From owner-chemistry@ccl.net Mon Aug 25 06:47:01 2014 From: "Russell W Driver rwdriver a kaist.ac.kr" To: CCL Subject: CCL: TINKER with cyclic amino acids and distance restraints Message-Id: <-50433-140825013731-5788-H2ilr9to/V5HfJ3ys6EsOA .. server.ccl.net> X-Original-From: "Russell W Driver" Date: Mon, 25 Aug 2014 01:37:30 -0400 Sent to CCL by: "Russell W Driver" [rwdriver%%kaist.ac.kr] Dear Computational Chemists, I am a new TINKER user running Windows executables on a standard desktop PC. I am having difficulty making .xyz files from the .pdbs of cyclic amino acid foldamers using the pdbxyz executable. Is this because the forcefields I am using (like MM2) lack parameters for these atom connectivities (types)? I have gMOLDEN for Windows but preparing the structures that way doesnt seem to help. Can anyone recommend an way around this? Or care to pass along a parameter patch for cyclic structures? Also, I would like to do calculations with distance and dihedral angle restraints. Can anyone show me an example of a keyfile (?) that contains script for dihedral angles and interatomic distance restraints? Much appreciated! Best regards, Russell Department of Chemistry KAIST rwdriver/a\kaist.ac.kr From owner-chemistry@ccl.net Mon Aug 25 07:22:01 2014 From: "fateme sabzalizade fatemesabzalizade__gmail.com" To: CCL Subject: CCL:G: error in gaussian 09 Message-Id: <-50434-140825020448-6890-fpkNlJJo5oGbsGY5X01a4w++server.ccl.net> X-Original-From: "fateme sabzalizade" Date: Mon, 25 Aug 2014 02:04:47 -0400 Sent to CCL by: "fateme sabzalizade" [fatemesabzalizade]^[gmail.com] Hi Dear Subscribers I want to use gaussian 09 for the optimised structure with B3LYP/6-311G***. but when I am running the input file, its giving me error like this: QPErr --- A syntax error was detected in the input line. #b3lyp/6-311g*** opt freq Last state="GCL" TCursr= 1046 LCursr= 15 Error termination via Lnk1e I do not know How to rectify the problem in using this basis set Thank you for your cooperation From owner-chemistry@ccl.net Mon Aug 25 08:09:01 2014 From: "Jean Jules Fifen julesfifen{=}gmail.com" To: CCL Subject: CCL:G: error in gaussian 09 Message-Id: <-50435-140825080725-15440-n1MHFmEV2EcKQBGe4PDqaA]|[server.ccl.net> X-Original-From: Jean Jules Fifen Content-Type: multipart/alternative; boundary=001a1133614e26393205017307d2 Date: Mon, 25 Aug 2014 15:07:16 +0300 MIME-Version: 1.0 Sent to CCL by: Jean Jules Fifen [julesfifen-#-gmail.com] --001a1133614e26393205017307d2 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Of course, the error is in your input file. type #b3lyp/6-311g** opt freq instead of #b3lyp/6-311g*** opt freq. The basis set 6-311g*** doesn't exist. Regards, On Mon, Aug 25, 2014 at 9:04 AM, fateme sabzalizade fatemesabzalizade__gmail.com wrote: > > Sent to CCL by: "fateme sabzalizade" [fatemesabzalizade]^[gmail.com] > Hi Dear Subscribers > > I want to use gaussian 09 for the optimised structure with > B3LYP/6-311G***. but when I am running the input file, its giving me erro= r > like this: > QPErr --- A syntax error was detected in the input line. > #b3lyp/6-311g*** opt freq > > Last state=3D"GCL" > TCursr=3D 1046 LCursr=3D 15 > Error termination via Lnk1e > > I do not know How to rectify the problem in using this basis set > Thank you for your cooperation > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 --------------------------------------------------------------------------- *Jean Jules FIFEN*, Ph.D. in Atomic & Molecular Physics Senior Lecturer, =E2=80=8BDepartment of Physics, Faculty of Science, The University of Ngaoundere, Cameroon. P.O. BOX 454 Ngaoundere Private: P.O. BOX 547 Ngaoundere Phone number: +972 54 3656845 /+972 55 8961001/ +237 75 21 61 39 ---------------------------------------------------------------------------= -------------------------------------- --001a1133614e26393205017307d2 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Of course, the error is in your input file.<= br>
type #b3lyp/6-311g** opt freq instead of #b3lyp/6-311g*** opt freq.
The basis set 6-311g*** doesn't exist.

Regards,


On Mon, Aug 25, 2014 at 9:04 AM, fateme sabzalizade fatemesabzalizade__gmail.com <owner-chemistry .. ccl.net> wrote:

Sent to CCL by: "fateme=C2=A0 sabzalizade" [fatemesabzalizade]^[<= a href=3D"http://gmail.com" target=3D"_blank">gmail.com]
Hi Dear Subscribers

I want to use=C2=A0 gaussian 09 for the optimised structure with
B3LYP/6-311G***. but when I am running the input file, its giving me error<= br> like this:
QPErr --- A syntax error was detected in the input line.
=C2=A0#b3lyp/6-311g*** opt freq

=C2=A0Last state=3D"GCL"
=C2=A0TCursr=3D 1046 LCursr=3D=C2=A0 =C2=A015
=C2=A0Error termination via Lnk1e

I do not know How to rectify the problem in using this basis set
Thank you for your cooperation



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY .. ccl.n= et or use:
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--
<= span style=3D"color:rgb(0,0,255)">--------------------------------------------------------------------= -------
Jean Jules FIFEN,
Ph.D. in= Atomic & Molecular Physics
Senior Lecturer,
=
=E2= =80=8BDepartment of Physics,
<= span style=3D"font-family:courier new,monospace">Faculty of Science,
The= University of Ngaoundere, Cameroon.
P.O. BOX 454 Ngaou= ndere
Private: P.O. BOX 547 Ngaoundere
Phone= number: +972 54 3656845 /+= 972 55 8961001/ +237 75 21 61 39
---= ---------------------------------------------------------------------------= -----------------------------------
=C2=A0
--001a1133614e26393205017307d2-- From owner-chemistry@ccl.net Mon Aug 25 08:46:00 2014 From: "Robert Molt r.molt.chemical.physics-,-gmail.com" To: CCL Subject: CCL:G: error in gaussian 09 Message-Id: <-50436-140825084512-12379-2vBO77S+gMROCdMQdnxKzg*|*server.ccl.net> X-Original-From: Robert Molt Content-Type: multipart/alternative; boundary=Apple-Mail-1--980709264 Date: Mon, 25 Aug 2014 08:45:03 -0400 Mime-Version: 1.0 (Apple Message framework v1085) Sent to CCL by: Robert Molt [r.molt.chemical.physics^gmail.com] --Apple-Mail-1--980709264 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii There is no basis set 6-311G*** You probably mean 6-31G** (2, not 3). Dr. Robert Molt Jr. r.molt.chemical.physics/a\gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 On Aug 25, 2014, at 2:04 AM, fateme sabzalizade = fatemesabzalizade__gmail.com wrote: >=20 > Sent to CCL by: "fateme sabzalizade" [fatemesabzalizade]^[gmail.com] > Hi Dear Subscribers >=20 > I want to use gaussian 09 for the optimised structure with > B3LYP/6-311G***. but when I am running the input file, its giving me = error > like this: > QPErr --- A syntax error was detected in the input line. > #b3lyp/6-311g*** opt freq >=20 > Last state=3D"GCL" > TCursr=3D 1046 LCursr=3D 15 > Error termination via Lnk1e >=20 > I do not know How to rectify the problem in using this basis set > Thank you for your cooperation >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail-1--980709264 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii There = is no basis = set

6-311G***

You probably = mean

6-31G**

(2, not = 3).

Dr. Robert Molt Jr.
r.molt.chemical.physics/a\= gmail.com
Nigel Richards Research Group
Department of = Chemistry & Chemical Biology
Indiana University-Purdue = University Indianapolis
LD 326
402 N. Blackford = St.
Indianapolis, IN 46202

On Aug 25, 2014, at 2:04 AM, fateme sabzalizade = fatemesabzalizade__gmail.com wrote:


Sent to CCL by: "fateme  sabzalizade" = [fatemesabzalizade]^[gmail.com]
Hi Dear Subscribers

I want to = use  gaussian 09 for the optimised structure = with
B3LYP/6-311G***. but when I am running the input file, its = giving me error
like this:
QPErr --- A syntax error was detected = in the input line.
#b3lyp/6-311g*** opt freq

Last = state=3D"GCL"
TCursr=3D 1046 LCursr=3D   15
Error = termination via Lnk1e

I do not know How to rectify the problem in = using this basis set
Thank you for your cooperation



-=3D= This is automatically added to each message by the mailing script = =3D-
To recover the email address of the author of the message, = please change
the strange characters on the top line to the /a\ sign. = You can also
look up the X-Original-From: line in the mail = header.

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<= /div>
= --Apple-Mail-1--980709264-- From owner-chemistry@ccl.net Mon Aug 25 09:21:01 2014 From: "Mozhdeh Mohammadpour mozhdehmohammadpour]*[gmail.com" To: CCL Subject: CCL:G: error in gaussian 09 Message-Id: <-50437-140825085217-17984-3Gv7iPWagFOS4xQ0m0WzHQ##server.ccl.net> X-Original-From: Mozhdeh Mohammadpour Content-Type: multipart/alternative; boundary=001a11c288f2c85852050173a7ec Date: Mon, 25 Aug 2014 17:22:11 +0430 MIME-Version: 1.0 Sent to CCL by: Mozhdeh Mohammadpour [mozhdehmohammadpour|a|gmail.com] --001a11c288f2c85852050173a7ec Content-Type: text/plain; charset=ISO-8859-1 Dear Fatemeh Sintax errors are related to mistakes in keywords . in your input *** is incorrect. change it to ** and run it again. if you want to skip this kind of problem, use Gaussview to build your input. On Mon, Aug 25, 2014 at 10:34 AM, fateme sabzalizade fatemesabzalizade__gmail.com wrote: > > Sent to CCL by: "fateme sabzalizade" [fatemesabzalizade]^[gmail.com] > Hi Dear Subscribers > > I want to use gaussian 09 for the optimised structure with > B3LYP/6-311G***. but when I am running the input file, its giving me error > like this: > QPErr --- A syntax error was detected in the input line. > #b3lyp/6-311g*** opt freq > > Last state="GCL" > TCursr= 1046 LCursr= 15 > Error termination via Lnk1e > > I do not know How to rectify the problem in using this basis set > Thank you for your cooperation> > > --001a11c288f2c85852050173a7ec Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Fatemeh
Sintax errors are related to mi= stakes in keywords . in your input *** is incorrect. change it to ** and ru= n it again. if you want to skip this kind of problem, use Gaussview to buil= d your input.


On Mon,= Aug 25, 2014 at 10:34 AM, fateme sabzalizade fatemesabzalizade__gmail.com <<= a href=3D"mailto:owner-chemistry/a\ccl.net" target=3D"_blank">owner-chemistry= /a\ccl.net> wrote:

Sent to CCL by: "fateme=A0 sabzalizade" [fatemesabzalizade]^[gmail.com]
Hi Dear Subscribers

I want to use=A0 gaussian 09 for the optimised structure with
B3LYP/6-311G***. but when I am running the input file, its giving me error<= br> like this:
QPErr --- A syntax error was detected in the input line.
=A0#b3lyp/6-311g*** opt freq

=A0Last state=3D"GCL"
=A0TCursr=3D 1046 LCursr=3D=A0 =A015
=A0Error termination via Lnk1e

I do not know How to rectify the problem in using this basis set
Thank you for your cooperation



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY/a\ccl.n= et or use:
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--001a11c288f2c85852050173a7ec-- From owner-chemistry@ccl.net Mon Aug 25 10:46:00 2014 From: "Olasunkanmi Lukman Olawale walecomuk%yahoo.co.uk" To: CCL Subject: CCL:G: error in gaussian 09 Message-Id: <-50438-140825081101-18279-GYEzD94zrQ6QUxQqPA3vZg#%#server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 25 Aug 2014 13:10:54 +0100 MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk_._yahoo.co.uk] Double-check your route section you put #b3lyp/6-311g*** opt freq instead of #b3lyp/6-311g** opt freq (triple * instead of double) Lukman Olawale Olasunkanmi Current Address: Department of Chemistry, Faculty of Agriculture, Science and Technology, North West University (Mafikeng Campus), South Africa. Cell: +27710156252 OR +27747614116 Permanent Address: Department of Chemistry, Obafemi Awolowo University, Ile-Ife, Nigeria. Cell: +234 805 240 1564 -------------------------------------------- On Mon, 25/8/14, fateme sabzalizade fatemesabzalizade__gmail.com wrote: Subject: CCL:G: error in gaussian 09 To: "Olasunkanmi, Olawale Lukman " Date: Monday, 25 August, 2014, 8:04 Sent to CCL by: "fateme  sabzalizade" [fatemesabzalizade]^[gmail.com] Hi Dear Subscribers I want to use  gaussian 09 for the optimised structure with B3LYP/6-311G***. but when I am running the input file, its giving me error like this: QPErr --- A syntax error was detected in the input line. #b3lyp/6-311g*** opt freq Last state="GCL" TCursr= 1046 LCursr=   15 Error termination via Lnk1e I do not know How to rectify the problem in using this basis set Thank you for your cooperation                     From owner-chemistry@ccl.net Mon Aug 25 12:37:01 2014 From: "Billy McCann thebillywayne^gmail.com" To: CCL Subject: CCL: Obtaining a compilation of OPLS-AA force field parameters Message-Id: <-50439-140825115213-8090-MbbGbW8e9BaNntTj+iWctA- -server.ccl.net> X-Original-From: Billy McCann Content-Type: multipart/alternative; boundary=047d7bdca5e4c9c16f0501762ad7 Date: Mon, 25 Aug 2014 11:51:44 -0400 MIME-Version: 1.0 Sent to CCL by: Billy McCann [thebillywayne|*|gmail.com] --047d7bdca5e4c9c16f0501762ad7 Content-Type: text/plain; charset=UTF-8 Hi Andrew. There have a couple of additions that I know of. One involved a biological fragment and the other was incorporating the "sigma hole" phenomenon. There are also OPLS-AA parameters which have been produced by Acevedo regarding ionic liquids, and a few which I've created. At least, I'm sure that my all-atom methanol, which drastically increased the accuracy of a substitution reaction over united-atom methanol, hasn't been published. In any case, you'll want to use the parameters which are included with BOSS, so TINKER's parameters would be ideal. Check out the papers that Jorgensen's published laterly. I follow his work fairly closely. That one biological fragment may be relevant to you, as might the sigma hole. But I've met Jorgensen and know a couple of people in his group. They're all really nice. Shoot Bill an email requesting the latest compilation. Regards, BW -- Billy Wayne McCann, Ph.D. irc://irc.freenode.net:bwayne "A rich man will always desire what his wealth cannot acquire." ~ Faust (Goethe) On Sun, Aug 24, 2014 at 9:09 PM, Andrew DeYoung andrewdaviddeyoung[*] gmail.com wrote: > Hi, > > Does anyone know where I can obtain a compilation of OPLS-AA force field > parameters? > > The OPLS-AA force field has been developed over many years by the > Jorgensen Group at Yale. The parameters have been developed and > disseminated in many publications over the years. I am wondering if there > is a compiled list of all the OPLS-AA parameters. I thought that perhaps > the Jorgensen Group website ( http://zarbi.chem.yale.edu/index.html ) > might have such a compilation, but I can't seem to find one there. > > I'm a user of the GROMACS MD package ( http://www.gromacs.org/ ). > GROMACS contains library force field files ( usually located in > /usr/local/gromacs/share/gromacs/top ), including ones for OPLS-AA. But > I'm not sure if these are "official" compilations. There are a lot of > comments sprinkled throughout these files, including several that seem to > indicate a variety of revisions. > > Another possible list of parameters is found at the TINKER website: > > http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm > > The heading of that file includes this comment: > > "The parameters supplied with TINKER are from "OPLS All-Atom Parameters > for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as > provided by W. L. Jorgensen, Yale University during June 2009. These > parameters are taken from those distributed with BOSS Version 4.8." > > So, that list appears to be fairly recent (July 2008 and June 2009). I > don't know if there have been many changes/additions to OPLS-AA in the last > few years; browsing through the literature, it seems perhaps not. But, > nevertheless, does anyone know where I can obtain a fairly recent and > official compilation of the OPLS-AA force field parameters? > > Thank you so very much for your time! > > Andrew DeYoung > Carnegie Mellon University > --047d7bdca5e4c9c16f0501762ad7 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Hi Andrew.=C2=A0

There have a couple of additions that I know of.=C2=A0 One involved a biolo= gical fragment and the other was incorporating the "sigma hole" p= henomenon.=C2=A0 There are also OPLS-AA parameters which have been produced= by Acevedo regarding ionic liquids, and a few which I've created.=C2= =A0 At least, I'm sure that my all-atom methanol, which drastically inc= reased the accuracy of a substitution reaction over united-atom methanol, h= asn't been published.=C2=A0

= In any case, you'll want to use the parameters which are included with = BOSS, so TINKER's parameters would be ideal.=C2=A0 Check out the papers= that Jorgensen's published laterly.=C2=A0 I follow his work fairly clo= sely.=C2=A0 That one biological fragment may be relevant to you, as might t= he sigma hole.

= But I've met Jorgensen and know a couple of people in his group.=C2=A0 = They're all really nice.=C2=A0 Shoot Bill an email requesting the lates= t compilation.=C2=A0


Regards,
BW




--
Billy Wayne McCann, Ph.D.
irc://irc.freenode.net:bwayne
 "A rich = man will always desire what his wealth cannot acquire." ~ Faust (Goeth= e)
=


On Sun, Aug 24, 2014 at 9:09 PM, Andrew = DeYoung andrewdaviddeyoung[*]gmail.com <owner-chemistry{=}ccl.net> wrote:
Hi,

Does anyone kno= w where I can obtain a compilation of OPLS-AA force field parameters?
The OPLS-AA force field has been developed over many years by the Jorgensen= Group at Yale. =C2=A0The parameters have been developed and disseminated i= n many publications over the years. =C2=A0I am wondering if there is a comp= iled list of all the OPLS-AA parameters. =C2=A0I thought that perhaps the J= orgensen Group website ( http://zarbi.chem.yale.edu/index.html ) might have su= ch a compilation, but I can't seem to find one there.

I'm a user of the GROMACS MD package ( http://www.gromacs.org/ ). =C2=A0GROMACS cont= ains library force field files ( usually located in /usr/local/gromacs/shar= e/gromacs/top ), including ones for OPLS-AA. =C2=A0But I'm not sure if = these are "official" compilations. =C2=A0There are a lot of comme= nts sprinkled throughout these files, including several that seem to indica= te a variety of revisions.

Another possible list of parameters is found at the TINKER website:
=
http://dasher.wustl.edu/tinker/distribution/params/opl= saa.prm

The heading of that file includes this comment:

"The parameters= supplied with TINKER are from "OPLS All-Atom Parameters for Organic M= olecules, Ions, Peptides & Nucleic Acids, July 2008" as provided b= y W. L. Jorgensen, Yale University during June 2009. These parameters are t= aken from those distributed with BOSS Version 4.8."

So, that list appears to be fairly recent (July 2008 and June 2009). = =C2=A0I don't know if there have been many changes/additions to OPLS-AA= in the last few years; browsing through the literature, it seems perhaps n= ot. =C2=A0But, nevertheless, does anyone know where I can obtain a fairly r= ecent and official compilation of the OPLS-AA force field parameters? =C2= =A0

Thank you so very much for your time!

Andrew DeYoung
Carnegie= Mellon University

--047d7bdca5e4c9c16f0501762ad7-- From owner-chemistry@ccl.net Mon Aug 25 14:32:00 2014 From: "BUSRA DERELI bsradereli++gmail.com" To: CCL Subject: CCL: Solvation Free Energy of Proton in THF Message-Id: <-50440-140825142303-23362-TDW8DeLmGFL+B04fAPCcJA[]server.ccl.net> X-Original-From: "BUSRA DERELI" Date: Mon, 25 Aug 2014 14:23:02 -0400 Sent to CCL by: "BUSRA DERELI" [bsradereli::gmail.com] Hello, I am trying to calculate pKa values of two systems, one is anionic and the other is cationic copper systems. I got so weird numbers not close to the experimental values when I computed the free energy of proton in THF which is the solvent of interest. I use M11-L local functional with SDD basis set on Cu atom and 6-31G(d) on all other atoms in the system. Thus, I want to compare the computed solvation free energy of proton in THF with the experimental value. In some literature reports, I have seen absolute solvation free energy of proton in a couple of solvents but not in THF. Thanks, Busra Dereli From owner-chemistry@ccl.net Mon Aug 25 17:31:00 2014 From: "Jean Jules Fifen julesfifen[*]gmail.com" To: CCL Subject: CCL: Solvation Free Energy of Proton in THF Message-Id: <-50441-140825171327-6368-1czBJ5ogQFgt1YxB1h67fQ^^^server.ccl.net> X-Original-From: Jean Jules Fifen Content-Type: multipart/alternative; boundary=001a1133785423143005017aa859 Date: Tue, 26 Aug 2014 00:13:21 +0300 MIME-Version: 1.0 Sent to CCL by: Jean Jules Fifen [julesfifen : gmail.com] --001a1133785423143005017aa859 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable What model did you use to compute the solvated free energy of the proton in THF? On Mon, Aug 25, 2014 at 9:23 PM, BUSRA DERELI bsradereli++gmail.com < owner-chemistry::ccl.net> wrote: > > Sent to CCL by: "BUSRA DERELI" [bsradereli::gmail.com] > Hello, > > I am trying to calculate pKa values of two systems, one is anionic and th= e > other is cationic copper systems. I got so weird numbers not close to the > experimental values when I computed the free energy of proton in THF whic= h > is > the solvent of interest. I use M11-L local functional with SDD basis set > on Cu > atom and 6-31G(d) on all other atoms in the system. Thus, I want to > compare the > computed solvation free energy of proton in THF with the experimental > value. In > some literature reports, I have seen absolute solvation free energy of > proton > in a couple of solvents but not in THF. > > Thanks, > Busra Dereli > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 --------------------------------------------------------------------------- *Jean Jules FIFEN*, Ph.D. in Atomic & Molecular Physics Senior Lecturer, =E2=80=8BDepartment of Physics, Faculty of Science, The University of Ngaoundere, Cameroon. P.O. BOX 454 Ngaoundere Private: P.O. BOX 547 Ngaoundere Phone number: +972 54 3656845 /+972 55 8961001/ +237 75 21 61 39 ---------------------------------------------------------------------------= -------------------------------------- --001a1133785423143005017aa859 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
What model did you use to compute the solvat= ed free energy of the proton in THF?


On Mon, Aug 25, 2014 at 9:23 PM, BUSRA DEREL= I bsradereli++gmail.com = <owner-chem= istry::ccl.net> wrote:

Sent to CCL by: "BUSRA=C2=A0 DERELI" [bsradereli::gmail.com]
Hello,

I am trying to calculate pKa values of two systems, one is anionic and the<= br> other is cationic copper systems. I got so weird numbers not close to the experimental values when I computed the free energy of proton in THF which = is
the solvent of interest. I use M11-L local functional with SDD basis set on= Cu
atom and 6-31G(d) on all other atoms in the system. Thus, I want to compare= the
computed solvation free energy of proton in THF with the experimental value= . In
some literature reports, I have seen absolute solvation free energy of prot= on
in a couple of solvents but not in THF.

Thanks,
Busra Dereli



-=3D This is automatically added to each message by the mailing script =3D-=
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--
<= span style=3D"color:rgb(0,0,255)">--------------------------------------------------------------------= -------
Jean Jules FIFEN,
Ph.D. in= Atomic & Molecular Physics
Senior Lecturer,
=
=E2= =80=8BDepartment of Physics,
<= span style=3D"font-family:courier new,monospace">Faculty of Science,
The= University of Ngaoundere, Cameroon.
P.O. BOX 454 Ngaou= ndere
Private: P.O. BOX 547 Ngaoundere
Phone= number: +972 54 3656845 /+= 972 55 8961001/ +237 75 21 61 39
---= ---------------------------------------------------------------------------= -----------------------------------
=C2=A0
--001a1133785423143005017aa859-- From owner-chemistry@ccl.net Mon Aug 25 18:25:00 2014 From: "busra dereli bsradereli_-_gmail.com" To: CCL Subject: CCL:G: Solvation Free Energy of Proton in THF Message-Id: <-50442-140825180220-2367-cbV0rbiQ1m7TA+HWI8aHlA+/-server.ccl.net> X-Original-From: busra dereli Content-Type: multipart/alternative; boundary=047d7b3430d0b0fe8905017b5605 Date: Tue, 26 Aug 2014 01:02:10 +0300 MIME-Version: 1.0 Sent to CCL by: busra dereli [bsradereli],[gmail.com] --047d7b3430d0b0fe8905017b5605 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable I used the SMD model in Gaussian. On Tue, Aug 26, 2014 at 12:13 AM, Jean Jules Fifen julesfifen[*]gmail.com < owner-chemistry^_^ccl.net> wrote: > What model did you use to compute the solvated free energy of the proton > in THF? > > > On Mon, Aug 25, 2014 at 9:23 PM, BUSRA DERELI bsradereli++gmail.com < > owner-chemistry^ccl.net> wrote: > >> >> Sent to CCL by: "BUSRA DERELI" [bsradereli::gmail.com] >> Hello, >> >> I am trying to calculate pKa values of two systems, one is anionic and t= he >> other is cationic copper systems. I got so weird numbers not close to th= e >> experimental values when I computed the free energy of proton in THF >> which is >> the solvent of interest. I use M11-L local functional with SDD basis set >> on Cu >> atom and 6-31G(d) on all other atoms in the system. Thus, I want to >> compare the >> computed solvation free energy of proton in THF with the experimental >> value. In >> some literature reports, I have seen absolute solvation free energy of >> proton >> in a couple of solvents but not in THF. >> >> Thanks, >> Busra Dereli >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY^ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST^ccl.net or use>> >> >> > > > -- > -------------------------------------------------------------------------= -- > *Jean Jules FIFEN*, > Ph.D. in Atomic & Molecular Physics > Senior Lecturer, > =E2=80=8BDepartment of Physics, > Faculty of Science, > The University of Ngaoundere, Cameroon. > P.O. BOX 454 Ngaoundere > Private: P.O. BOX 547 Ngaoundere > Phone number: +972 54 3656845 /+972 55 8961001/ +237 75 21 61 39 > > -------------------------------------------------------------------------= ---------------------------------------- > > --047d7b3430d0b0fe8905017b5605 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I used the SMD model in Gaussian.


On Tue, Aug 26, 2014 at 12:13 AM= , Jean Jules Fifen julesfifen[*]gmail.com = <owner-chemistry^_^ccl.net> wrote:
What model di= d you use to compute the solvated free energy of the proton in THF?


On Mon, Aug 25, 2014 at 9:23= PM, BUSRA DERELI bsradereli++gmail.com <owner-chemistry^ccl.net> wrote:

Sent to CCL by: "BUSRA=C2=A0 DERELI" [bsradereli::gmail.com]
Hello,

I am trying to calculate pKa values of two systems, one is anionic and the<= br> other is cationic copper systems. I got so weird numbers not close to the experimental values when I computed the free energy of proton in THF which = is
the solvent of interest. I use M11-L local functional with SDD basis set on= Cu
atom and 6-31G(d) on all other atoms in the system. Thus, I want to compare= the
computed solvation free energy of proton in THF with the experimental value= . In
some literature reports, I have seen absolute solvation free energy of prot= on
in a couple of solvents but not in THF.

Thanks,
Busra Dereli



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY^ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEMISTRY-REQUEST^ccl.net or use

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

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

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=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

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--
---------------= ------------------------------------------------------------<= br> Jean Jules FIFEN,
Ph.D. in= Atomic & Molecular Physics
Senior Lecturer,
=
=E2= =80=8BDepartment of Physics,
<= span style=3D"font-family:courier new,monospace">Faculty of Science,
The= University of Ngaoundere, Cameroon.
P.O. BOX 454 Ngaou= ndere
Private: P.O. BOX 547 Ngaoundere
Phone= number: +972 54 3656845 /<= a href=3D"tel:%2B972%2055%208961001" value=3D"+972558961001" target=3D"_bla= nk">+972 55 8961001/ +237 75 21 61 39 =
---= ---------------------------------------------------------------------------= -----------------------------------
=C2=A0

--047d7b3430d0b0fe8905017b5605--