From owner-chemistry@ccl.net Sat Apr 30 03:11:00 2011 From: "Sue Lam chsue2004 a yahoo.com" To: CCL Subject: CCL:G: implicit solvation Message-Id: <-44499-110430030809-9435-WFClny3615vpaWI5NX71kg_+_server.ccl.net> X-Original-From: Sue Lam Content-Type: multipart/alternative; boundary="0-1778243014-1304147277=:28494" Date: Sat, 30 Apr 2011 00:07:57 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004**yahoo.com] --0-1778243014-1304147277=:28494 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Servaas, =A0 For the point 2, do you think we could also do the solvent=A0field calculat= ion (single point), on the basis of the gas-phase optimized structure to ge= t the solvent correction? =A0 Sue --- On Fri, 4/29/11, servaas servaas.michielssens**student.kuleuven.be wrote: > From: servaas servaas.michielssens**student.kuleuven.be Subject: CCL:G: implicit solvation To: "L, Sue " Date: Friday, April 29, 2011, 4:08 PM Sent to CCL by: servaas [servaas.michielssens[*]student.kuleuven.be] According to the procedure described in Comment on the correct use of continuum solvent models (J. Phys. Chem. A 2010, 114, 13442-13444). One should proceed as follows using gaussian 09: 1. Optimize structure in vacuum and do frequency analysis, from this one can find the free energy correction in the gas phase (dGcorr_gas) 2.Optimize the structure in solvent if you are using another solvent model than SMD I think you should add the keyword cav, dis and rep. The energy you get includes all corrections, also the non electrostatic ones. So this it is actually E_solv + Gnes from the above paper. 3. So to find the free energy in solvent one can simply add everything: dGcorr_gas + E_solv + Gnes. I hope that helps, Servaas On Thu, 2011-04-28 at 19:53 +0200, Arne Dieckmann adieckma[#]googlemail.com wrote: > Sent to CCL by: Arne Dieckmann [adieckma ~ googlemail.com] > Dear Dave, >=20 > I am aware of that. However, as I understand it frequency calculations sh= ould be done in vacuum as the equations are derived from an ideal gas assum= ption. >=A0 Am I wrong here? And what would be the energy I need to use from the P= CM calculation?=20 >=20 > Cheers, > Arne >=20 > On Apr 28, 2011, at 17:01, "Close, David M. CLOSED^mail.etsu.edu" wrote: >=20 > >=20 > > Sent to CCL by: "Close, David M." [CLOSED++mail.etsu.edu] > > Arne: > >=A0 You need to do a frequency calculation and then you will have all th= e thermodynamic parameters including the free energy, the zero-point energy= , etc. > >=A0 Regards, Dave Close > >=20 > > -----Original Message----- > >> From: owner-chemistry+closed=3D=3Detsu.edu(!)ccl.net [mailto:owner-che= mistry+closed=3D=3Detsu.edu(!)ccl.net] On Behalf Of Arne Dieckmann adieckma= ]_[googlemail.com > > Sent: Thursday, April 28, 2011 8:53 AM > > To: Close, David M. > > Subject: CCL:G: implicit solvation > >=20 > >=20 > > Sent to CCL by: "Arne Dieckmann" [adieckma---googlemail.com] > > Dear all,=20 > >=20 > > I am performing Gaussian calculations using implicit solvation (CPCM). = Afterwards, I would like to apply thermal corrections from gas phase calcul= ations to obtain free energy differences of certain molecules. The Gaussian= output contains several energy values when using implicit solvation, e.g. = "After PCM corrections, the SCF energy is=A0 -193.093761350" and "Total fre= e energy in solution with all non electrostatic terms". Which one would I u= se to add the correction for free energy?=20 > >=20 > >=20 > > Thanks in advance,=20 > > Arnehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/c= hemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>=20 > -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0--0-1778243014-1304147277=:28494 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable --0-1778243014-1304147277=:28494-- From owner-chemistry@ccl.net Sat Apr 30 11:11:01 2011 From: "Bhargav Trivedi bhargavatrivedi*|*gmail.com" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44500-110430062047-15339-p1QPwjrIrL314PrmQgs/GA_._server.ccl.net> X-Original-From: "Bhargav Trivedi" Date: Sat, 30 Apr 2011 06:20:45 -0400 Sent to CCL by: "Bhargav Trivedi" [bhargavatrivedi[-]gmail.com] Dear all, I would like to learn computational chemistry. Please tell me how can I prepare for it. I am an M Sc PhD with Physical chemistry & an academician since last 16 years. I teach thermodynamics and electrochemistry to under graduates. Thanks a lot: Dr. Bhargav Trivedi, Associate Professor of Chemistry, J & J College of science, Nadiad, Gujarat. India From owner-chemistry@ccl.net Sat Apr 30 11:49:00 2011 From: "John Merle jkmerle(0)yahoo.com" To: CCL Subject: CCL: peptides/amino acids and implicit solvation Message-Id: <-44501-110430114606-9808-P36v8uIzw+zOfOhsGsMwOw*_*server.ccl.net> X-Original-From: John Merle Content-Type: text/plain; charset=us-ascii Date: Sat, 30 Apr 2011 08:45:43 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: John Merle [jkmerle__yahoo.com] Is anyone aware of articles in the literature that describe methods of treating solvation for reactions of amino acids and peptides that have different gas phase and solution protonation states. I would like to calculate solvation free energies and enthalpies for these types of reactions. Thanks, John Merle From owner-chemistry@ccl.net Sat Apr 30 13:00:00 2011 From: "Arne Dieckmann adieckma[a]googlemail.com" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44502-110430124434-4586-mfsPZe4eJ7ug6tGqeFLgDQ|a|server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Sat, 30 Apr 2011 18:44:20 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Arne Dieckmann [adieckma]|[googlemail.com] I would suggest "Introduction to Computational Chemistry" by Jensen. It's a perfect book for beginners. Arne On Apr 30, 2011, at 12:20 PM, Bhargav Trivedi bhargavatrivedi*|*gmail.com wrote: > > Sent to CCL by: "Bhargav Trivedi" [bhargavatrivedi[-]gmail.com] > Dear all, > I would like to learn computational chemistry. Please tell me how can I prepare for it. > I am an M Sc PhD with Physical chemistry & an academician since last 16 years. I teach thermodynamics and electrochemistry to under graduates. > Thanks a lot: > Dr. Bhargav Trivedi, > Associate Professor of Chemistry, > J & J College of science, > Nadiad, Gujarat. > India> > From owner-chemistry@ccl.net Sat Apr 30 13:35:00 2011 From: "Deepangi Pandit deepangi.pandit\a/gmail.com" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44503-110430133053-8123-tvgWYgaXviiiv2ZuBR7q7g]^[server.ccl.net> X-Original-From: Deepangi Pandit Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 30 Apr 2011 13:30:43 -0400 MIME-Version: 1.0 Sent to CCL by: Deepangi Pandit [deepangi.pandit_-_gmail.com] Hi Bhargav: You can refer "Essentials of Computational Chemistry: Theories and Models" by Christopher J. Cramer http://kimia.unnes.ac.id/kasmui/textbooks/Essentials%20of%20Computational%20Chemistry%20Theories%20and%20Models%202d%20Ed%20-%20Christopher%20J.%20Cramer.pdf ShortURL http://alturl.com/jks5j Also please feel free to browse http://static.msi.umn.edu/tutorial/chemistryphysics/IntroCompChem.pdf I believe these are good starting points and based on your interests you can explore the topic/s further. Regards, Deepa On Sat, Apr 30, 2011 at 6:20 AM, Bhargav Trivedi bhargavatrivedi*|*gmail.com wrote: > > Sent to CCL by: "Bhargav  Trivedi" [bhargavatrivedi[-]gmail.com] > Dear all, > I would like to learn computational chemistry. Please tell me how can I prepare for it. > I am an M Sc PhD with Physical chemistry & an academician since last 16 years. I teach thermodynamics and electrochemistry to under graduates. > Thanks a lot: > Dr. Bhargav Trivedi, > Associate Professor of Chemistry, > J & J College of science, > Nadiad, Gujarat. > India>      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 Sat Apr 30 14:48:00 2011 From: "Christopher Cramer cramer+/-umn.edu" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44504-110430144641-17455-j4/kCW3ZZPy7I9aAJqu87w|server.ccl.net> X-Original-From: Christopher Cramer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Sat, 30 Apr 2011 13:46:27 -0500 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Christopher Cramer [cramer-$-umn.edu] My... The least you can do if you're going to steal the book, and post it online for piracy, is choose a later printing -- then people won't have to refer to so many errata. Now I recall why I've been reluctant to devote the time to a 3rd edition... CJC On Apr 30, 2011, at 12:30 PM, Deepangi Pandit deepangi.pandita/gmail.com wrote: > > Sent to CCL by: Deepangi Pandit [deepangi.pandit_-_gmail.com] > Hi Bhargav: > You can refer "Essentials of Computational Chemistry: Theories and > Models" by Christopher J. Cramer > > http://kimia.unnes.ac.id/kasmui/textbooks/Essentials%20of%20Computational%20Chemistry%20Theories%20and%20Models%202d%20Ed%20-%20Christopher%20J.%20Cramer.pdf > > ShortURL > > http://alturl.com/jks5j > > Also please feel free to browse > > http://static.msi.umn.edu/tutorial/chemistryphysics/IntroCompChem.pdf > > I believe these are good starting points and based on your interests > you can explore the topic/s further. > > Regards, > Deepa > > > > On Sat, Apr 30, 2011 at 6:20 AM, Bhargav Trivedi > bhargavatrivedi*|*gmail.com wrote: >> >> Sent to CCL by: "Bhargav Trivedi" [bhargavatrivedi[-]gmail.com] >> Dear all, >> I would like to learn computational chemistry. Please tell me how can I prepare for it. >> I am an M Sc PhD with Physical chemistry & an academician since last 16 years. I teach thermodynamics and electrochemistry to under graduates. >> Thanks a lot: >> Dr. Bhargav Trivedi, >> Associate Professor of Chemistry, >> J & J College of science, >> Nadiad, Gujarat. >> India> > -- Christopher J. Cramer Elmore H. Northey Professor University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-7541 Mobile: (952) 297-2575 email: cramer : umn.edu jabber: cramer : jabber.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") From owner-chemistry@ccl.net Sat Apr 30 15:42:01 2011 From: "Nuno A. G. Bandeira nuno.bandeira _ ist.utl.pt" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44505-110430153352-26105-9AT4PsOJrUiMZ+GN6gms0A * server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 30 Apr 2011 21:33:26 +0200 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira,ist.utl.pt] Best introduction I ever read was Donald McQuarrie's Quantum Chemistry. It's recently been re-edited. Have a look http://www.amazon.com/gp/product/1891389505/ref=pd_lpo_k2_dp_sr_1?pf_rd_p=1278548962&pf_rd_s=lpo-top-stripe-1&pf_rd_t=201&pf_rd_i=093570213X&pf_rd_m=ATVPDKIKX0DER&pf_rd_r=1TBT0W97693DN023PQNB -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN -- From owner-chemistry@ccl.net Sat Apr 30 22:26:00 2011 From: "David A Mannock dmannock(-)ualberta.ca" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44506-110430171326-9912-jsbe+4iVfhSRyLv9GQKmvw-*-server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=20cf3071cd26547c0b04a2294263 Date: Sat, 30 Apr 2011 15:13:16 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock(~)ualberta.ca] --20cf3071cd26547c0b04a2294263 Content-Type: text/plain; charset=ISO-8859-1 Chris, as a newbie to computational chemistry, I try to use every resource that I can get hold of. I have to admit that I sometimes pirate electronic copies to help me search texts which are often long and complicated. A recent point relevant to this issue is Jacob Israelachvili's "Intermolecular and surface forces", 2nd Edn. As our lab copy disappeared into a black hole known as my colleagues basement, I found a pirated online copy of this essential text. I later bought a second-hand hard copy, while awaiting the appearance of the 3rd Edition, which was due to appear in 2010, but came out in 2011. I have read the 1991 2nd edition cover to cover and have returned to it in order to refresh my memory many times. After talking to Jacob Israelachvili, he explained the delays in getting the 3rd edition to press and told me when it would be available. Within a week of it coming off the presses, I had bought a copy from Amazon out of my own pocket. The new edition is several hundred pages longer than the previous copy and an electronic version would be useful to me. It is a beautifully written masterpiece in my opinion. However, many publishers are slow in their move into the electronic realm. This is where the future lies. My job ends here on June 30th, 2011, but I still have responsibilities for writing up papers for a student. I will not have access to online library facilities here because of local University policy. Despite this, I would still be willing to buy a new edition of your book to help with my calculations on my Linux box. I would do this out of my own pocket if need be. As I see it, one of the main purposes of text books is to put all of the knowledge in a certain area in one place for ease of reference. I think that this is very valuable for those of us who do research and those who teach. Putting together a new edition of your book would be recognized as a valuable contribution by people in this scientific area, but rather than be pessimistic about piracy, ask your publishers to make an electronic copy available for sale at 50% of the price of the softcover. A university could either buy a yearly site license for distribution to students at a lower price, or the institution could host a copy which could be read online, but not downloaded. There will always be people who want to get something for nothing and who are willing to remove the encryption on electronic media, the simplest solution is to make the text available at a lower cost for academic use and make some money rather than none. You should be talking to your publisher about this policy, as it will help their bottom line and your standard of living in your retirement!! So cheer up and realize that old dogs, like myself, would rather sit on a sun lounger on my back porch reading your new edition, than sitting at a computer screen in the lab or in my study! David Mannock On Sat, Apr 30, 2011 at 12:46 PM, Christopher Cramer cramer+/-umn.edu < owner-chemistry*_*ccl.net> wrote: > > Sent to CCL by: Christopher Cramer [cramer-$-umn.edu] > My... > > The least you can do if you're going to steal the book, and post it online > for piracy, is choose a later printing -- then people won't have to refer to > so many errata. > > Now I recall why I've been reluctant to devote the time to a 3rd edition... > > CJC > > On Apr 30, 2011, at 12:30 PM, Deepangi Pandit deepangi.pandita/gmail.comwrote: > > > > > Sent to CCL by: Deepangi Pandit [deepangi.pandit_-_gmail.com] > > Hi Bhargav: > > You can refer "Essentials of Computational Chemistry: Theories and > > Models" by Christopher J. Cramer > > > > > http://kimia.unnes.ac.id/kasmui/textbooks/Essentials%20of%20Computational%20Chemistry%20Theories%20and%20Models%202d%20Ed%20-%20Christopher%20J.%20Cramer.pdf > > > > ShortURL > > > > http://alturl.com/jks5j > > > > Also please feel free to browse > > > > http://static.msi.umn.edu/tutorial/chemistryphysics/IntroCompChem.pdf > > > > I believe these are good starting points and based on your interests > > you can explore the topic/s further. > > > > Regards, > > Deepa > > > > > > > > On Sat, Apr 30, 2011 at 6:20 AM, Bhargav Trivedi > > bhargavatrivedi*|*gmail.com wrote: > >> > >> Sent to CCL by: "Bhargav Trivedi" [bhargavatrivedi[-]gmail.com] > >> Dear all, > >> I would like to learn computational chemistry. Please tell me how can I > prepare for it. > >> I am an M Sc PhD with Physical chemistry & an academician since last 16 > years. I teach thermodynamics and electrochemistry to under graduates. > >> Thanks a lot: > >> Dr. Bhargav Trivedi, > >> Associate Professor of Chemistry, > >> J & J College of science, > >> Nadiad, Gujarat. > >> India> > > > > -- > > Christopher J. Cramer > Elmore H. Northey Professor > University of Minnesota > Department of Chemistry > 207 Pleasant St. SE > Minneapolis, MN 55455-0431 > -------------------------- > Phone: (612) 624-0859 || FAX: (612) 626-7541 > Mobile: (952) 297-2575 > email: cramer,+,umn.edu > jabber: cramer,+,jabber.umn.edu > http://pollux.chem.umn.edu/~cramer > (website includes information about the textbook "Essentials > of Computational Chemistry: Theories and Models, 2nd Edition")> > > --20cf3071cd26547c0b04a2294263 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Chris, as a newbie to computational chemistry, I try to use every resource = that I can get hold of. I have to admit that I sometimes pirate electronic = copies to help me search texts which are often long and complicated. A rece= nt point relevant to this issue is Jacob Israelachvili's "Intermol= ecular and surface forces", 2nd Edn. As our lab copy disappeared into = a black hole known as my colleagues basement, I found a pirated online copy= of this essential text. I later bought a second-hand hard copy, while awai= ting the appearance of the 3rd Edition, which was due to appear in 2010, bu= t came out in 2011. I have read the 1991 2nd edition cover to cover and hav= e returned to it in order to refresh my memory many times. After talking to= Jacob Israelachvili, he explained the delays in getting the 3rd edition to= press and told me when it would be available. Within a week of it coming o= ff the presses, I had bought a copy from Amazon out of my own pocket. The n= ew edition is several hundred pages longer than the previous copy and an el= ectronic version would be useful to me. It is a beautifully written masterp= iece in my opinion. However, many publishers are slow in their move into th= e electronic realm. This is where the future lies.

My job ends here on June 30th, 2011, but I still have responsibilities = for writing up papers for a student. I will not have access to online libra= ry facilities here because of local University policy. Despite this, I woul= d still be willing to buy a new edition of your book to help with my calcul= ations on my Linux box. I would do this out of my own pocket if need be.
As I see it, one of the main purposes of text books is to put all of th= e knowledge in a certain area in one place for ease of reference. I think t= hat this is very valuable for those of us who do research and those who tea= ch. Putting together a new edition of your book would be recognized as a va= luable contribution by people in this scientific area, but rather than be p= essimistic about piracy, ask your publishers to make an electronic copy ava= ilable for sale at 50% of the price of the softcover. A university could ei= ther buy a yearly site license for distribution to students at a lower pric= e, or the institution could host a copy which could be read online, but not= downloaded. There will always be people who want to get something for noth= ing and who are willing to remove the encryption on electronic media, the s= implest solution is to make the text available at a lower cost for academic= use and make some money rather than none. You should be talking to your pu= blisher about this policy, as it will help their bottom line and your stand= ard of living in your retirement!! So cheer up and realize that old dogs, l= ike myself, would rather sit on a sun lounger on my back porch reading your= new edition, than sitting at a computer screen in the lab or in my study! = David Mannock=A0

On Sat, Apr 30, 2011 at 12:46 PM, Christophe= r Cramer cramer+/-umn.edu = <owner-chemistry*_*ccl.net&= gt; wrote:

Sent to CCL by: Christopher Cramer [cramer-$-umn.edu]
My...

The least you can do if you're going to steal the book, and post it onl= ine for piracy, is choose a later printing -- then people won't have to= refer to so many errata.

Now I recall why I've been reluctant to devote the time to a 3rd editio= n...

CJC

On Apr 30, 2011, at 12:30 PM, Deepangi Pandit deepangi.pandita/gmail.com wrote:

>
> Sent to CCL by: Deepangi Pandit [deepangi.pandit_-_gmail.com]
> Hi Bhargav:
> You can refer "Essentials of Computational Chemistry: Theories an= d
> Models" by Christopher J. Cramer
>
> http://kimia.unnes.ac.id/kasmui/= textbooks/Essentials%20of%20Computational%20Chemistry%20Theories%20and%20Mo= dels%202d%20Ed%20-%20Christopher%20J.%20Cramer.pdf
>
> ShortURL
>
> http://alturl.co= m/jks5j
>
> Also please feel free to browse
>
> http://static.msi.umn.edu/tutorial/chemistryp= hysics/IntroCompChem.pdf
>
> I believe these are good starting points and based on your interests > you can explore the topic/s further.
>
> Regards,
> Deepa
>
>
>
> On Sat, Apr 30, 2011 at 6:20 AM, Bhargav Trivedi
> bhargavatrivedi*|*gmail= .com <owner-chemistry~!~ccl.net> wrote:
>>
>> Sent to CCL by: "Bhargav =A0Trivedi" [bhargavatrivedi[-]= gmail.com]
>> Dear all,
>> I would like to learn computational chemistry. Please tell me how = can I prepare for it.
>> I am an M Sc PhD with Physical chemistry & an academician sinc= e last 16 years. I teach thermodynamics and electrochemistry to under gradu= ates.
>> Thanks a lot:
>> Dr. Bhargav Trivedi,
>> Associate Professor of Chemistry,
>> J & J College of science,
>> Nadiad, Gujarat.
>> India>
>

--

Christopher J. Cramer
Elmore H. Northey Professor
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
--------------------------
Phone: =A0(612)= 624-0859 || FAX: =A0(612) 626-7541
Mobile: (952) 2= 97-2575
email: =A0cramer,+,umn.edu=
jabber: =A0cramer,+,jab= ber.umn.edu
http://p= ollux.chem.umn.edu/~cramer
(website includes information about the textbook "Essentials
=A0 =A0of Computational Chemistry: =A0Theories and Models, 2nd Edition&quo= t;)



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--20cf3071cd26547c0b04a2294263-- From owner-chemistry@ccl.net Sat Apr 30 23:24:00 2011 From: "Deepangi Pandit deepangi.pandit[-]gmail.com" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44507-110430232309-20573-qL9bYlEteyel55xJT5pyDw(-)server.ccl.net> X-Original-From: Deepangi Pandit Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 30 Apr 2011 23:22:28 -0400 MIME-Version: 1.0 Sent to CCL by: Deepangi Pandit [deepangi.pandit a gmail.com] I am not sure if you have already looked at the CCL link on the same topic. It is good to get an overview. http://www.ccl.net/cca/documents/dyoung/topics-orig/compchem.html DP On Sat, Apr 30, 2011 at 12:44 PM, Arne Dieckmann adieckma[a]googlemail.com wrote: > > Sent to CCL by: Arne Dieckmann [adieckma]|[googlemail.com] > I would suggest "Introduction to Computational Chemistry" by Jensen. It's a perfect book for beginners. > > Arne > > On Apr 30, 2011, at 12:20 PM, Bhargav Trivedi bhargavatrivedi*|*gmail.com wrote: > >> >> Sent to CCL by: "Bhargav  Trivedi" [bhargavatrivedi[-]gmail.com] >> Dear all, >> I would like to learn computational chemistry. Please tell me how can I prepare for it. >> I am an M Sc PhD with Physical chemistry & an academician since last 16 years. I teach thermodynamics and electrochemistry to under graduates. >> Thanks a lot: >> Dr. Bhargav Trivedi, >> Associate Professor of Chemistry, >> J & J College of science, >> Nadiad, Gujarat. >> India>      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> > >
Hi Servaas,
 
For the point 2, do you think we could also do the solvent field = calculation (single point), on the basis of the gas-phase optimized structu= re to get the solvent correction?
 
Sue


--- On Fri, 4/29/11, servaas servaas.michielssens**s= tudent.kuleuven.be <owner-chemistry^-^ccl.net> wrote:

From: servaas servaas.michielssens**student.kuleu= ven.be <owner-chemistry^-^ccl.net>
Subject: CCL:G: implicit solvatio= n
To: "L, Sue " <chsue2004^-^yahoo.com>
Date: Friday, Apr= il 29, 2011, 4:08 PM


Sent to CCL by: servaas [servaas.michielssens[*]= student.kuleuven.be]
According to the procedure described in Comment on = the correct use of
continuum solvent models (J. Phys. Chem. A 2010, 114,= 13442-13444). One
should proceed as follows using gaussian 09:
1. Op= timize structure in vacuum and do frequency analysis, from this one
can = find the free energy correction in the gas phase (dGcorr_gas)
2.Optimize= the structure in solvent if you are using another solvent
model than SM= D I think you should add the keyword cav, dis and rep. The
energy you ge= t includes all corrections, also the non electrostatic
ones. So this it = is actually E_solv + Gnes from the above paper.
3. So to find the free e= nergy in solvent one can simply add everything:
dGcorr_gas + E_solv + Gn= es.


I hope that helps,

Servaas

On Thu, 2011-04-28 = at 19:53 +0200, Arne Dieckmann
adieckma[#]googlemail.com wrote:
> Sent to CCL by: Arne Dieckmann [adieckma ~ googlemail.com]<= BR>> Dear Dave,
>
> I am aware of that. However, as I under= stand it frequency calculations should be done in vacuum as the equations a= re derived from an ideal gas assumption.

>  Am I wrong here?= And what would be the energy I need to use from the PCM calculation?
&= gt;
> Cheers,
> Arne
>
> On Apr 28, 2011, at 17:0= 1, "Close, David M. CLOSED^mail.etsu.edu" <owner-chemistry/./ccl.net>= wrote:
>
> >
> > Sent to CCL by: "Close, David M= ." [CLOSED++mail.etsu.edu]
> > Arne:
> >  You need t= o do a frequency calculation and then you will have all the thermodynamic p= arameters including the free energy, the zero-point energy, etc.
> &g= t;  Regards, Dave Close
> >
> > -----Original Messa= ge-----
> >> From: owner-chemistry+closed=3D=3Detsu.edu(!)ccl.net [mailto:owner-chemistry+clo= sed=3D=3Detsu.edu(!)ccl.net] On Behalf Of Arne Dieckmann adieckma]_[googlem= ail.com
> > Sent: Thursday, April 28, 2011 8:53 AM
> > To= : Close, David M.
> > Subject: CCL:G: implicit solvation
> &= gt;
> >
> > Sent to CCL by: "Arne Dieckmann" [adieckma-= --googlemail.com]
> > Dear all,
> >
> > I am p= erforming Gaussian calculations using implicit solvation (CPCM). Afterwards= , I would like to apply thermal corrections from gas phase calculations to = obtain free energy differences of certain molecules. The Gaussian output co= ntains several energy values when using implicit solvation, e.g. "After PCM= corrections, the SCF energy is  -193.093761350" and "Total free energ= y in solution with all non electrostatic terms". Which one would I use to a= dd the correction for free energy?
> >
> >
> >= ; Thanks in advance,
> > Arnehttp://www.ccl.net/cgi-bin/ccl/send_= ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/s= pammers.txt>
>



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