From owner-chemistry@ccl.net Tue Jan 7 09:38:01 2014 From: "Close, David M. CLOSED%a%mail.etsu.edu" To: CCL Subject: CCL: SCF energy Message-Id: <-49520-140107093655-24399-O1mvq+UlTIgkTjwM3LR7Ow%x%server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 7 Jan 2014 14:36:44 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED^^^mail.etsu.edu] I'm not sure if I can answer your question with the information provided. The difference in energy you provided is roughly the energy of a proton. You don 't tell us the molecule you are studying. All you say is "two different structure in acidic or neutral conditions"? What is the difference is these structures? Has one structure lost a proton? If so, how are you accounting for this in making the comparison between the two structures? Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu^^^ccl.net [mailto:owner-chemistry+closed==etsu.edu^^^ccl.net] On Behalf Of mahnaz gh mahnaz271163%a%yahoo.com Sent: Monday, January 06, 2014 2:11 PM To: Close, David M. Subject: CCL: SCF energy Sent to CCL by: "mahnaz gh" [mahnaz271163 _ yahoo.com] hi there I have a molecule which have two different structure in acidic or neutral conditions. In order to determine which of them is the more stable structure, I used the SCF done term, the values is as follows: SCF done 1 = -1330.29275098 and SCF done 2 = -1330.76227822. Could you please help me and tell which of them is the more stable one and is the difference enough to distinguish between the structures? Regardshttp://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 Jan 7 11:09:00 2014 From: "partha kundu partha1kundu%gmail.com" To: CCL Subject: CCL:G: SCF energy Message-Id: <-49521-140107105802-26269-in8UpaX1aKOTbTmdl7tGDw-*-server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary=bcaec52bf0c984ae7e04ef6354cc Date: Tue, 7 Jan 2014 21:19:24 +0530 MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu^gmail.com] --bcaec52bf0c984ae7e04ef6354cc Content-Type: text/plain; charset=ISO-8859-1 Dear Dave Close, Since its an electronic energy calculation, the energy of a proton should be zero, right? I also had a similar question and got the answer from Gaussian help. Regards. Partha On Tue, Jan 7, 2014 at 8:06 PM, Close, David M. CLOSED%a%mail.etsu.edu < owner-chemistry[-]ccl.net> wrote: > > Sent to CCL by: "Close, David M." [CLOSED^^^mail.etsu.edu] > I'm not sure if I can answer your question with the information > provided. The difference in energy you provided is roughly the energy of a > proton. You don 't tell us the molecule you are studying. All you say is > "two different structure in acidic or neutral conditions"? What is the > difference is these structures? Has one structure lost a proton? If so, > how are you accounting for this in making the comparison between the two > structures? > Regards, Dave Close. > > -----Original Message----- > > From: owner-chemistry+closed==etsu.edu*_*ccl.net [mailto: > owner-chemistry+closed==etsu.edu*_*ccl.net] On Behalf Of mahnaz gh > mahnaz271163%a%yahoo.com > Sent: Monday, January 06, 2014 2:11 PM > To: Close, David M. > Subject: CCL: SCF energy > > > Sent to CCL by: "mahnaz gh" [mahnaz271163 _ yahoo.com] hi there I have a > molecule which have two different structure in acidic or neutral > conditions. In order to determine which of them is the more stable > structure, I used the SCF done term, the values is as follows: SCF done 1 = > -1330.29275098 and SCF done 2 = -1330.76227822. Could you please help me > and tell which of them is the more stable one and is the difference enough > to distinguish between the structures? > Regardshttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > --bcaec52bf0c984ae7e04ef6354cc Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Dave Close,
Since its an electroni= c energy calculation, the energy of a proton should be zero, right? I also = had a similar question and got the answer from Gaussian help.
Rega= rds.

Partha

On T= ue, Jan 7, 2014 at 8:06 PM, Close, David M. CLOSED%a%mail.etsu.edu <owner-chemistry[-]ccl.net>= wrote:

Sent to CCL by: "Close, David M." [CLOSED^^^mail.etsu.edu]
=A0 I'm not sure if I can answer your question with the information pro= vided. =A0The difference in energy you provided is roughly the energy of a = proton. You don 't tell us the molecule you are studying. =A0All you sa= y is "two different structure in acidic or neutral conditions"? = =A0What is the difference is these structures? =A0Has one structure lost a = proton? If so, how are you accounting for this in making the comparison bet= ween the two structures?
=A0 Regards, Dave Close.

-----Original Message-----
> From: owner-chemistry+closed=3D=3Detsu.edu*_*ccl= .net [mailto:owner-chemistr= y+closed=3D=3Detsu.edu*_*ccl.net] On Behalf Of = mahnaz gh mahnaz271163%a%yah= oo.com
Sent: Monday, January 06, 2014 2:11 PM
To: Close, David M.
Subject: CCL: SCF energy


Sent to CCL by: "mahnaz =A0gh" [mahnaz271163 _ yahoo.com] hi there I have a molecule whic= h have two different structure in acidic or neutral conditions. In order to= determine which of them is the more stable structure, I used the SCF done = term, the values is as follows: SCF done 1 =3D -1330.29275098 and SCF done = 2 =3D -1330.76227822. Could you please help me and tell which of them is th= e more stable one and is the difference enough to distinguish between the s= tructures?
Regardshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net= /chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


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

E-mail to administrators: CHEM= ISTRY-REQUEST[-]ccl.net or use
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.shtml

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/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0 h= ttp://www.ccl.net/spammers.txt

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



--bcaec52bf0c984ae7e04ef6354cc-- From owner-chemistry@ccl.net Tue Jan 7 11:58:00 2014 From: "Susi Lehtola susi.lehtola- -alumni.helsinki.fi" To: CCL Subject: CCL:G: SCF energy Message-Id: <-49522-140107115412-16701-ZDfCGHKfKMaFXEGddkFELQ_._server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Tue, 7 Jan 2014 18:54:00 +0200 Mime-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola_+_alumni.helsinki.fi] On Mon, 6 Jan 2014 14:11:00 -0500 "mahnaz gh mahnaz271163%a%yahoo.com" wrote: > hi there > I have a molecule which have two different structure in acidic or neutral conditions. In order to determine which of them is the more stable structure, I used the SCF done term, the values is as follows: SCF done 1 = -1330.29275098 and SCF done 2 = -1330.76227822. Could you please help me and tell which of them is the more stable one and is the difference enough to distinguish between the structures? > Regards First of all, the electronic energy doesn't define the stability of a molecule by itself. You also have to take into account the zero point energy for the nuclei. Second, also the thermodynamics can play a part. The minimum might not be defined by the least energy (or enthalpy), but by the largest entropy. http://goldbook.iupac.org/S05900.html On Tue, 7 Jan 2014 21:19:24 +0530 "partha kundu partha1kundu%gmail.com" wrote: > Dear Dave Close, > Since its an electronic energy calculation, the energy of a proton should > be zero, right? I also had a similar question and got the answer from > Gaussian help. > Regards. No. The electronic energy of a gas-phase hydrogen atom is -1/2 Hartrees. Here the difference between the two systems was -0.46953 which is pretty close to that. -- --------------------------------------------------------------- Mr. Susi Lehtola, PhD Research Associate susi.lehtola..alumni.helsinki.fi Department of Applied Physics http://www.helsinki.fi/~jzlehtol Aalto University Finland --------------------------------------------------------------- Susi Lehtola, FT Tutkijatohtori susi.lehtola..alumni.helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Aalto-yliopisto --------------------------------------------------------------- From owner-chemistry@ccl.net Tue Jan 7 12:32:00 2014 From: "Brian Skinn brian.skinn a gmail.com" To: CCL Subject: CCL:G: SCF energy Message-Id: <-49523-140107120631-25661-d+ZdTwaTG3lMTXB8NZdTZg%server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=047d7b5dae360c4f3704ef64650e Date: Tue, 7 Jan 2014 12:05:57 -0500 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [brian.skinn(~)gmail.com] --047d7b5dae360c4f3704ef64650e Content-Type: text/plain; charset=ISO-8859-1 Partha, No, the energy of the proton is not zero -- if nothing else, it contributes some additional nuclear-nuclear repulsion to the total energy. It also provides a center onto which some electron density can shift, which will influence the calculated energy -- perhaps negligibly, perhaps not. Are you performing your simulations on the isolated structures, or with surrounding solvent molecules? In the gas phase, or with a PCM/COSMO solvation model? The question, "which structure is more stable?" means different things in different situations, and getting a good answer to the question you're interested in depends critically on running the proper simulations. Best regards, Brian On Tue, Jan 7, 2014 at 10:49 AM, partha kundu partha1kundu%gmail.com < owner-chemistry+/-ccl.net> wrote: > Dear Dave Close, > Since its an electronic energy calculation, the energy of a proton should > be zero, right? I also had a similar question and got the answer from > Gaussian help. > Regards. > > Partha > > On Tue, Jan 7, 2014 at 8:06 PM, Close, David M. CLOSED%a%mail.etsu.edu < > owner-chemistry__ccl.net> wrote: > >> >> Sent to CCL by: "Close, David M." [CLOSED^^^mail.etsu.edu] >> I'm not sure if I can answer your question with the information >> provided. The difference in energy you provided is roughly the energy of a >> proton. You don 't tell us the molecule you are studying. All you say is >> "two different structure in acidic or neutral conditions"? What is the >> difference is these structures? Has one structure lost a proton? If so, >> how are you accounting for this in making the comparison between the two >> structures? >> Regards, Dave Close. >> >> -----Original Message----- >> > From: owner-chemistry+closed==etsu.edu*_*ccl.net [mailto: >> owner-chemistry+closed==etsu.edu*_*ccl.net] On Behalf Of mahnaz gh >> mahnaz271163%a%yahoo.com >> Sent: Monday, January 06, 2014 2:11 PM >> To: Close, David M. >> Subject: CCL: SCF energy >> >> >> Sent to CCL by: "mahnaz gh" [mahnaz271163 _ yahoo.com] hi there I have >> a molecule which have two different structure in acidic or neutral >> conditions. In order to determine which of them is the more stable >> structure, I used the SCF done term, the values is as follows: SCF done 1 = >> -1330.29275098 and SCF done 2 = -1330.76227822. Could you please help me >> and tell which of them is the more stable one and is the difference enough >> to distinguish between the structures? >> Regardshttp:// >> www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>> E-mail to subscribers: CHEMISTRY__ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST__ccl.net or use>> >> >> > --047d7b5dae360c4f3704ef64650e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Partha,

No, the energy of the = proton is not zero -- if nothing else, it contributes some additional nucle= ar-nuclear repulsion to the total energy.=A0 It also provides a center onto= which some electron density can shift, which will influence the calculated= energy -- perhaps negligibly, perhaps not.

Are you performing your simulations on the isolated structures, o= r with surrounding solvent molecules?=A0 In the gas phase, or with a PCM/CO= SMO solvation model?=A0 The question, "which structure is more stable?= " means different things in different situations, and getting a good a= nswer to the question you're interested in depends critically on runnin= g the proper simulations.


Best regards,
Brian



On Tue, Jan 7, 2014 at 10:49 AM, parth= a kundu partha1kundu%gmail.com <o= wner-chemistry+/-ccl.net> wrote:
Dear Dave Close,<= br>
Since its an electronic energy calculation, the energy of a proton= should be zero, right? I also had a similar question and got the answer fr= om Gaussian help.
Regards.

Partha

On T= ue, Jan 7, 2014 at 8:06 PM, Close, David M. CLOSED%a%mail.etsu.edu <owner-chemistry__cc= l.net> wrote:

Sent to CCL by: "Close, David M." [CLOSED^^^mail.etsu.edu]
=A0 I'm not sure if I can answer your question with the information pro= vided. =A0The difference in energy you provided is roughly the energy of a = proton. You don 't tell us the molecule you are studying. =A0All you sa= y is "two different structure in acidic or neutral conditions"? = =A0What is the difference is these structures? =A0Has one structure lost a = proton? If so, how are you accounting for this in making the comparison bet= ween the two structures?
=A0 Regards, Dave Close.

-----Original Message-----
> From: owner-chemistry+closed=3D=3Detsu.edu*_*ccl= .net [mailto:owner-chemistry+closed=3D=3Detsu.edu*_*ccl.net<= /a>] On Behalf Of mahnaz gh mahnaz271163%a%yahoo.com
Sent: Monday, January 06, 2014 2:11 PM
To: Close, David M.
Subject: CCL: SCF energy


Sent to CCL by: "mahnaz =A0gh" [mahnaz271163 _ yahoo.com] hi there I have a molecule whic= h have two different structure in acidic or neutral conditions. In order to= determine which of them is the more stable structure, I used the SCF done = term, the values is as follows: SCF done 1 =3D -1330.29275098 and SCF done = 2 =3D -1330.76227822. Could you please help me and tell which of them is th= e more stable one and is the difference enough to distinguish between the s= tructures?
Regardshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net= /chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


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

E-mail to administrators: CHEMISTRY-REQUEST__ccl.net or use
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.shtml

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/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0 h= ttp://www.ccl.net/spammers.txt

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




--047d7b5dae360c4f3704ef64650e-- From owner-chemistry@ccl.net Tue Jan 7 13:07:00 2014 From: "Hao-Bo Guo guohaobo-,-gmail.com" To: CCL Subject: CCL:G: SCF energy Message-Id: <-49524-140107123015-11408-sZ0aopmznGkSL1n5yRqRYg_-_server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/alternative; boundary=bcaec52160c946e1a404ef64ba75 Date: Tue, 7 Jan 2014 12:30:07 -0500 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo::gmail.com] --bcaec52160c946e1a404ef64ba75 Content-Type: text/plain; charset=ISO-8859-1 Hi Partha, What you need to take into account is the solvation enthalpy (free energy) of different species (HA, A(-) and H(+)), and with corrections to standard state etc. From your data, the dE value of -294 kcal/mol seems reasonable with contributions for proton hydration (~-270 kcal/mol) and the counterion A(-). There are tons of papers on this issue. If you don't mind could check this one: J. Chem. Theory Comput. 2013, 9, 555. Hao-Bo On Tue, Jan 7, 2014 at 10:49 AM, partha kundu partha1kundu%gmail.com < owner-chemistry[#]ccl.net> wrote: > Dear Dave Close, > Since its an electronic energy calculation, the energy of a proton should > be zero, right? I also had a similar question and got the answer from > Gaussian help. > Regards. > > Partha > > On Tue, Jan 7, 2014 at 8:06 PM, Close, David M. CLOSED%a%mail.etsu.edu < > owner-chemistry__ccl.net> wrote: > >> >> Sent to CCL by: "Close, David M." [CLOSED^^^mail.etsu.edu] >> I'm not sure if I can answer your question with the information >> provided. The difference in energy you provided is roughly the energy of a >> proton. You don 't tell us the molecule you are studying. All you say is >> "two different structure in acidic or neutral conditions"? What is the >> difference is these structures? Has one structure lost a proton? If so, >> how are you accounting for this in making the comparison between the two >> structures? >> Regards, Dave Close. >> >> -----Original Message----- >> > From: owner-chemistry+closed==etsu.edu*_*ccl.net [mailto: >> owner-chemistry+closed==etsu.edu*_*ccl.net] On Behalf Of mahnaz gh >> mahnaz271163%a%yahoo.com >> Sent: Monday, January 06, 2014 2:11 PM >> To: Close, David M. >> Subject: CCL: SCF energy >> >> >> Sent to CCL by: "mahnaz gh" [mahnaz271163 _ yahoo.com] hi there I have >> a molecule which have two different structure in acidic or neutral >> conditions. In order to determine which of them is the more stable >> structure, I used the SCF done term, the values is as follows: SCF done 1 = >> -1330.29275098 and SCF done 2 = -1330.76227822. Could you please help me >> and tell which of them is the more stable one and is the difference enough >> to distinguish between the structures? >> Regardshttp:// >> www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>> E-mail to subscribers: CHEMISTRY__ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST__ccl.net or use>> >> >> > --bcaec52160c946e1a404ef64ba75 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Partha,
What you need to take into a= ccount is the solvation enthalpy (free energy) of different species (HA, A(= -) and H(+)), and with corrections to standard state etc. From your data, t= he dE value of -294 kcal/mol seems reasonable with contributions for proton= hydration (~-270 kcal/mol) and the counterion A(-).
There are tons of papers on this issue. If you don't mind co= uld check this one: J. Chem. Theory Comput. 2013, 9, 555.
Hao-Bo


On Tu= e, Jan 7, 2014 at 10:49 AM, partha kundu partha1kundu%gmail.com <owner-chemistry[#]ccl.net> wrote:=
Dear Dave Close,<= br>
Since its an electronic energy calculation, the energy of a proton= should be zero, right? I also had a similar question and got the answer fr= om Gaussian help.
Regards.

Partha

On T= ue, Jan 7, 2014 at 8:06 PM, Close, David M. CLOSED%a%mail.etsu.edu <owner-chemistry__cc= l.net> wrote:

Sent to CCL by: "Close, David M." [CLOSED^^^mail.etsu.edu]
=A0 I'm not sure if I can answer your question with the information pro= vided. =A0The difference in energy you provided is roughly the energy of a = proton. You don 't tell us the molecule you are studying. =A0All you sa= y is "two different structure in acidic or neutral conditions"? = =A0What is the difference is these structures? =A0Has one structure lost a = proton? If so, how are you accounting for this in making the comparison bet= ween the two structures?
=A0 Regards, Dave Close.

-----Original Message-----
> From: owner-chemistry+closed=3D=3Detsu.edu*_*ccl= .net [mailto:owner-chemistry+closed=3D=3Detsu.edu*_*ccl.net<= /a>] On Behalf Of mahnaz gh mahnaz271163%a%yahoo.com
Sent: Monday, January 06, 2014 2:11 PM
To: Close, David M.
Subject: CCL: SCF energy


Sent to CCL by: "mahnaz =A0gh" [mahnaz271163 _ yahoo.com] hi there I have a molecule whic= h have two different structure in acidic or neutral conditions. In order to= determine which of them is the more stable structure, I used the SCF done = term, the values is as follows: SCF done 1 =3D -1330.29275098 and SCF done = 2 =3D -1330.76227822. Could you please help me and tell which of them is th= e more stable one and is the difference enough to distinguish between the s= tructures?
Regardshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net= /chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


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

E-mail to administrators: CHEMISTRY-REQUEST__ccl.net or use
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.shtml

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/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0 h= ttp://www.ccl.net/spammers.txt

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




--bcaec52160c946e1a404ef64ba75--