nm f=0.0014 <S**2>=0.907
     34A -> 39A       -0.49500
     38A -> 41A        0.21184
     38A -> 45A       -0.79827
     17B -> 38B        0.12297
     34B -> 39B        0.14647

Excited State 34: 2.925-A      9.2364 eV 134.23 nm f=0.0009 <S**2>=1.889
     33A -> 39A       -0.23112
     35A -> 39A        0.38314
     37A -> 40A       -0.22231
     37A -> 41A       -0.15865
     38A -> 42A        0.32733
     38A -> 44A       -0.43797
     33B -> 39B        0.30788
     37B -> 40B        0.49995
     37B -> 41B        0.20700

Excited State 35: 3.142-A      9.2651 eV 133.82 nm f=0.0013 <S**2>=2.217
     34A -> 39A        0.44645
     37A -> 42A        0.49409
     37A -> 44A       -0.12113
     38A -> 41A       -0.14607
     38A -> 45A       -0.31704
     37B -> 42B       -0.56897
     37B -> 44B        0.13839

Excited State 36: 3.386-A      9.2747 eV 133.68 nm f=0.0006 <S**2>=2.617
     32A -> 39A       -0.13283
     33A -> 39A        0.30256
     37A -> 40A       -0.24142
     37A -> 41A        0.43285
     37A -> 43A       -0.17761
     38A -> 42A        0.13933
     38A -> 44A       -0.10509
     18B -> 38B        0.15408
     32B -> 39B        0.15236
     33B -> 39B       -0.27891
     37B -> 40B        0.28228
     37B -> 41B       -0.53128
     37B -> 43B        0.14745

Excited State 37: 2.837-A      9.2904 eV 133.45 nm f=0.0004 <S**2>=1.762
     31A -> 39A        0.11133
     34A -> 39A       -0.57541
     36A -> 40A       -0.10845
     37A -> 42A        0.32198
     38A -> 41A        0.28753
     38A -> 45A        0.44283
     31B -> 39B       -0.10182
     37B -> 42B       -0.43343

Excited State 38: 2.081-A      9.3046 eV 133.25 nm f=0.0018 <S**2>=0.833
     37A -> 40A       -0.22476
     38A -> 44A        0.13151
     18B -> 38B        0.90012
     37B -> 40B       -0.22910
     37B -> 41B        0.10153

Excited State 39: 2.128-A      9.3159 eV 133.09 nm f=0.0097 <S**2>=0.883
     33A -> 39A        0.17420
     35A -> 39A       -0.16068
     37A -> 40A        0.63369
     37A -> 43A        0.22447
     38A -> 44A        0.14606
     18B -> 38B        0.31566
     33B -> 39B        0.16236
     37B -> 40B        0.55470

Excited State 40: 2.042-A      9.3756 eV 132.24 nm f=0.0000 <S**2>=0.792
     38A -> 45A        0.11905
     38A -> 48A       -0.10673
     17B -> 38B        0.96711

Starting geometry was C3v but changed to C1 (Omega: Change in point group or standard orientation.)

2) I optimized the molecule in S0 state using the same functional and basis set (B3LYP/cc-pVTZ).

Markus

Am 31.10.2011 14:48, schrieb Soren Eustis soreneustis#gmail.com:

Sent to CCL by: Soren Eustis [soreneustis{:}gmail.com]
Marcus,

   I have seen this before.  Unfortunately, it is generally not a good
sign.  Often this means that your excited state is not stable (i.e. bond
dissociation), or your molecule is crossing to a lower potential energy
surface.

   Two questions:  1) what are the few lowest excited state energies
output by gaussian before it fails? 2) did you fully optimize this in the
S0 state with the same functional and basis set?  If not, that could be
your issue.  

Soren



Soren N. Eustis, Ph.D.
ETH  Zürich
Institute for Biogeochemistry and Pollutant Dynamics
CHN F33
Universitätstrasse 16
8092 Zürich
Switzerland

+41 44 632 9348 (Office)
+41 44 632 1438(Fax)

soren-#-env.ethz.ch






On 10/31/11 10:48 , "Markus Schütz schuhtib=-=physik.tu-berlin.de"
<owner-chemistry-#-ccl.net> wrote:

Sent to CCL by: =?ISO-8859-15?Q?Markus_Sch=FCtz?= [schuhtib *
physik.tu-berlin.de]
Am 27.10.2011 19:05, schrieb Markus Schütz schuhtib!A!physik.tu-berlin.de:

Sent to CCL by: =?ISO-8859-15?Q?Markus_Sch=FCtz?=
[schuhtib::physik.tu-berlin.de]
Hello,

I tried to calculate the second excited state of adamantane cation
(opt and freq) in TDDFT ( # TD(root=2,NStates=40) b3lyp/cc-pvtz opt
sym=loose). Unfortunately the calculation ended with

'You need to solve for more vectors in order to follow this state.'

So I set the keyword for NStates first to 10 then to 25 and finally
also to 40, but the message is the same.
I tried another way: From a cis calculation I wanted to get the force
contants using them for the TDDFT calculation. But the cis calculation
also ended with the message above (NStates=25). Is it useful to set
NStates much higher or is there another way to do the TDDFT calculation?

By the way, I also tried a cis calculation (# CIS=(Root=2, NStates=40)
hf/cc-pvtz opt(calcFC) freq sym=loose). This delivers the message

'Tx not orthogonal to T.'

I couldn't find any solution for this problem.

Regards,
Markus

Sorry,

forgot to say I'm using Gaussian09.

-- 
Markus Schütz
Institut für Optik und Atomare Physik
AG Dopfer
Sekretariat EW 3-1
Technische Universität Berlin
Hardenbergstraße 36
10623 Berlin

Tel +49 (0)30 314 29808

Raum EW 337>

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-- 
Markus Schütz
Institut für Optik und Atomare Physik
AG Dopfer
Sekretariat EW 3-1
Technische Universität Berlin
Hardenbergstraße 36
10623 Berlin

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--------------060606030808040608030804-- From owner-chemistry@ccl.net Tue Nov 1 11:04:00 2011 From: "Sue Lam chsue2004]_[yahoo.com" To: CCL Subject: CCL:G: Solvent-corrected Gibbs free energies Message-Id: <-45799-111101110000-5676-mnMnXCVRSL761vubJmvm3w,server.ccl.net> X-Original-From: Sue Lam Content-Type: multipart/alternative; boundary="-887514071-1879295465-1320159588=:64311" Date: Tue, 1 Nov 2011 07:59:48 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004+/-yahoo.com] ---887514071-1879295465-1320159588=:64311 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Andreas and Arne, Thanks for your help. =C2=A0 Best regards, Sue --- On Tue, 11/1/11, Andreas Klamt klamt[#]cosmologic.de wrote: > From: Andreas Klamt klamt[#]cosmologic.de Subject: CCL:G: Solvent-corrected Gibbs free energies To: "L, Sue " Date: Tuesday, November 1, 2011, 4:56 AM Sent to CCL by: Andreas Klamt [klamt[-]cosmologic.de] Sear Sue, perhaps have a look at=20 Ho J., Klamt A., Coote M.L. Comment on the correct use of continuum solvent= models. J. Phys. Chem. A (2010), 114(51), 13442=E2=80=9313444 This exactly handles your questions. Best regards Andreas Am 31.10.2011 19:24, schrieb Arne Dieckmann adieckma(_)googlemail.com:=20 Sent to CCL by: Arne Dieckmann [adieckma]=3D[googlemail.com] Dear Sue,=20 here is a link to the Gaussian 03 User Reference Guide answering your quest= ion:=20 http://www.inc.bme.hu/common/g03_man/g_ur/k_scrf.htm You have to use the total free energy in solution with all non-electrostati= c terms.=20 Cheers, Arne - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -=20 Dr. Arne Dieckmann Houk Research Lab University of California, Los Angeles=20 email: adieckma[A]googlemail.com On Oct 31, 2011, at 7:12 AM, Sue Lam chsue2004^^^yahoo.com wrote: Dear Arne, Thanks for your reply. Sorry for the confusion. Below is an example from the Gaussian manual. For the output file in Gaussi= an 03, we could obtain (1) Total free energy in solution: with all non electrostatic terms =20 (2) Solvent-phase electronic energies, which is the value associated with S= CF(Done) I am not sure which value I should use if I include the thermal correction = to Gibbs free energy from the vibrational frequency calculation. SCF Done: E(RHF) =3D -98.569083211 A.U. after 5 cycles=20 Convg =3D 0.4249D-05 -V/T =3D 2.0033=20 S**2 =3D 0.0000=20 --------------------------------------------------------------------=20 Variational PCM results =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20 (a.u.) =3D -98.568013=20 (a.u.) =3D -98.569083 Total free energy in solution:=20 with all non electrostatic terms (a.u.) =3D -98.573228 --------------------------------------------------------------------=20 (Polarized solute)-Solvent (kcal/mol) =3D -3.27=20 --------------------------------------------------------------------=20 Cavitation energy (kcal/mol) =3D 5.34=20 Dispersion energy (kcal/mol) =3D -3.08=20 Repulsion energy (kcal/mol) =3D 0.34=20 Total non electrostatic (kcal/mol) =3D 2.60 =20 --------------------------------------------------------------------=20 =20 Best regards, Sue =20 --- On Mon, 10/31/11, Arne Dieckmann adieckma**googlemail.com wrote: > From: Arne Dieckmann adieckma**googlemail.com Subject: CCL:G: Solvent-corrected Gibbs free energies To: "L, Sue " Date: Monday, October 31, 2011, 12:48 PM Sent to CCL by: Arne Dieckmann [adieckma###googlemail.com] Hi Sue,=20 the two methods you are describing are exactly the same, as you are only ch= anging the order in which different quantities are added.=20 Cheers,=20 Arne On Oct 30, 2011, at 9:08 PM, Sue L chsue2004^^yahoo.com wrote: Sent to CCL by: "Sue L" [chsue2004]_[yahoo.com] Dear CCL users, Could someone help me with the following question? If I want to calculate the solvent-corrected Gibbs free energies of the mol= ecules based on the gas-phase optimized geometry usinf gaussian 03. Which o= f the following methods is more appropriate? > From the vibrational frequency calculation of the gas-phase optimized struc= ture, I could obtain the thermal correction to Gibbs Free Energy > From the single-point PCM calculation, I could obtain the total free energy= in solution: with all non electrostatic terms as well as solvent-phase ele= ctronic energies (The energy value associated with SCF(Done)) (1) The solvent-corrected Gibbs free energies =3D the total free energy in = solution + thermal correction to Gibbs Free Energy Or (2) The solvent-corrected Gibbs free energies =3D gas-phase Gibbs free ener= gies + (solvent-phase electronic energies - gas-phase electronic energies) Thank you very much for your kind help. Best regards, Sue--130478739-893504848-1320070366=3D:1570 Content-Type: text/html; charset=3Diso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Arne,

Thanks for your re= ply. Sorry for the confusion.

Below is an example from the Gaussian manual. = For the output file in Gaussian 03, we could obtain

(1) Total free ene= rgy in solution: with all non electrostatic terms

(2) Solvent-phase electroni= c energies, which is the val= ue associated with SCF(Done)

I am not sure which valu= e I should use if I include the thermal correction= to Gibbs free energy from t= he vibrational frequency calculation.

SCF Done:= E(RHF) =3D -98= .569083211 A.U. after 5 cycles

&= nbsp; Convg =3D = ; 0.4249D-05 &nbs= p; -V/T =3D 2.0033

&= nbsp; S**2 =3D = 0.0000

-----------------------------------------------= ---------------------

Variational PCM results

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D

<psi(f)|&n= bsp; H |p= si(f)> &n= bsp; (a.= u.) =3D -9= 8.568013

<psi(f)|H+V(f)/2|psi(f)> &nbs= p; (a.u.) =3D -98.569083

Total free energy in solution:

<= /SPAN>with all non electrostatic terms&nb= sp; (a.u.) =3D -98.573228

-----------------------------------------------= ---------------------

(Polarized solute)-Solvent &n= bsp; (kcal/mol) =3D -3.27

-----------------------------------------------= ---------------------

Cavitation energy = ; = (kcal/mol) =3D &nb= sp; 5.34

Dispersion energy = ; &n= bsp; (kcal/mol) =3D -3.08

Repulsion energy = (kcal/mol) =3D &nbs= p; 0.34

Total non electrostatic &nb= sp; (kcal/mol) =3D 2.60

-----------------------------------------------= ---------------------

Best regards,

Sue

=

--- On Mon, 10/31/11, Arne Dieckmann adieckma**goog= lemail.com <owner-chemistry::ccl.net> wrote:

From: Arne Dieckmann adieckma**googlemail.com <= ;owner-chemistry::ccl.net>
Subject: CCL:G: Solvent-corrected Gibbs fr= ee energies
To: "L, Sue " <chsue2004::yahoo.com>
Date: Monday, = October 31, 2011, 12:48 PM

Sent to CCL by: Arne Dieckmann [adieckma###googl= email.com]
Hi Sue,

the two methods you are describing are exactl= y the same, as you are only changing the order in which different quantitie= s are added.

Cheers,
Arne

On Oct 30, 2011, at 9:= 08 PM, Sue L chsue2004^^yahoo.com wrote:

>
> Sent to CCL b= y: "Sue L" [chsue2004]_[yahoo.com]
> Dear CCL users,
> > Could someone help me with the following question?
>
> = If I want to calculate the solvent-corrected Gibbs free energies of the mol= ecules based on the gas-phase optimized geometry usinf gaussian 03. Which o= f the following methods is more appropriate?
>
>> From the = vibrational frequency calculation of the gas-phase optimized stru cture, I could obtain the thermal correction to Gibbs Free Energy
> <= BR>>> From the single-point PCM calculation, I could obtain the total= free energy in solution: with all non electrostatic terms as well as solvent-pha= se electronic energies (The energy value associated with SCF(Done))
>=
> (1) The solvent-corrected Gibbs free energies =3D the total free = energy in solution + thermal correction to Gibbs Free Energy
>
&g= t; Or
>
> (2) The solvent-corrected Gibbs free energies =3D ga= s-phase Gibbs free energies + (solvent-phase electronic energies - ga= s-phase electronic energies)
>
> Thank you very much for your = kind help.
>
> Best regards,
> Sue>
>

<= BR>the strange characters on the top line to the :: sign. You can= also
E-mail to subscribers: CHEMISTRY::ccl.net or use:
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CHEMISTRY[]ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST[]ccl.net or usehttp://www.ccl.net/che= mistry/sub_unsub.shtmlJob: http://www.ccl.net/jobs=20http://w= ww.ccl.net/spammers.txt--=20 PD. Dr. Andreas Klamt CEO / Gesch=C3=A4ftsf=C3=BChrer COSMOlogic GmbH & Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone =09+49-2171-731681 fax =09+49-2171-731689 e-mail =09klamt[]cosmologic.de web =09www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt -=3D This is automatically added to each message by the mailing script =3D-=t= he strange characters on the top line to the [A] sign. You can also look up t= he X-Original-From: line in the mail header. E-mail to subscribers: CHEMIST= RY[A]ccl.net or use:E-mail t= o administrators: CHEMISTRY-REQUEST[A]ccl.net or use http://www.ccl.net/cgi-b= in/ccl/send_ccl_messagehttp://www.ccl.net/chemistry= /sub_unsub.shtmlJob= : http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/anno= uncements/conferences/ Search Messages: http://www.ccl.net/chemistry/search= ccl/index.shtmlhttp= ://www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/ ---887514071-1879295465-1320159588=:64311 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

Hi Andreas and Arne,

Thanks for your help.

Best regards,

Sue

--- On Tue, 11/1/11, Andreas Klamt klamt[#]cosmologic.de= <owner-chemistry[A]ccl.net> wrote:

From: Andreas Klamt klamt[#]cosmologic.de <own= er-chemistry[A]ccl.net>
Subject: CCL:G: Solvent-corrected Gibbs free en= ergies
To: "L, Sue " <chsue2004[A]yahoo.com>
Date: Tuesda= y, November 1, 2011, 4:56 AM

Sent to CCL by: Andreas Klamt [klamt[-]cosmologic.de= ] Sear Sue,

perhaps have a look at
= Ho J., Klamt A., Coote M.L. Comment on the correct use of= continuum solvent models. J. Phys. Chem. A (2010), 114(51), 13442=E2=80=93= 13444

This exactly handles your questions.

Best regards
Andreas

Am 31.10.2011 19:24, schrieb Arne Dieckmann adieckm= a(_)googlemail.com:=20

Sent to CCL by: Arne Dieckmann [adieckma]=3D=
[googlemail.com]
Dear Sue,=20

here is a link to the Gaussian 03 User Reference Guide answering your quest=
ion:=20

http://www.i=
nc.bme.hu/common/g03_man/g_ur/k_scrf.htm

You have to use the total free energy in solution with all non-electrostati=
c terms.=20


Cheers,
Arne


- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -=20
Dr. Arne Dieckmann
Houk Research Lab
University of California, Los Angeles=20
email: adieckma[A]googlemail.com


On Oct 31, 2011, at 7:12 AM, Sue Lam chsue2004^^^yahoo.com wrote:

Dear Arne,
Thanks for your reply. Sorry for the confusion.
Below is an example from the Gaussian manual. For the output file in Gaussi=
an 03, we could obtain
(1) Total free energy in solution: with all non electrostatic terms =20
(2) Solvent-phase electronic energies, which is the value associated with S=
CF(Done)
I am not sure which value I should use if I include the thermal correction =
to Gibbs free energy from the vibrational frequency calculation.
SCF Done:  E(RHF) =3D  -98.569083211     A.U. after    5 cycles=20
          Convg  =3D    0.4249D-05             -V/T =3D  2.0033=20
          S**2   =3D   0.0000=20
--------------------------------------------------------------------=20
Variational PCM results
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20
<psi(f)|   H   |psi(f)>                 (a.u.) =3D     -98.568013=20
<psi(f)|H+V(f)/2|psi(f)>                (a.u.) =3D     -98.569083
Total free energy in solution:=20
 with all non electrostatic terms       (a.u.) =3D     -98.573228
--------------------------------------------------------------------=20
(Polarized solute)-Solvent               (kcal/mol) =3D      -3.27=20
--------------------------------------------------------------------=20
Cavitation energy                        (kcal/mol) =3D       5.34=20
Dispersion energy                        (kcal/mol) =3D      -3.08=20
Repulsion energy                         (kcal/mol) =3D       0.34=20
Total non electrostatic                  (kcal/mol) =3D       2.60 =20
--------------------------------------------------------------------=20
=20
Best regards,
Sue
=20

--- On Mon, 10/31/11, Arne Dieckmann adieckma**googlemail.com <owner-che=
mistry::ccl.net> wrote:

From: Arne Dieckmann adieckma**googlemail.co=
m <owner-chemistry::ccl.net>

Subject: CCL:G: Solvent-corrected Gibbs free energi=
es
To: "L, Sue " <chsue2004::yahoo.com>
Date: Monday, October 31, 2011, 12:48 PM



Sent to CCL by: Arne Dieckmann [adieckma###googlemail.com]
Hi Sue,=20

the two methods you are describing are exactly the same, as you are only ch=
anging the order in which different quantities are added.=20


Cheers,=20
Arne


On Oct 30, 2011, at 9:08 PM, Sue L chsue2004^^yahoo.com wrote:

Sent to CCL by: "Sue  L" [chsue2004]_[yahoo.=
com]
Dear CCL users,

Could someone help me with the following question?

If I want to calculate the solvent-corrected Gibbs free energies of the mol=
ecules based on the gas-phase optimized geometry usinf gaussian 03. Which o=
f the following methods is more appropriate?

From the vibrational frequency calculation o=
f the gas-phase optimized structure, I could obtain the thermal correction =
to Gibbs Free Energy

From the single-point PCM calculation, I cou=
ld obtain the total free energy in solution: with all non electrostatic ter=
ms as well as solvent-phase electronic energies (The energy value associate=
d with SCF(Done))

(1) The solvent-corrected Gibbs free energies =3D t=
he total free energy in solution + thermal correction to Gibbs Free Energy

Or

(2) The solvent-corrected Gibbs free energies =3D gas-phase Gibbs free ener=
gies + (solvent-phase electronic energies  - gas-phase electronic energies)

Thank you very much for your kind help.

Best regards,
Sue--130478739-893504848-1320070366=3D:1570

Content-Type: text/html; charset=3Diso-8859-1
Content-Transfer-Encoding: quoted-printable

<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr>&l=
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0in 10pt" class=3DMsoNormal><SPAN style=3D"mso-fareast-language: ZH-H=
K"><FONT size=3D3><FONT face=3DCalibri>Dear Arne,<?xml:na=
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<o:p></o:p></FONT></FONT></SPAN></DIV>
<P style=3D"MARGIN: 0in 0in 10pt" class=3DMsoNormal><SPAN style=3D=
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ri>Thanks for your reply. Sorry for the confusion.<o:p></o:p>=
;</FONT></FONT></SPAN></DIV>
<P style=3D"MARGIN: 0in 0in 10pt" class=3DMsoNormal><SPAN style=3D=
"LINE-HEIGHT: 115%; FONT-FAMILY: 'Arial','sans-serif'; FONT-SIZE: 10pt; mso=
-fareast-language: ZH-HK">Below is an example from the Gaussian manual. =
</SPAN><SPAN style=3D"mso-fareast-language: ZH-HK"><FONT siz=
e=3D3><FONT face=3DCalibri>For the output file in Gaussian 03, we =
could obtain<o:p></o:p></FONT></FONT></SPAN>&=
lt;/DIV>
<P style=3D"MARGIN: 0in 0in 10pt" class=3DMsoNormal><SPAN style=3D=
"mso-fareast-language: ZH-HK"><FONT size=3D3><FONT face=3DCalib=
ri>(1) Total free energy in solution: with all non electrostatic terms&a=
mp;nbsp;<SPAN style=3D"mso-spacerun: yes">&nbsp;</SPAN><=
/FONT></FONT></SPAN></DIV>
<P style=3D"MARGIN: 0in 0in 10pt" class=3DMsoNormal><SPAN style=3D=
"mso-fareast-language: ZH-HK"><FONT size=3D3 face=3DCalibri>(2) &l=
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Arial','sans-serif'; FONT-SIZE: 10pt; mso-fareast-language: ZH-HK">S<=
/SPAN><SPAN style=3D"LINE-HEIGHT: 115%; FONT-FAMILY: 'Arial','sans-se=
rif'; FONT-SIZE: 10pt">olvent-phase electronic energies</SPAN><=
SPAN style=3D"LINE-HEIGHT: 115%; FONT-FAMILY: 'Arial','sans-serif'; FONT-SI=
ZE: 10pt; mso-fareast-language: ZH-HK">, which is the value </SPAN>=
;<SPAN style=3D"LINE-HEIGHT: 115%; FONT-FAMILY: 'Arial','sans-serif'; FO=
NT-SIZE: 10pt">associated with SCF(Done</SPAN><SPAN style=3D"LI=
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<P style=3D"MARGIN: 0in 0in 10pt" class=3DMsoNormal><SPAN style=3D=
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ot sure which value I should use if I include the </FONT></SPAN>=
;<SPAN style=3D"LINE-HEIGHT: 115%; FONT-FAMILY: 'Arial','sans-serif'; FO=
NT-SIZE: 10pt">thermal correction to Gibbs free energy</SPAN><S=
PAN style=3D"LINE-HEIGHT: 115%; FONT-FAMILY: 'Arial','sans-serif'; FONT-SIZ=
E: 10pt; mso-fareast-language: ZH-HK"> from the </SPAN><SPAN st=
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t">vibrational frequency calculation</SPAN><SPAN style=3D"LINE-=
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<SPAN style=3D"FONT-FAMILY: 'Courier New'; COLOR: black; FONT-SIZE: 10pt=
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"mso-spacerun: yes">&nbsp; </SPAN>E(RHF) =3D<SPAN style=3D"=
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;
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&nbsp;&nbsp; </SPAN>Convg<SPAN style=3D"mso-spacerun: yes"=
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;nbsp;&nbsp;&nbsp; </SPAN>0.4249D-05<SPAN style=3D"mso-spa=
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>-=
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8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><SPAN =
style=3D"FONT-FAMILY: 'Courier New'; COLOR: black; FONT-SIZE: 10pt; mso-far=
east-font-family: 'Times New Roman'">&lt;psi(f)|<SPAN style=3D"ms=
o-spacerun: yes">&nbsp;&nbsp; </SPAN>H<SPAN style=3D"ms=
o-spacerun: yes">&nbsp;&nbsp; </SPAN>|psi(f)&gt;<SP=
AN style=3D"mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&=
amp;nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>(a.u.) =3D<SPA=
N style=3D"mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; &=
lt;/SPAN>-98.568013 <o:p></o:p></SPAN></DIV>
<P style=3D"LINE-HEIGHT: normal; MARGIN: 0in 0in 0pt; tab-stops: 45.8pt =
91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.=
8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><SPAN =
style=3D"FONT-FAMILY: 'Courier New'; COLOR: black; FONT-SIZE: 10pt; mso-far=
east-font-family: 'Times New Roman'">&lt;psi(f)|H+V(f)/2|psi(f)&=
gt;<SPAN style=3D"mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&a=
mp;nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>(a.u.) =3D<SPAN=
 style=3D"mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; &l=
t;/SPAN>-98.569083<B><o:p></o:p></B></SPAN>=
;</DIV>
<P style=3D"LINE-HEIGHT: normal; MARGIN: 0in 0in 0pt; tab-stops: 45.8pt =
91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.=
8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><B>=
<SPAN style=3D"FONT-FAMILY: 'Courier New'; COLOR: #003399; FONT-SIZE: 10=
pt; mso-fareast-font-family: 'Times New Roman'">Total free energy in sol=
ution: <o:p></o:p></SPAN></B></DIV>
<P style=3D"LINE-HEIGHT: normal; MARGIN: 0in 0in 0pt; tab-stops: 45.8pt =
91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.=
8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><B>=
<SPAN style=3D"FONT-FAMILY: 'Courier New'; COLOR: #003399; FONT-SIZE: 10=
pt; mso-fareast-font-family: 'Times New Roman'"><SPAN style=3D"mso-sp=
acerun: yes">&nbsp;</SPAN>with all non electrostatic terms<=
SPAN style=3D"mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp; </SPAN>(a.u.) =3D<SPAN style=3D"mso-spacerun=
: yes">&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>-98.573228&=
lt;/SPAN></B><B style=3D"mso-bidi-font-weight: normal"><S=
PAN style=3D"FONT-FAMILY: 'Courier New'; COLOR: black; FONT-SIZE: 10pt; mso=
-fareast-font-family: 'Times New Roman'"><o:p></o:p></SPA=
N></B></DIV>
<P style=3D"LINE-HEIGHT: normal; MARGIN: 0in 0in 0pt; tab-stops: 45.8pt =
91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.=
8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><SPAN =
style=3D"FONT-FAMILY: 'Courier New'; COLOR: black; FONT-SIZE: 10pt; mso-far=
east-font-family: 'Times New Roman'">-----------------------------------=
--------------------------------- <o:p></o:p></SPAN></=
DIV>
<P style=3D"LINE-HEIGHT: normal; MARGIN: 0in 0in 0pt; tab-stops: 45.8pt =
91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.=
8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><SPAN =
style=3D"FONT-FAMILY: 'Courier New'; COLOR: black; FONT-SIZE: 10pt; mso-far=
east-font-family: 'Times New Roman'">(Polarized solute)-Solvent<SPAN =
style=3D"mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&=
;nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp; </SPAN>(kcal/mol) =3D<SPAN style=3D"mso-spac=
erun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN&=
gt;-3.27 <o:p></o:p></SPAN></DIV>
<P style=3D"LINE-HEIGHT: normal; MARGIN: 0in 0in 0pt; tab-stops: 45.8pt =
91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.=
8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><SPAN =
style=3D"FONT-FAMILY: 'Courier New'; COLOR: black; FONT-SIZE: 10pt; mso-far=
east-font-family: 'Times New Roman'">-----------------------------------=
--------------------------------- <o:p></o:p></SPAN></=
DIV>
<P style=3D"LINE-HEIGHT: normal; MARGIN: 0in 0in 0pt; tab-stops: 45.8pt =
91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.=
8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><SPAN =
style=3D"FONT-FAMILY: 'Courier New'; COLOR: black; FONT-SIZE: 10pt; mso-far=
east-font-family: 'Times New Roman'">Cavitation energy<SPAN style=3D"=
mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&am=
p;nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&am=
p;nbsp;&nbsp;&nbsp; </SPAN>(kcal/mol) =3D<SPAN style=3D"ms=
o-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp; </SPAN>5.34 <o:p></o:p></SPAN></DIV>
<P style=3D"LINE-HEIGHT: normal; MARGIN: 0in 0in 0pt; tab-stops: 45.8pt =
91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.=
8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><SPAN =
style=3D"FONT-FAMILY: 'Courier New'; COLOR: black; FONT-SIZE: 10pt; mso-far=
east-font-family: 'Times New Roman'">Dispersion energy<SPAN style=3D"=
mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&am=
p;nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp; </SPAN><SPAN style=3D"mso-spacerun: yes">=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
;nbsp;</SPAN>(kcal/mol) =3D<SPAN style=3D"mso-spacerun: yes">&a=
mp;nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>-3.08 <o:p=
></o:p></SPAN></DIV>
<P style=3D"LINE-HEIGHT: normal; MARGIN: 0in 0in 0pt; tab-stops: 45.8pt =
91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.=
8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><SPAN =
style=3D"FONT-FAMILY: 'Courier New'; COLOR: black; FONT-SIZE: 10pt; mso-far=
east-font-family: 'Times New Roman'">Repulsion energy<SPAN style=3D"m=
so-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
;nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
;nbsp;&nbsp;&nbsp;&nbsp; </SPAN>(kcal/mol) =3D<SPAN st=
yle=3D"mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp; </SPAN>0.34 <B><o:p></o:p></B>=
</SPAN></DIV>
<P style=3D"LINE-HEIGHT: normal; MARGIN: 0in 0in 0pt; tab-stops: 45.8pt =
91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.=
8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><SPAN =
style=3D"FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt; mso-fareast-font-fami=
ly: 'Times New Roman'; mso-bidi-font-weight: bold">Total non electrostat=
ic<SPAN style=3D"mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&am=
p;nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>=
;(kcal/mol) =3D<SPAN style=3D"mso-spacerun: yes">&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>2.60 </SPAN><=
;SPAN style=3D"FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt; mso-fareast-fon=
t-family: 'Times New Roman'"><SPAN style=3D"mso-spacerun: yes">&am=
p;nbsp;</SPAN><o:p></o:p></SPAN></DIV>
<P style=3D"LINE-HEIGHT: normal; MARGIN: 0in 0in 0pt; tab-stops: 45.8pt =
91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.=
8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class=3DMsoNormal><SPAN =
style=3D"FONT-FAMILY: 'Courier New'; COLOR: black; FONT-SIZE: 10pt; mso-far=
east-font-family: 'Times New Roman'">-----------------------------------=
--------------------------------- <o:p></o:p></SPAN></=
DIV>
<P style=3D"MARGIN: 0in 0in 10pt" class=3DMsoNormal><SPAN style=3D=
"LINE-HEIGHT: 115%; FONT-FAMILY: 'Arial','sans-serif'; FONT-SIZE: 10pt; mso=
-fareast-language: ZH-HK"><o:p>&nbsp;</o:p></SPAN>=
</DIV>
<P style=3D"MARGIN: 0in 0in 10pt" class=3DMsoNormal><SPAN style=3D=
"LINE-HEIGHT: 115%; FONT-FAMILY: 'Arial','sans-serif'; FONT-SIZE: 10pt; mso=
-fareast-language: ZH-HK">Best regards,<o:p></o:p></SPAN&=
gt;</DIV>
<P style=3D"MARGIN: 0in 0in 10pt" class=3DMsoNormal><SPAN style=3D=
"LINE-HEIGHT: 115%; FONT-FAMILY: 'Arial','sans-serif'; FONT-SIZE: 10pt; mso=
-fareast-language: ZH-HK">Sue<o:p></o:p></SPAN></DI=
V>
<P style=3D"MARGIN: 0in 0in 10pt" class=3DMsoNormal><SPAN style=3D=
"mso-fareast-language: ZH-HK"><o:p><FONT size=3D3 face=3DCalibr=
i>&nbsp;</FONT></o:p></SPAN></DIV><BR>=
<BR>--- On <B>Mon, 10/31/11, Arne Dieckmann adieckma**googlemai=
l.com <I>&lt;owner-chemistry::ccl.net&gt;</I></B>=
 wrote:<BR>
<BLOCKQUOTE style=3D"BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT=
: 5px; MARGIN-LEFT: 5px"><BR>From: Arne Dieckmann adieckma**google=
mail.com &lt;owner-chemistry::ccl.net&gt;<BR>Subject: CCL:G: =
Solvent-corrected Gibbs free energies<BR>To: "L, Sue " &lt;chsue2=
004::yahoo.com&gt;<BR>Date: Monday, October 31, 2011, 12:48 PM<=
;BR><BR>
<DIV class=3DplainMail><BR>Sent to CCL by: Arne Dieckmann [adie=
ckma###googlemail.com]<BR>Hi Sue, <BR><BR>the two methods=
 you are describing are exactly the same, as you are only changing the orde=
r in which different quantities are added. <BR><BR><BR>Ch=
eers, <BR>Arne<BR><BR><BR>On Oct 30, 2011, at 9:08 =
PM, Sue L chsue2004^^yahoo.com wrote:<BR><BR>&gt; <BR>=
;&gt; Sent to CCL by: "Sue&nbsp; L" [chsue2004]_[yahoo.com]<BR&g=
t;&gt; Dear CCL users,<BR>&gt; <BR>&gt; Could someo=
ne help me with the following question?<BR>&gt; <BR>&gt=
; If I want to calculate the solvent-corrected Gibbs free energies of the m=
olecules based on the gas-phase optimized geometry usinf gaussian 03. Which=
 of the following methods is more appropriate?<BR>&gt; <BR>=
&gt;&gt; From the vibrational frequency calculation of the
 gas-phase optimized stru
cture, I could obtain the thermal correction to Gibbs Free Energy<BR>=
&gt; <BR>&gt;&gt; From the single-point PCM calculation, =
I could obtain the total free
energy in solution: with all non electrostatic terms as well as solvent-pha=
se electronic energies (The energy value associated with SCF(Done))<BR&g=
t;&gt; <BR>&gt; (1) The solvent-corrected Gibbs free energies=
 =3D the total free energy in solution + thermal correction to Gibbs Free E=
nergy<BR>&gt; <BR>&gt; Or<BR>&gt; <BR>&=
amp;gt; (2) The solvent-corrected Gibbs free energies =3D gas-phase Gibbs f=
ree energies + (solvent-phase electronic energies&nbsp; - gas-phase ele=
ctronic energies)<BR>&gt; <BR>&gt; Thank you very much =
for your kind help.<BR>&gt; <BR>&gt; Best regards,<B=
R>&gt; Sue&gt; <BR>&gt;<BR><BR><BR>&=
lt;BR<BR<BR>the strange characters on the top line to the :: sign.=
 You can also<BR<BR><BR>E-mail to subscribers: <A
href=3D"http://us.mc1205.mail.yahoo.com/mc/compose?to=3DCHEMISTRY::ccl.n=
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bsp; <A href=3D"http://www.ccl=
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lank>http://www.ccl.net/chemistry/aboutccl/instructions/<=
;/A><BR><BR><BR></DIV></BLOCKQUOTE></td=
></tr></table>

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--=20
PD. Dr. Andreas Klamt
CEO / Gesch=C3=A4ftsf=C3=BChrer
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D-51381 Leverkusen, Germany

phone  =09+49-2171-731681
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HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
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---887514071-1879295465-1320159588=:64311-- From owner-chemistry@ccl.net Tue Nov 1 11:39:01 2011 From: "Werner Schroedinger werner.schroedinger*|*googlemail.com" To: CCL Subject: CCL: Study folding and/or molecular dynamics of flexible part of a protein Message-Id: <-45800-111101113354-30814-cJ33iu7WORPfWEq0nbDjDQ_-_server.ccl.net> X-Original-From: "Werner Schroedinger" Date: Tue, 1 Nov 2011 11:33:52 -0400 Sent to CCL by: "Werner Schroedinger" [werner.schroedinger^-^googlemail.com] In some PDB protein structure I would like to study flexibility in some concrete part of the molecule (small loop). I would like to perform a) protein folding where all the protein is rigid except the selected part, which remains totally flexible b) molecular dynamics, where it is only flexible the previously selected part Although this approach could seem unrealistic, I would like to know which method/programs, etc, would you recommend for performing this. From owner-chemistry@ccl.net Tue Nov 1 12:13:00 2011 From: "Vera Cathrine vera.cathrine]|[yahoo.com" To: CCL Subject: CCL: G09: rigid scan Message-Id: <-45801-111101115341-17333-+levQvfSkSHQQiSC9EbEag%x%server.ccl.net> X-Original-From: "Vera Cathrine" Date: Tue, 1 Nov 2011 11:53:36 -0400 Sent to CCL by: "Vera Cathrine" [vera.cathrine : yahoo.com] Dear All, I am dealing with a two fragments system (lets say hbd donor and hbd acceptor) in G09. These fragments from hydrogen bond together. I would like to do a rigid scan along a dihedral angle inside the hbd donor fragment. When I scan the dihedral angle in the first fragment (hbd donor), the second fragment (hbd acceptor) is also rotates with the second fragment (move around). I am interested in relation of the dihedral barrier in second fragment and hbd distance with the second fragment. How I can avoid this In rigid scan? I could not find any way to freeze the atom in rigid scanning. Is the problem due to the z-matrix definition of whole system? Thank you for your suggestion in advance. Best regards, Vera From owner-chemistry@ccl.net Tue Nov 1 14:24:00 2011 From: "Wojciech Kolodziejczyk dziecial:_:icnanotox.org" To: CCL Subject: CCL:G: G09: rigid scan Message-Id: <-45802-111101142125-23057-RfXnB0r2drVyhZfpbeaQWA!A!server.ccl.net> X-Original-From: Wojciech Kolodziejczyk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 1 Nov 2011 19:01:21 +0100 MIME-Version: 1.0 Sent to CCL by: Wojciech Kolodziejczyk [dziecial a icnanotox.org] Hi In gaussian you are able to make rotation around angle using opt=modredundant keyword or scan keyword. It depends what you want to get. First of all. Are you interested in relaxing your compound after every step? If yes you should use scan and your second fragment will rotate with the first one as long as your Z-MATRIX is built to rotate it. I mean that in Z-MATRIX every angle and distance depends on atom above. So if you change one distance it will move other part that is connected with this one. Of course you can use modredundand keyword. It will rotate only part that is bonded. So if you have two moieties that are not bonded and you will rotate only one the second will not move. So mainly. Try to rebuild your Z-MATRIX first and then read about modredundant keyword I hope I did help W. 2011/11/1 Vera Cathrine vera.cathrine]|[yahoo.com : > > Sent to CCL by: "Vera Cathrine" [vera.cathrine : yahoo.com] > Dear All, > > I am dealing with a two fragments system (lets say hbd donor and hbd acceptor) in G09. These fragments from hydrogen bond together. I would like to do a rigid scan along a dihedral angle inside the hbd donor fragment. When I scan the dihedral angle in the first fragment (hbd donor), the second fragment (hbd acceptor) is also rotates with the second fragment (move around). I am interested in relation of the dihedral barrier in second fragment and hbd distance with the second fragment. How I can avoid this In rigid scan? I could not find any way to freeze the atom in rigid scanning. Is the problem due to the z-matrix definition of whole system? Thank you for your suggestion in advance. > Best regards, > Vera> 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 Tue Nov 1 14:59:01 2011 From: "David Gallagher gallagher.da\a/gmail.com" To: CCL Subject: CCL: ParaSurf (electronic property prediction) FREE to Academics Message-Id: <-45803-111101143046-26419-1czBJ5ogQFgt1YxB1h67fQ-.-server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="------------020209070302080003070509" Date: Tue, 01 Nov 2011 11:30:35 -0700 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da/a\gmail.com] This is a multi-part message in MIME format. --------------020209070302080003070509 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit *ParaSurf*^(TM)*now available FREE to Academics.* . 3D QSAR & QSPR - novel electronic properties & descriptors . Chemical & physical property prediction . Novel surface-integral models for properties . Properties can also be used for grid-based techniques analogous to CoMFA^(TM) . High quality molecular electrostatics A special academic version of ParaSurf'10 that includes most of the functionality of the commercial release, is now available at no cost to bona fide academics. For more information click here... ParaSurf^(TM) uses semiempirical molecular-orbital methods to calculate electronic properties on the surface of molecules for use in QSPR, 3D-QSAR, ligand docking and reactivity prediction. The CypScore technique for predicting drug metabolism by cyctochrome P450 is based on descriptors available in the full version of ParaSurf . ParaSurf^(TM)is available from Cepos InSilico in Europe and CAChe Research in the Americas. --------------020209070302080003070509 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit ParaSurf™ now available FREE to Academics.

   •   3D QSAR & QSPR - novel electronic properties & descriptors
   •   Chemical & physical property prediction
   •   Novel surface-integral models for properties
   •   Properties can also be used for grid-based techniques analogous to CoMFA™
   •   High quality molecular electrostatics

A special academic version of ParaSurf’10 that includes most of the functionality of the commercial release, is now available at no cost to bona fide academics. For more information click here...

ParaSurf™ uses semiempirical molecular-orbital methods to calculate electronic properties on the surface of molecules for use in QSPR, 3D-QSAR, ligand docking and reactivity prediction. The CypScore technique for predicting drug metabolism by cyctochrome P450 is based on descriptors available in the full version of ParaSurf.

ParaSurf™ is available from Cepos InSilico in Europe and CAChe Research in the Americas.

--------------020209070302080003070509-- From owner-chemistry@ccl.net Tue Nov 1 15:34:01 2011 From: "Michael A Wilson Michael.A.Wilson_._nasa.gov" To: CCL Subject: CCL: Study folding and/or molecular dynamics of flexible part of a protein Message-Id: <-45804-111101130258-20116-39vPaIrKn2gwGd/PMiIYvw~~server.ccl.net> X-Original-From: Michael A Wilson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Date: Tue, 1 Nov 2011 10:02:21 -0700 MIME-Version: 1.0 Sent to CCL by: Michael A Wilson [Michael.A.Wilson*nasa.gov] Regarding (a): the PLOP program from Matt Jacobson's group at UCSF, which can be used to predict and optimize loop structure ( http://http://www.jacobsonlab.org ). I'm sure there are other codes to do constrained structure prediction. Regarding (b): most MD codes will allow you to constrain (either rigidly or with harmonic restraints) selected atoms, so it would be straightforward to do something like restrain all backbone atoms, except in the region of interest. Mike On 11/1/2011 8:33 AM, Werner Schroedinger werner.schroedinger*|*googlemail.com wrote: > Sent to CCL by: "Werner Schroedinger" [werner.schroedinger^-^googlemail.com] > In some PDB protein structure I would like to study flexibility in some concrete part of the molecule (small loop). I would like to perform > > a) protein folding where all the protein is rigid except the selected part, which remains totally flexible b) molecular dynamics, where it is only flexible the previously selected part > > Although this approach could seem unrealistic, I would like to know which method/programs, etc, would you recommend for performing this.> > > From owner-chemistry@ccl.net Tue Nov 1 16:08:01 2011 From: "Simmie, John john.simmie-x-nuigalway.ie" To: CCL Subject: CCL: G09: rigid scan Message-Id: <-45805-111101144748-22140-/U4zO9Z7t+sfBGToymCDgQ[#]server.ccl.net> X-Original-From: "Simmie, John" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 1 Nov 2011 18:47:39 -0000 MIME-Version: 1.0 Sent to CCL by: "Simmie, John" [john.simmie^^nuigalway.ie] I have found that the Opt=ModRedundant option offers more control over scans Making it easier to freeze coordinates etc Have you explored this possibility? >Sent to CCL by: "Vera Cathrine" [vera.cathrine : yahoo.com] Dear All, >I am dealing with a two fragments system (lets say hbd donor and hbd acceptor) in G09. These fragments from hydrogen >bond together. I would like to do a rigid scan along a dihedral angle inside the hbd donor fragment. When I scan the dihedral >angle in the first fragment (hbd donor), the second fragment (hbd acceptor) is also rotates with the second fragment (move >around). I am interested in relation of the dihedral barrier in second fragment and hbd distance with the second fragment. >How I can avoid this In rigid scan? I could not find any way to freeze the atom in rigid scanning. Is the problem due to the z->matrix definition of whole system? Thank you for your suggestion in advance. >Best regards, >Vera From owner-chemistry@ccl.net Tue Nov 1 16:43:00 2011 From: "Arne Dieckmann adieckmann(a)ucla.edu" To: CCL Subject: CCL: NBO Message-Id: <-45806-111101150237-13730-XUQEXHVlfzNF6nv+aLCCkQ(!)server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 1 Nov 2011 12:02:02 -0700 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Arne Dieckmann [adieckmann%%ucla.edu] Dear all, I am about to perform a NBO analysis for some structures which were optimized using M062X/6-31+G(d,p). Is it legitimite to perform the transformation to the NBOs directly using this method or should they be derived from a HF calculation? Cheers, Arne - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dr. Arne Dieckmann Houk Research Lab University of California, Los Angeles email: adieckma#googlemail.com From owner-chemistry@ccl.net Tue Nov 1 22:55:00 2011 From: "Andrew Orry andy/a\molsoft.com" To: CCL Subject: CCL: Study folding and/or molecular dynamics of flexible part of a protein Message-Id: <-45807-111101174702-22569-Y2rcXl1SFYz+0EnSu9e9jw^^server.ccl.net> X-Original-From: Andrew Orry Content-Type: multipart/alternative; boundary="------------040306000407070804050104" Date: Tue, 01 Nov 2011 14:50:32 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy^^molsoft.com] This is a multi-part message in MIME format. --------------040306000407070804050104 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Werner You might find this new method helpful: Arnautova /et al/ Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins. 2011 Feb;79(2):477-98http://www.ncbi.nlm.nih.gov/pubmed/21069716 Conformational sampling is carried out using the biased probability Monte Carlo method in a new Internal Coordinate Mechanics force field. It is incorporated into MolSoft's software http://www.molsoft.com/icm_pro.html. Thanks, Andy -- Andrew Orry Ph.D. MolSoft LLC Senior Research Scientist 11199 Sorrento Valley Road, S209 San Diego CA 92121 Tel: 858-625-2000 x108 Fax: 828-625-2888 www.molsoft.com On 11/1/2011 8:33 AM, Werner Schroedinger werner.schroedinger*|*googlemail.com wrote: > Sent to CCL by: "Werner Schroedinger" [werner.schroedinger^-^googlemail.com] > In some PDB protein structure I would like to study flexibility in some concrete part of the molecule (small loop). I would like to perform > > a) protein folding where all the protein is rigid except the selected part, which remains totally flexible b) molecular dynamics, where it is only flexible the previously selected part > > Although this approach could seem unrealistic, I would like to know which method/programs, etc, would you recommend for performing this.> -- Andrew Orry Ph.D. MolSoft LLC Senior Research Scientist 11199 Sorrento Valley Road, S209 San Diego CA 92121 Tel: 858-625-2000 x108 Fax: 828-625-2888 www.molsoft.com --------------040306000407070804050104 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Werner

You might find this new method helpful:

Arnautova et al Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins. 2011 Feb;79(2):477-98 http://www.ncbi.nlm.nih.gov/pubmed/21069716

Conformational sampling is carried out using the biased probability Monte Carlo method in a new Internal Coordinate Mechanics force field. It is incorporated into MolSoft's software http://www.molsoft.com/icm_pro.html.

Thanks,
Andy

-- 
Andrew Orry Ph.D.
MolSoft LLC
Senior Research Scientist
11199 Sorrento Valley Road, S209
San Diego
CA 92121
Tel: 858-625-2000 x108
Fax: 828-625-2888
www.molsoft.com

On 11/1/2011 8:33 AM, Werner Schroedinger werner.schroedinger*|*googlemail.com wrote:

Sent to CCL by: "Werner  Schroedinger" [werner.schroedinger^-^googlemail.com]
In some PDB protein structure I would like to study flexibility in some concrete part of the molecule (small loop). I would like to perform

a) protein folding where all the protein is rigid except the selected part, which remains totally flexible b) molecular dynamics, where it is only flexible the previously selected part

Although this approach could seem unrealistic, I would like to know which method/programs, etc, would you recommend for performing this.E-mail to subscribers: CHEMISTRY||ccl.net or use:
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-- 
Andrew Orry Ph.D.
MolSoft LLC
Senior Research Scientist
11199 Sorrento Valley Road, S209
San Diego
CA 92121
Tel: 858-625-2000 x108
Fax: 828-625-2888
www.molsoft.com

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