From owner-chemistry@ccl.net Fri May 2 01:01:00 2014 From: "alain.borel+*+epfl.ch" To: CCL Subject: CCL: Name of authors during review ...!!! Message-Id: <-49972-140502005928-14167-zxcczLYp0krpCIk8gIodMg|-|server.ccl.net> X-Original-From: alain.borel:-:epfl.ch Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Fri, 02 May 2014 06:59:20 +0200 MIME-Version: 1.0 Sent to CCL by: alain.borel]^[epfl.ch "tarzan p tarzan11_11..yahoo.com" a écrit : > It is often(or probably always ...) that a submitted article to > journal goes for a peer review. Of course the reviewers are > confidential. Justified. > But why is that the reviewers get to know the names of the authors > and his affiliation during the review process ..? Unfair ...!!! > Will it not put a sort of bias into the reviewers head ...?? > Will it be not possible for the journal editors to adopt a policy of > non-disclosure of the authors till the work is accepted...? Some journals do: http://www.arj.no/2010/09/04/double-blind-peer-review/ http://www.nature.com/ngeo/journal/v6/n6/full/ngeo1853.html On the other hand, some other journals feel that the reviewers should not be kept secret and prefer a full disclosure policy: http://www.biomedcentral.com/authors/authorfaq/medical Both approaches (as well as the "usual" way) have their advantages and drawbacks, in my opinion. Alain Borel EPFL Library Rolex Learning Center Station 20 CH-1015 Lausanne Swizterland From owner-chemistry@ccl.net Fri May 2 01:35:00 2014 From: "Ambrish K Srivastava ambrishphysics() gmail.com" To: CCL Subject: CCL: Name of authors during review ...!!! Message-Id: <-49973-140502010217-14692-0uNEXa0hfSZNMb8oMTJlUA_-_server.ccl.net> X-Original-From: Ambrish K Srivastava Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 2 May 2014 10:32:11 +0530 MIME-Version: 1.0 Sent to CCL by: Ambrish K Srivastava [ambrishphysics=gmail.com] Dear Tarzan, I share your views on peer review policy and request journal editors to promote double-blinded peer review system instead of single-blinded one. Of course, it doesn't mean that one should not trust on single-blinded peer review, but due to extended collaborations and world wide scientific communications, it may introduce some kind of bias.. which is neither desired by editor nor acceptable by authors. Needless to say that researchers must be identified by their quality of work, not that their names/affiliations should suggest their work-quality. Thanks! On 5/2/14, tarzan p tarzan11_11..yahoo.com wrote: > > Sent to CCL by: "tarzan p" [tarzan11_11=-=yahoo.com] > Dear All........ > It is often(or probably always ...) that a submitted article to journal goes > for a peer review. Of course the reviewers are confidential. Justified. > But why is that the reviewers get to know the names of the authors and his > affiliation during the review process ..? Unfair ...!!! > Will it not put a sort of bias into the reviewers head ...?? > Will it be not possible for the journal editors to adopt a policy of > non-disclosure of the authors till the work is accepted...? > > I hope to get some views..... > with best wishes and happy computing ....> > > -- *Ambrish K. Srivastava CSIR Junior Research Fellow Department of Physics University of Lucknow Lucknow, India-226007* From owner-chemistry@ccl.net Fri May 2 08:36:00 2014 From: "torstein.fjermestad a unito.it" To: CCL Subject: CCL: [SPAM] CCL: Standard state conversions Message-Id: <-49974-140502082635-2648-Q5SjJ7Nj5VwV7lG80kgEOA]|[server.ccl.net> X-Original-From: torstein.fjermestad{=}unito.it Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Fri, 02 May 2014 14:26:12 +0200 MIME-Version: 1.0 Sent to CCL by: torstein.fjermestad:+:unito.it Dear Kathrin, This is the first time I answer a question to CCL so I hope I get it right. As far as I have understood, the standard state of a species is completely arbitrary. You can choose whatever you want. You just have to make sure that you specify the concentrations of the corresponding species in units of the chosen standard state. In your example A(g) + B(aq) -> C(aq) it would probably be most practical to choose 1 atm for A(g) and 1 M for B(aq) and C(aq). This is because the concentration of gases is usually given in atm while the concentration of dissolved species is usually given in M. However, it is completely arbitrary. You could for instance choose the standard state 2.248583 atm for A(g), 3.45 atm for B(aq) and 4.2345 M for C(aq). In that case make sure you specify the concentration of A(g) in units of 2.248583 atm, the concentration of B(aq) in units of 3.45 atm, and the concentration of C(aq) in units of 4.2345 M. To Prof. Cramer: please correct me if I am wrong. Regards, Torstein Fjermestad On 01.05.2014 20:53, Kathrin Helen Hopmann kathrin.hopmann(a)uit.no wrote: > Sent to CCL by: "Kathrin Helen Hopmann" [kathrin.hopmann[*]uit.no] > > Dear all, > I have a question regarding standard state conversion when computing > free energies. > As far as I understand, if I compute a free energy with e.g. DFT (in > gas phase or also using PCM), the energy will be a standard state > free > energy at 1 atm. If I wish to convert to a solution reaction, i.e. a > 1 > M standard state, a correction term has to be added to each species > amounting to +1.89 kcal/mol at 298 K. If the number of moles remains > the same during the reaction, this correction cancels out, but if I > have a reaction of the type: > A + B -> C > the correction term will not cancel out and the overall reaction > energy will in this case be lowered by 1.89 kcal/mol (compared to the > computed value). > > I have the following question: What if the reacting species have > different standard states? E.g. if A is a gas (such as H2) reacting > with B, which is dissolved in a solvent, to form complex C (also > dissolved): > A(g) + B(aq) -> C(aq) > If I compute the free energies for the species in this reaction with > DFT (all in 1 atm standard state) and I wish to do a standard state > conversion to obtain the free energy for this reaction in solution, > would the correction term of 1.89 kcal/mol be applied to A, the gas? > I appreciate your thoughts on this. > > best regards > Kathrin H. Hopmann > CTCC, University of Troms, Norway > kathrin.hopmann^uit.no > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ From owner-chemistry@ccl.net Fri May 2 11:19:00 2014 From: "Kathrin Helen Hopmann kathrin.hopmann!A!uit.no" To: CCL Subject: CCL: SPAM CCL: Standard state conversions Message-Id: <-49975-140502110832-10036-eJX8e3k/uaMacvxBZLCB/g===server.ccl.net> X-Original-From: "Kathrin Helen Hopmann" Date: Fri, 2 May 2014 11:08:31 -0400 Sent to CCL by: "Kathrin Helen Hopmann" [kathrin.hopmann(-)uit.no] Chris and Torstein - Thank you very much for your answers! I believe you are right, I can probably use any standard state, as long as I specify it clearly. However, the convention for solution reactions seems to be 1M standard state. I have seen at least one paper where the correction term for the conversion 1atm -> 1M seems to have been applied to H2 as well. I was wondering if it is correct to do so, but I assume it is, as long as one states it clearly. Something else that puzzles me is what to do about activation free energies (barriers). Would the correction also be applied to barriers? I have seen people do this, but I am unsure about it. Assume I compute this reaction: A(aq) + B(aq) -> [TS_A-B](aq) -> C(aq) + D(aq) Clearly, for the reaction free energy, the correction cancels out. But it would not for the TS (which is a complex of A and B). But should the correction at all be applied to the TS? A colleague of mine suggested that it would not be meaningful to do so ... but I am unsure. best regards Kathrin H. Hopmann University of Troms, CTCC, Norway kathrin.hopmann!^!uit.no > "torstein.fjermestad a unito.it" wrote: > > Sent to CCL by: torstein.fjermestad:+:unito.it > Dear Kathrin, > > This is the first time I answer a question to CCL so I hope I get it > right. > As far as I have understood, the standard state of a species is > completely arbitrary. You can choose whatever you want. You just have to > make sure that you specify the concentrations of the corresponding > species in units of the chosen standard state. In your example > > A(g) + B(aq) -> C(aq) > > it would probably be most practical to choose 1 atm for A(g) and 1 M > for B(aq) and C(aq). This is because the concentration of gases is > usually given in atm while the concentration of dissolved species is > usually given in M. However, it is completely arbitrary. You could for > instance choose the standard state 2.248583 atm for A(g), 3.45 atm for > B(aq) and 4.2345 M for C(aq). In that case make sure you specify the > concentration of A(g) in units of 2.248583 atm, the concentration of > B(aq) in units of 3.45 atm, and the concentration of C(aq) in units of > 4.2345 M. > > To Prof. Cramer: please correct me if I am wrong. > > Regards, > Torstein Fjermestad > > > On 01.05.2014 20:53, Kathrin Helen Hopmann kathrin.hopmann(a)uit.no > wrote: > > Sent to CCL by: "Kathrin Helen Hopmann" [kathrin.hopmann[*]uit.no] > > > > Dear all, > > I have a question regarding standard state conversion when computing > > free energies. > > As far as I understand, if I compute a free energy with e.g. DFT (in > > gas phase or also using PCM), the energy will be a standard state > > free > > energy at 1 atm. If I wish to convert to a solution reaction, i.e. a > > 1 > > M standard state, a correction term has to be added to each species > > amounting to +1.89 kcal/mol at 298 K. If the number of moles remains > > the same during the reaction, this correction cancels out, but if I > > have a reaction of the type: > > A + B -> C > > the correction term will not cancel out and the overall reaction > > energy will in this case be lowered by 1.89 kcal/mol (compared to the > > computed value). > > > > I have the following question: What if the reacting species have > > different standard states? E.g. if A is a gas (such as H2) reacting > > with B, which is dissolved in a solvent, to form complex C (also > > dissolved): > > A(g) + B(aq) -> C(aq) > > If I compute the free energies for the species in this reaction with > > DFT (all in 1 atm standard state) and I wish to do a standard state > > conversion to obtain the free energy for this reaction in solution, > > would the correction term of 1.89 kcal/mol be applied to A, the gas? > > I appreciate your thoughts on this. > > > > best regards > > Kathrin H. Hopmann > > CTCC, University of Troms, Norway > > kathrin.hopmann^uit.no > > > > > > > > -= This is automatically added to each message by the mailing script > > =- > > To recover the email address of the author of the message, please > > change> Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/ > From owner-chemistry@ccl.net Fri May 2 11:54:00 2014 From: "Jim Kress jimkress35]![gmail.com" To: CCL Subject: CCL: Name of authors during review ...!!! Message-Id: <-49976-140502112726-25603-smXrMjw04ds741Ap2/9UAw]=[server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 2 May 2014 11:27:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35=-=gmail.com] Why should the names of the reviewers be confidential? It is only reasonable, given the level of personal and professional antipathy present in todays "Science" that the authors of an article be allowed to see who reviewed their work. As we have seen exposed in the media, e.g. on the topic of "Global Warming", reviewers who object to your political views will ignore the scientific aspects of your work and deny publication, just on the basis of their personal animosity toward you and/or your politics. Authors should be allowed to ensure this type of nonscientific bias is not allowed to interfere with the publication of their scientific work. Jim Kress -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com[*]ccl.net [mailto:owner-chemistry+jimkress35==gmail.com[*]ccl.net] On Behalf Of tarzan p tarzan11_11..yahoo.com Sent: Thursday, May 01, 2014 11:19 PM To: Kress, Jim Subject: CCL: Name of authors during review ...!!! Sent to CCL by: "tarzan p" [tarzan11_11=-=yahoo.com] Dear All........ It is often(or probably always ...) that a submitted article to journal goes for a peer review. Of course the reviewers are confidential. Justified. But why is that the reviewers get to know the names of the authors and his affiliation during the review process ..? Unfair ...!!! Will it not put a sort of bias into the reviewers head ...?? Will it be not possible for the journal editors to adopt a policy of non-disclosure of the authors till the work is accepted...? I hope to get some views..... with best wishes and happy computing ....http://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 Fri May 2 12:56:00 2014 From: "Christopher Cramer cramer+*+umn.edu" To: CCL Subject: CCL: SPAM CCL: Standard state conversions Message-Id: <-49977-140502125433-2415-T08lkNJdpyCC7L2T68jD7A]~[server.ccl.net> X-Original-From: Christopher Cramer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Fri, 2 May 2014 11:54:11 -0500 Mime-Version: 1.0 (Mac OS X Mail 7.2 \(1874\)) Sent to CCL by: Christopher Cramer [cramer[-]umn.edu] Kathrin, Within the context of transition-state theory (TST), one most certainly MUST adopt a standard-state concentration convention for a TS structure (and 1 M would be typical for solution). After all, the fundamental development of TST is to consider the transition state (the “activated complex”) to be in equilibrium with the reactants. And, thus, it corresponds precisely to the A + B —> C case you already outlined below when you called C a “product”. Chris On May 2, 2014, at 10:08, Kathrin Helen Hopmann kathrin.hopmann!A!uit.no wrote: > > Sent to CCL by: "Kathrin Helen Hopmann" [kathrin.hopmann(-)uit.no] > > Chris and Torstein - Thank you very much for your answers! > > I believe you are right, I can probably use any standard state, as long as I specify it clearly. However, the convention for solution reactions seems to be 1M standard state. > I have seen at least one paper where the correction term for the conversion 1atm -> 1M seems to have been applied to H2 as well. I was wondering if it is correct to do so, but I assume it is, as long as one states it clearly. > > Something else that puzzles me is what to do about activation free energies (barriers). Would the correction also be applied to barriers? I have seen people do this, but I am unsure about it. Assume I compute this reaction: > > A(aq) + B(aq) -> [TS_A-B](aq) -> C(aq) + D(aq) > > Clearly, for the reaction free energy, the correction cancels out. But it would not for the TS (which is a complex of A and B). But should the correction at all be applied to the TS? A colleague of mine suggested that it would not be meaningful to do so ... but I am unsure. > > best regards > Kathrin H. Hopmann > University of Troms, CTCC, Norway > kathrin.hopmann^_^uit.no > > > > >> "torstein.fjermestad a unito.it" wrote: >> >> Sent to CCL by: torstein.fjermestad:+:unito.it >> Dear Kathrin, >> >> This is the first time I answer a question to CCL so I hope I get it >> right. >> As far as I have understood, the standard state of a species is >> completely arbitrary. You can choose whatever you want. You just have to >> make sure that you specify the concentrations of the corresponding >> species in units of the chosen standard state. In your example >> >> A(g) + B(aq) -> C(aq) >> >> it would probably be most practical to choose 1 atm for A(g) and 1 M >> for B(aq) and C(aq). This is because the concentration of gases is >> usually given in atm while the concentration of dissolved species is >> usually given in M. However, it is completely arbitrary. You could for >> instance choose the standard state 2.248583 atm for A(g), 3.45 atm for >> B(aq) and 4.2345 M for C(aq). In that case make sure you specify the >> concentration of A(g) in units of 2.248583 atm, the concentration of >> B(aq) in units of 3.45 atm, and the concentration of C(aq) in units of >> 4.2345 M. >> >> To Prof. Cramer: please correct me if I am wrong. >> >> Regards, >> Torstein Fjermestad >> >> >> On 01.05.2014 20:53, Kathrin Helen Hopmann kathrin.hopmann(a)uit.no >> wrote: >>> Sent to CCL by: "Kathrin Helen Hopmann" [kathrin.hopmann[*]uit.no] >>> >>> Dear all, >>> I have a question regarding standard state conversion when computing >>> free energies. >>> As far as I understand, if I compute a free energy with e.g. DFT (in >>> gas phase or also using PCM), the energy will be a standard state >>> free >>> energy at 1 atm. If I wish to convert to a solution reaction, i.e. a >>> 1 >>> M standard state, a correction term has to be added to each species >>> amounting to +1.89 kcal/mol at 298 K. If the number of moles remains >>> the same during the reaction, this correction cancels out, but if I >>> have a reaction of the type: >>> A + B -> C >>> the correction term will not cancel out and the overall reaction >>> energy will in this case be lowered by 1.89 kcal/mol (compared to the >>> computed value). >>> >>> I have the following question: What if the reacting species have >>> different standard states? E.g. if A is a gas (such as H2) reacting >>> with B, which is dissolved in a solvent, to form complex C (also >>> dissolved): >>> A(g) + B(aq) -> C(aq) >>> If I compute the free energies for the species in this reaction with >>> DFT (all in 1 atm standard state) and I wish to do a standard state >>> conversion to obtain the free energy for this reaction in solution, >>> would the correction term of 1.89 kcal/mol be applied to A, the gas? >>> I appreciate your thoughts on this. >>> >>> best regards >>> Kathrin H. Hopmann >>> CTCC, University of Troms, Norway >>> kathrin.hopmann^uit.no >>> >>> >>> >>> -= This is automatically added to each message by the mailing script >>> =- >>> To recover the email address of the author of the message, please >>> change> Conferences: >>> http://server.ccl.net/chemistry/announcements/conferences/> > -- Christopher J. Cramer Elmore H. Northey Professor and Associate Dean for Academic Affairs University of Minnesota Department of Chemistry and College of Science & Engineering Minneapolis, MN 55455-0431 Phone: (612) 624-0859 (Chemistry) Phone: (612) 624-9371 (CSE) -------------------------- Mobile: (952) 297-2575 Email: cramer|umn.edu Twitter: |ChemProfCramer Website: http://pollux.chem.umn.edu From owner-chemistry@ccl.net Fri May 2 13:30:00 2014 From: "Robert Molt r.molt.chemical.physics^^^gmail.com" To: CCL Subject: CCL: Name of authors during review ...!!! Message-Id: <-49978-140502131403-15306-pAWTHyMAzDDAJxvpFN522g:_:server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 02 May 2014 13:13:54 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics%x%gmail.com] The concept of "nonscientific bias" is a bit ill-defined. People who believe [A] is true, scientifically, believe they do so as a reflection of science, not politics. People who believe [not A] is true, scientifically, believe they do so as a reflection of science, not politics. At what point is it "bias" that a person is decidedly in one camp, vs. the person has analyzed the evidence and come to an "informed opinion?" Double-blind makes sense to me; judge the scientific evidence on its own merit, not biased by who writes it or judges it. Zero-blind also makes sense; let everyone have at one another in a public debate. I do not understand single-blind (why go halfway?). Dr. Robert Molt Jr., Ph.D. r.molt.chemical.physics**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 5/2/14 11:27 AM, Jim Kress jimkress35]![gmail.com wrote: > Sent to CCL by: "Jim Kress" [jimkress35=-=gmail.com] > Why should the names of the reviewers be confidential? It is only > reasonable, given the level of personal and professional antipathy present > in todays "Science" that the authors of an article be allowed to see who > reviewed their work. As we have seen exposed in the media, e.g. on the > topic of "Global Warming", reviewers who object to your political views will > ignore the scientific aspects of your work and deny publication, just on the > basis of their personal animosity toward you and/or your politics. > > Authors should be allowed to ensure this type of nonscientific bias is not > allowed to interfere with the publication of their scientific work. > > Jim Kress > > -----Original Message----- >> From: owner-chemistry+jimkress35==gmail.com(-)ccl.net > [mailto:owner-chemistry+jimkress35==gmail.com(-)ccl.net] On Behalf Of tarzan p > tarzan11_11..yahoo.com > Sent: Thursday, May 01, 2014 11:19 PM > To: Kress, Jim > Subject: CCL: Name of authors during review ...!!! > > > Sent to CCL by: "tarzan p" [tarzan11_11=-=yahoo.com] Dear All........ > It is often(or probably always ...) that a submitted article to journal goes > for a peer review. Of course the reviewers are confidential. Justified. > But why is that the reviewers get to know the names of the authors and his > affiliation during the review process ..? Unfair ...!!! > Will it not put a sort of bias into the reviewers head ...?? > Will it be not possible for the journal editors to adopt a policy of > non-disclosure of the authors till the work is accepted...? > > I hope to get some views..... > with best wishes and happy computing ....http://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 Fri May 2 14:05:00 2014 From: "Francois Berenger berenger]|[riken.jp" To: CCL Subject: CCL: Name of authors during review ...!!! Message-Id: <-49979-140502012204-22864-KIOz1CjwtzHKBtg7Z07rEw . server.ccl.net> X-Original-From: Francois Berenger Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 02 May 2014 14:21:50 +0900 MIME-Version: 1.0 Sent to CCL by: Francois Berenger [berenger+/-riken.jp] I heard some computer science conferences do this: submitted manuscripts are anonymized. On 05/02/2014 12:19 PM, tarzan p tarzan11_11..yahoo.com wrote: > Sent to CCL by: "tarzan p" [tarzan11_11=-=yahoo.com] > Dear All........ > It is often(or probably always ...) that a submitted article to journal goes for a peer review. Of course the reviewers are confidential. Justified. > But why is that the reviewers get to know the names of the authors and his affiliation during the review process ..? Unfair ...!!! > Will it not put a sort of bias into the reviewers head ...?? > Will it be not possible for the journal editors to adopt a policy of non-disclosure of the authors till the work is accepted...? > > I hope to get some views..... > with best wishes and happy computing ....> > -- Best regards, Francois Berenger. From owner-chemistry@ccl.net Fri May 2 14:40:00 2014 From: "berger!A!chem.helsinki.fi" To: CCL Subject: CCL: Name of authors during review ...!!! Message-Id: <-49980-140502042945-18542-+B9LyJaL94XpOt5f2i/kcQ . server.ccl.net> X-Original-From: berger%chem.helsinki.fi Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 2 May 2014 11:29:32 +0300 MIME-Version: 1.0 Sent to CCL by: berger:_:chem.helsinki.fi Dear all, with the years I made lots of experiences with single and double blind reveiewing. In my point of view both are bad. As a referee you should write respectful and high quality reviews. This is only warranted if xou haveto sign the comments with your good name and take take full personal reponsibility for the review. sincerily, Raphael J F Berger > Sent to CCL by: Ambrish K Srivastava [ambrishphysics=gmail.com] > Dear Tarzan, > I share your views on peer review policy and request journal editors > to promote double-blinded peer review system instead of single-blinded > one. Of course, it doesn't mean that one should not trust on > single-blinded peer review, but due to extended collaborations and > world wide scientific communications, it may introduce some kind of > bias.. which is neither desired by editor nor acceptable by authors. > Needless to say that researchers must be identified by their quality > of work, not that their names/affiliations should suggest their > work-quality. > > Thanks! > > On 5/2/14, tarzan p tarzan11_11..yahoo.com > wrote: >> >> Sent to CCL by: "tarzan p" [tarzan11_11=-=yahoo.com] >> Dear All........ >> It is often(or probably always ...) that a submitted article to journal >> goes >> for a peer review. Of course the reviewers are confidential. Justified. >> But why is that the reviewers get to know the names of the authors and >> his >> affiliation during the review process ..? Unfair ...!!! >> Will it not put a sort of bias into the reviewers head ...?? >> Will it be not possible for the journal editors to adopt a policy of >> non-disclosure of the authors till the work is accepted...? >> >> I hope to get some views..... >> with best wishes and happy computing ....> >> >> > > > -- > *Ambrish K. Srivastava > CSIR Junior Research Fellow > Department of Physics > University of Lucknow > Lucknow, India-226007*> > > From owner-chemistry@ccl.net Fri May 2 15:15:01 2014 From: "Fabio Cardenas fabiocarden{:}gmail.com" To: CCL Subject: CCL:G: Gaussian/Computer related question Message-Id: <-49981-140502062410-3625-ABhcrPLlDGtgWllI+8VTkA_+_server.ccl.net> X-Original-From: "Fabio Cardenas" Date: Fri, 2 May 2014 06:24:09 -0400 Sent to CCL by: "Fabio Cardenas" [fabiocarden++gmail.com] Dear CCL users, As member of a small community college I am very exited that we received Gaussian 09 and GV5 for Windows OS as a Donation. I have use the software in the past on a computer center and I find it very helpful for my research. However, I have never use the software to run directly on a Windows computer. Since the IT shop people in our department are not familiar with the software, I have few questions that I was hopping you could help me answer. Taking into account that the type of calculations we would run are on organic small molecules (ground states, Transition states, TDDFT and similar) and are not high performance computer demanding, we will probably use medium size level such b3lyp/6-31g(d,p), then the questions are: 1. If we buy a multicore processor (quad core for example) can the software use all cores without the installation of any extra software? 2. Are there any specifications on the computer hardware and software that you would recommend. From owner-chemistry@ccl.net Fri May 2 15:50:00 2014 From: "Michel Petitjean petitjean.chiral::gmail.com" To: CCL Subject: CCL: Name of authors during review ...!!! Message-Id: <-49982-140502140652-31899-zVUuSLa9REs/yTi0LdfGbA__server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=UTF-8 Date: Fri, 2 May 2014 20:06:22 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral() gmail.com] As a past editor-in-chief of two journals, please let me add a reason why anonymous review is useful. Often, authors are unhappy with reviews, and sometimes the editor is hassled by unhappy authors (fortunately, not often). It is part of the job of the editor to manage such situations (I did that). But imagine what could happen when a non anonymous reviewer is hassled by the author? You know, editors receive contributions from very diverse authors, not all fair, and even from sects (yes indeed). Remember that reviewers are volounteers and benevolent. If they should face to such authors, imagine the consequences, not only for the reviewers themselves, but for all the scientific community: would reviewers still accept to help? I agree that anonymous review can be criticized, but until now it has more advantages than drawbacks. About the double blind review, most time it is not useful, and this is discussed on the websites cited in a previous post. Nevertheless, possibly it could make sense for some maths journals, eventually as an author choice. May be that should be experienced. All my best, Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral|-|gmail.com (preferred), michel.petitjean|-|univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html 2014-05-02 17:27 GMT+02:00 Jim Kress jimkress35]![gmail.com : > > Sent to CCL by: "Jim Kress" [jimkress35=-=gmail.com] > Why should the names of the reviewers be confidential? It is only > reasonable, given the level of personal and professional antipathy present > in todays "Science" that the authors of an article be allowed to see who > reviewed their work. As we have seen exposed in the media, e.g. on the > topic of "Global Warming", reviewers who object to your political views will > ignore the scientific aspects of your work and deny publication, just on the > basis of their personal animosity toward you and/or your politics. > > Authors should be allowed to ensure this type of nonscientific bias is not > allowed to interfere with the publication of their scientific work. > > Jim Kress > > -----Original Message----- >> From: owner-chemistry+jimkress35==gmail.com(-)ccl.net > [mailto:owner-chemistry+jimkress35==gmail.com(-)ccl.net] On Behalf Of tarzan p > tarzan11_11..yahoo.com > Sent: Thursday, May 01, 2014 11:19 PM > To: Kress, Jim > Subject: CCL: Name of authors during review ...!!! > > > Sent to CCL by: "tarzan p" [tarzan11_11=-=yahoo.com] Dear All........ > It is often(or probably always ...) that a submitted article to journal goes > for a peer review. Of course the reviewers are confidential. Justified. > But why is that the reviewers get to know the names of the authors and his > affiliation during the review process ..? Unfair ...!!! > Will it not put a sort of bias into the reviewers head ...?? > Will it be not possible for the journal editors to adopt a policy of > non-disclosure of the authors till the work is accepted...? > > I hope to get some views..... > with best wishes and happy computing ....http://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 Fri May 2 16:25:00 2014 From: "Sebastian Kozuch seb.kozuch/a\gmail.com" To: CCL Subject: CCL: SPAM CCL: Standard state conversions Message-Id: <-49983-140502141342-6056-yD+7oyxVEEZHDKijaOImAg[A]server.ccl.net> X-Original-From: Sebastian Kozuch Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 02 May 2014 13:08:13 -0500 MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [seb.kozuch/./gmail.com] One important detail: You cannot use "any standard state". You can use any state you want as long as it is coherent. However, the concept of "standard state" was built for tabulating values, and therefore it must be unique, i.e. 1 atm for gases, 1 M for solutions, etc. If you want to use any other state, you can always use an extra term of the type of RT ln P or similar. Now, regarding H2, if it is in solution you must use 1 M as a standard state, as ridiculous as it sounds. But again, you can "theoretically change" its chemical potential by adding RT ln [H2], with a very low concentration. Please check any physical chemistry book for the details. Best, Sebastian On 5/2/2014 10:08 AM, Kathrin Helen Hopmann kathrin.hopmann!A!uit.no wrote: > Sent to CCL by: "Kathrin Helen Hopmann" [kathrin.hopmann(-)uit.no] > > Chris and Torstein - Thank you very much for your answers! > > I believe you are right, I can probably use any standard state, as long as I specify it clearly. However, the convention for solution reactions seems to be 1M standard state. > I have seen at least one paper where the correction term for the conversion 1atm -> 1M seems to have been applied to H2 as well. I was wondering if it is correct to do so, but I assume it is, as long as one states it clearly. > > Something else that puzzles me is what to do about activation free energies (barriers). Would the correction also be applied to barriers? I have seen people do this, but I am unsure about it. Assume I compute this reaction: > > A(aq) + B(aq) -> [TS_A-B](aq) -> C(aq) + D(aq) > > Clearly, for the reaction free energy, the correction cancels out. But it would not for the TS (which is a complex of A and B). But should the correction at all be applied to the TS? A colleague of mine suggested that it would not be meaningful to do so ... but I am unsure. > > best regards > Kathrin H. Hopmann > University of Troms, CTCC, Norway > kathrin.hopmann^_^uit.no > > > > >> "torstein.fjermestad a unito.it" wrote: >> >> Sent to CCL by: torstein.fjermestad:+:unito.it >> Dear Kathrin, >> >> This is the first time I answer a question to CCL so I hope I get it >> right. >> As far as I have understood, the standard state of a species is >> completely arbitrary. You can choose whatever you want. You just have to >> make sure that you specify the concentrations of the corresponding >> species in units of the chosen standard state. In your example >> >> A(g) + B(aq) -> C(aq) >> >> it would probably be most practical to choose 1 atm for A(g) and 1 M >> for B(aq) and C(aq). This is because the concentration of gases is >> usually given in atm while the concentration of dissolved species is >> usually given in M. However, it is completely arbitrary. You could for >> instance choose the standard state 2.248583 atm for A(g), 3.45 atm for >> B(aq) and 4.2345 M for C(aq). In that case make sure you specify the >> concentration of A(g) in units of 2.248583 atm, the concentration of >> B(aq) in units of 3.45 atm, and the concentration of C(aq) in units of >> 4.2345 M. >> >> To Prof. Cramer: please correct me if I am wrong. >> >> Regards, >> Torstein Fjermestad >> >> >> On 01.05.2014 20:53, Kathrin Helen Hopmann kathrin.hopmann(a)uit.no >> wrote: >>> Sent to CCL by: "Kathrin Helen Hopmann" [kathrin.hopmann[*]uit.no] >>> >>> Dear all, >>> I have a question regarding standard state conversion when computing >>> free energies. >>> As far as I understand, if I compute a free energy with e.g. DFT (in >>> gas phase or also using PCM), the energy will be a standard state >>> free >>> energy at 1 atm. If I wish to convert to a solution reaction, i.e. a >>> 1 >>> M standard state, a correction term has to be added to each species >>> amounting to +1.89 kcal/mol at 298 K. If the number of moles remains >>> the same during the reaction, this correction cancels out, but if I >>> have a reaction of the type: >>> A + B -> C >>> the correction term will not cancel out and the overall reaction >>> energy will in this case be lowered by 1.89 kcal/mol (compared to the >>> computed value). >>> >>> I have the following question: What if the reacting species have >>> different standard states? E.g. if A is a gas (such as H2) reacting >>> with B, which is dissolved in a solvent, to form complex C (also >>> dissolved): >>> A(g) + B(aq) -> C(aq) >>> If I compute the free energies for the species in this reaction with >>> DFT (all in 1 atm standard state) and I wish to do a standard state >>> conversion to obtain the free energy for this reaction in solution, >>> would the correction term of 1.89 kcal/mol be applied to A, the gas? >>> I appreciate your thoughts on this. >>> >>> best regards >>> Kathrin H. Hopmann >>> CTCC, University of Troms, Norway >>> kathrin.hopmann^uit.no >>> >>> >>> >>> -= This is automatically added to each message by the mailing script >>> =- >>> To recover the email address of the author of the message, please >>> change> Conferences: >>> http://server.ccl.net/chemistry/announcements/conferences/> > -- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ..........Sebastian Kozuch........... xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ......University of North Texas...... ..........Denton, Texas, USA......... ........ seb.kozuch[*]gmail.com ....... http://yfaat.ch.huji.ac.il/kozuch.htm xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx From owner-chemistry@ccl.net Fri May 2 17:00:00 2014 From: "Andreas Klamt klamt++cosmologic.de" To: CCL Subject: CCL: Name of authors during review ...!!! Message-Id: <-49984-140502161508-6865-Ei3E39QvJDuCFGkZrmOLdQ#%#server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 02 May 2014 22:15:04 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt : cosmologic.de] Trying to anonymize the submitted articles is hopeless: Being experts in the field many reviewers will immediately know who wrote the submitted manuscript. This leads nowhere. Basically I vote for double-open. Indeed, I often already wrote my name into a review, because the authors would anyway have identified me as reviewer. If I have good arguments to criticize or reject an article, I have no problem to stand to these. I need not be protected by anonymity. But the problem is that this system would reduce the number of reviewers to those who are sufficiently independent. And this minority will most likely be unable to stand the flood of manuscripts. Really a hopeless situation: I am afraid, that we will have to live with the current system. Regards Andreas Am 02.05.2014 07:21, schrieb Francois Berenger berenger]|[riken.jp: > > Sent to CCL by: Francois Berenger [berenger+/-riken.jp] > I heard some computer science conferences do this: > submitted manuscripts are anonymized. > > On 05/02/2014 12:19 PM, tarzan p tarzan11_11..yahoo.com wrote: >> Sent to CCL by: "tarzan p" [tarzan11_11=-=yahoo.com] >> Dear All........ >> It is often(or probably always ...) that a submitted article to >> journal goes for a peer review. Of course the reviewers are >> confidential. Justified. >> But why is that the reviewers get to know the names of the authors >> and his affiliation during the review process ..? Unfair ...!!! >> Will it not put a sort of bias into the reviewers head ...?? >> Will it be not possible for the journal editors to adopt a policy of >> non-disclosure of the authors till the work is accepted...? >> >> I hope to get some views..... >> with best wishes and happy computing ....> >> > > -- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt . cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt From owner-chemistry@ccl.net Fri May 2 21:45:00 2014 From: "Chang, Christopher Christopher.Chang.(a).nrel.gov" To: CCL Subject: CCL: Name of authors during review ...!!! Message-Id: <-49985-140502145746-1766-CyCsZSqo7KvyT5nC12+6BQ(a)server.ccl.net> X-Original-From: "Chang, Christopher" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 2 May 2014 12:57:05 -0600 MIME-Version: 1.0 Sent to CCL by: "Chang, Christopher" [Christopher.Chang:nrel.gov] A little devil's advocacy... I've certainly heard my share of prognostications of who-that-reviewer-was or who-that-author-is from PIs based on style and subject matter, with business conducted accordingly. I doubt double-blind would work ideally, based on the close-knit communities of scientists in narrow fields. Zero-blind has its own hazards of quid pro quo. I suspect much trust is laid at the feet of editors to make the appropriate judgments, given their knowledge of the field and who-dislikes-whom (or, whose-work). If authors feel a review is off-base, they respond to the editor accordingly. Ultimately, completely unfair single-blind reviews can't stand without tarnishing the editorial integrity of a journal, which I imagine editors are very careful to uphold. So, single-blind with editorial oversight doesn't sound so bad... -----Original Message----- > From: owner-chemistry+christopher.chang==nrel.gov() ccl.net [mailto:owner-chemistry+christopher.chang==nrel.gov() ccl.net] On Behalf Of Robert Molt r.molt.chemical.physics^^^gmail.com Sent: Friday, May 02, 2014 11:14 AM To: Chang, Christopher Subject: CCL: Name of authors during review ...!!! Sent to CCL by: Robert Molt [r.molt.chemical.physics%x%gmail.com] The concept of "nonscientific bias" is a bit ill-defined. People who believe [A] is true, scientifically, believe they do so as a reflection of science, not politics. People who believe [not A] is true, scientifically, believe they do so as a reflection of science, not politics. At what point is it "bias" that a person is decidedly in one camp, vs. the person has analyzed the evidence and come to an "informed opinion?" Double-blind makes sense to me; judge the scientific evidence on its own merit, not biased by who writes it or judges it. Zero-blind also makes sense; let everyone have at one another in a public debate. I do not understand single-blind (why go halfway?). Dr. Robert Molt Jr., Ph.D. r.molt.chemical.physics===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 5/2/14 11:27 AM, Jim Kress jimkress35]![gmail.com wrote: > Sent to CCL by: "Jim Kress" [jimkress35=-=gmail.com] Why should the > names of the reviewers be confidential? It is only reasonable, given > the level of personal and professional antipathy present in todays > "Science" that the authors of an article be allowed to see who > reviewed their work. As we have seen exposed in the media, e.g. on > the topic of "Global Warming", reviewers who object to your political > views will ignore the scientific aspects of your work and deny > publication, just on the basis of their personal animosity toward you and/or your politics. > > Authors should be allowed to ensure this type of nonscientific bias is > not allowed to interfere with the publication of their scientific work. > > Jim Kress > > -----Original Message----- >> From: owner-chemistry+jimkress35==gmail.com(-)ccl.net > [mailto:owner-chemistry+jimkress35==gmail.com(-)ccl.net] On Behalf Of > tarzan p tarzan11_11..yahoo.com > Sent: Thursday, May 01, 2014 11:19 PM > To: Kress, Jim > Subject: CCL: Name of authors during review ...!!! > > > Sent to CCL by: "tarzan p" [tarzan11_11=-=yahoo.com] Dear All........ > It is often(or probably always ...) that a submitted article to > journal goes for a peer review. Of course the reviewers are confidential. Justified. > But why is that the reviewers get to know the names of the authors and > his affiliation during the review process ..? Unfair ...!!! > Will it not put a sort of bias into the reviewers head ...?? > Will it be not possible for the journal editors to adopt a policy of > non-disclosure of the authors till the work is accepted...? > > I hope to get some views..... > with best wishes and happy computing > ....http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/ > chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://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 Fri May 2 22:20:00 2014 From: "Christopher Cramer cramer++umn.edu" To: CCL Subject: CCL: Name of authors during review ...!!! Message-Id: <-49986-140502201650-19470-TaEf+E5KojmGyT2IovWgDw:server.ccl.net> X-Original-From: Christopher Cramer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Fri, 2 May 2014 19:16:23 -0500 Mime-Version: 1.0 (Mac OS X Mail 7.2 \(1874\)) Sent to CCL by: Christopher Cramer [cramer]![umn.edu] Andreas and I have had occasion in the past to disagree — emphatically. So, it is a pleasure in this instance to AGREE with him — emphatically. Unless you can guarantee that power differentials will never exist between authors and reviewers, good luck with your double open system. Oops... you can NEVER guarantee that (I criticized your paper openly and then you got my grant proposal to review? uh oh…) And, of COURSE you can easily determine who WROTE the paper (if you’re remotely qualified to referee it). So double-blind is laughable. We editors choose multiple referees for a reason — we look for a consensus of opinions, not a single individual with a vendetta. Is it remotely possible that brilliant, unconventional work could be mowed down by an unlucky combination of reviewers? Sure. The perfect system does NOT exist. But, I would say that current peer review systems are like democracy — the worst of all possible choices, except for all the others… Chris On May 2, 2014, at 15:15, Andreas Klamt klamt++cosmologic.de wrote: > > Sent to CCL by: Andreas Klamt [klamt : cosmologic.de] > Trying to anonymize the submitted articles is hopeless: Being experts in the field many reviewers will immediately know who wrote the submitted manuscript. This leads nowhere. > > Basically I vote for double-open. Indeed, I often already wrote my name into a review, because the authors would anyway have identified me as reviewer. If I have good arguments to criticize or reject an article, I have no problem to stand to these. I need not be protected by anonymity. > > But the problem is that this system would reduce the number of reviewers to those who are sufficiently independent. And this minority will most likely be unable to stand the flood of manuscripts. > > Really a hopeless situation: I am afraid, that we will have to live with the current system. > > Regards > > Andreas > > Am 02.05.2014 07:21, schrieb Francois Berenger berenger]|[riken.jp: >> >> Sent to CCL by: Francois Berenger [berenger+/-riken.jp] >> I heard some computer science conferences do this: >> submitted manuscripts are anonymized. >> >> On 05/02/2014 12:19 PM, tarzan p tarzan11_11..yahoo.com wrote: >>> Sent to CCL by: "tarzan p" [tarzan11_11=-=yahoo.com] >>> Dear All........ >>> It is often(or probably always ...) that a submitted article to journal goes for a peer review. Of course the reviewers are confidential. Justified. >>> But why is that the reviewers get to know the names of the authors and his affiliation during the review process ..? Unfair ...!!! >>> Will it not put a sort of bias into the reviewers head ...?? >>> Will it be not possible for the journal editors to adopt a policy of non-disclosure of the authors till the work is accepted...? >>> >>> I hope to get some views..... >>> with best wishes and happy computing ....> >>> >> >> > > > -- > Prof. Dr. Andreas Klamt > CEO / Geschäftsführer > COSMOlogic GmbH & Co. KG > Imbacher Weg 46 > D-51379 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt-.-cosmologic.de > web www.cosmologic.de > > [University address: Inst. of Physical and > Theoretical Chemistry, University of Regensburg] > > HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamthttp://www.ccl.net/chemistry/sub_unsub.shtml> > -- Christopher J. Cramer Elmore H. Northey Professor and Associate Dean for Academic Affairs University of Minnesota Department of Chemistry and College of Science & Engineering Minneapolis, MN 55455-0431 Phone: (612) 624-0859 (Chemistry) Phone: (612) 624-9371 (CSE) -------------------------- Mobile: (952) 297-2575 Email: cramer * umn.edu Twitter: * ChemProfCramer Website: http://pollux.chem.umn.edu From owner-chemistry@ccl.net Fri May 2 22:55:00 2014 From: "Brian Skinn bskinn]_[alum.mit.edu" To: CCL Subject: CCL: SPAM CCL: Standard state conversions Message-Id: <-49987-140502215246-4449-3FGNnPUlwe5pwOlFssdnsQ .. server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=001a11c289be22ddc404f8752721 Date: Fri, 2 May 2014 21:52:18 -0400 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [bskinn*alum.mit.edu] --001a11c289be22ddc404f8752721 Content-Type: text/plain; charset=UTF-8 Kathrin, One subtlety to your question is the distinction between (a) conversion > from gas phase to aquated thermodynamic standard states; and (b) the real-world equilibrium between gas-phase and aquated species. Rarely in an actual system will a gas at 1 atm be in equilibrium with a 1 M aqueous solution of that dissolved gas (per Henry's Law), whereas thermodynamic standard states have the 'luxury' of ignoring such physical constraints. Best regards, Brian On Fri, May 2, 2014 at 11:08 AM, Kathrin Helen Hopmann kathrin.hopmann!A! uit.no wrote: > > Sent to CCL by: "Kathrin Helen Hopmann" [kathrin.hopmann(-)uit.no] > > Chris and Torstein - Thank you very much for your answers! > > I believe you are right, I can probably use any standard state, as long as > I specify it clearly. However, the convention for solution reactions seems > to be 1M standard state. > I have seen at least one paper where the correction term for the > conversion 1atm -> 1M seems to have been applied to H2 as well. I was > wondering if it is correct to do so, but I assume it is, as long as one > states it clearly. > > Something else that puzzles me is what to do about activation free > energies (barriers). Would the correction also be applied to barriers? I > have seen people do this, but I am unsure about it. Assume I compute this > reaction: > > A(aq) + B(aq) -> [TS_A-B](aq) -> C(aq) + D(aq) > > Clearly, for the reaction free energy, the correction cancels out. But it > would not for the TS (which is a complex of A and B). But should the > correction at all be applied to the TS? A colleague of mine suggested that > it would not be meaningful to do so ... but I am unsure. > > best regards > Kathrin H. Hopmann > University of Troms, CTCC, Norway > kathrin.hopmann^_^uit.no > > > > > > "torstein.fjermestad a unito.it" wrote: > > > > Sent to CCL by: torstein.fjermestad:+:unito.it > > Dear Kathrin, > > > > This is the first time I answer a question to CCL so I hope I get it > > right. > > As far as I have understood, the standard state of a species is > > completely arbitrary. You can choose whatever you want. You just have to > > make sure that you specify the concentrations of the corresponding > > species in units of the chosen standard state. In your example > > > > A(g) + B(aq) -> C(aq) > > > > it would probably be most practical to choose 1 atm for A(g) and 1 M > > for B(aq) and C(aq). This is because the concentration of gases is > > usually given in atm while the concentration of dissolved species is > > usually given in M. However, it is completely arbitrary. You could for > > instance choose the standard state 2.248583 atm for A(g), 3.45 atm for > > B(aq) and 4.2345 M for C(aq). In that case make sure you specify the > > concentration of A(g) in units of 2.248583 atm, the concentration of > > B(aq) in units of 3.45 atm, and the concentration of C(aq) in units of > > 4.2345 M. > > > > To Prof. Cramer: please correct me if I am wrong. > > > > Regards, > > Torstein Fjermestad > > > > > > On 01.05.2014 20:53, Kathrin Helen Hopmann kathrin.hopmann(a)uit.no > > wrote: > > > Sent to CCL by: "Kathrin Helen Hopmann" [kathrin.hopmann[*]uit.no] > > > > > > Dear all, > > > I have a question regarding standard state conversion when computing > > > free energies. > > > As far as I understand, if I compute a free energy with e.g. DFT (in > > > gas phase or also using PCM), the energy will be a standard state > > > free > > > energy at 1 atm. If I wish to convert to a solution reaction, i.e. a > > > 1 > > > M standard state, a correction term has to be added to each species > > > amounting to +1.89 kcal/mol at 298 K. If the number of moles remains > > > the same during the reaction, this correction cancels out, but if I > > > have a reaction of the type: > > > A + B -> C > > > the correction term will not cancel out and the overall reaction > > > energy will in this case be lowered by 1.89 kcal/mol (compared to the > > > computed value). > > > > > > I have the following question: What if the reacting species have > > > different standard states? E.g. if A is a gas (such as H2) reacting > > > with B, which is dissolved in a solvent, to form complex C (also > > > dissolved): > > > A(g) + B(aq) -> C(aq) > > > If I compute the free energies for the species in this reaction with > > > DFT (all in 1 atm standard state) and I wish to do a standard state > > > conversion to obtain the free energy for this reaction in solution, > > > would the correction term of 1.89 kcal/mol be applied to A, the gas? > > > I appreciate your thoughts on this. > > > > > > best regards > > > Kathrin H. Hopmann > > > CTCC, University of Troms, Norway > > > kathrin.hopmann^uit.no > > > > > > > > > > > > -= This is automatically added to each message by the mailing script > > > =- > > > To recover the email address of the author of the message, please > > > change> Conferences: > > > http://server.ccl.net/chemistry/announcements/conferences/> > > --001a11c289be22ddc404f8752721 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Kathrin,

One subtlety to your question = is the distinction between (a) conversion from gas phase to aquated thermod= ynamic standard states; and (b) the real-world equilibrium between gas-phas= e and aquated species. =C2=A0Rarely in an actual system will a gas at 1 atm= be in equilibrium with a 1 M aqueous solution of that dissolved gas (per H= enry's Law), whereas thermodynamic standard states have the 'luxury= ' of ignoring such physical constraints.

Best regards,
Brian



On Fri,= May 2, 2014 at 11:08 AM, Kathrin Helen Hopmann kathrin.hopmann!A!uit.no <owner-chemistry-.-ccl.net> wrote:

Sent to CCL by: "Kathrin =C2=A0Helen Hopmann" [kathrin.hopmann(-)= uit.no]

Chris and Torstein - Thank you very much for your answers!

I believe you are right, I can probably use any standard state, as long as = I specify it clearly. However, the convention for solution reactions seems = to be 1M standard state.
I have seen at least one paper where the correction term for the conversion= 1atm -> 1M seems to have been applied to H2 as well. I was wondering if= it is correct to do so, but I assume it is, as long as one states it clear= ly.

Something else that puzzles me is what to do about activation free energies= (barriers). Would the correction also be applied to barriers? I have seen = people do this, but I am unsure about it. Assume I compute this reaction:
A(aq) + B(aq) -> [TS_A-B](aq) -> C(aq) + D(aq)

Clearly, for the reaction free energy, the correction cancels out. But it w= ould not for the TS (which is a complex of A and B). But should the correct= ion at all be applied to the TS? A colleague of mine suggested that it woul= d not be meaningful to do so ... but I am unsure.

best regards
Kathrin H. Hopmann
University of Troms, CTCC, Norway
kathrin.hopmann^_^uit.no



> "torstein.fjermestad a unito.it" =C2=A0wrote:
>
> Sent to CCL by: torstein.fjermestad:+:unito.it
> Dear Kathrin,
>
> This is the first time I answer a question to CCL so I hope I get it > right.
> As far as I have understood, the standard state of a species is
> completely arbitrary. You can choose whatever you want. You just have = to
> make sure that you specify the concentrations of the corresponding
> species in units of the chosen standard state. In your example
>
> A(g) + B(aq) -> C(aq)
>
> it would probably be most practical to choose 1 atm for A(g) and 1 M > for B(aq) and C(aq). This is because the concentration of gases is
> usually given in atm while the concentration of dissolved species is > usually given in M. However, it is completely arbitrary. You could for=
> instance choose the standard state 2.248583 atm for A(g), 3.45 atm for=
> B(aq) and 4.2345 M for C(aq). In that case make sure you specify the > concentration of A(g) in units of 2.248583 atm, the concentration of > B(aq) in units of 3.45 atm, and the concentration of C(aq) in units of=
> 4.2345 M.
>
> To Prof. Cramer: please correct me if I am wrong.
>
> Regards,
> Torstein Fjermestad
>
>
> On 01.05.2014 20:53, Kathrin Helen Hopmann kathrin.hopmann(a)uit.no
> wrote:
> > Sent to CCL by: "Kathrin Helen =C2=A0Hopmann" [kathrin.= hopmann[*]uit.no]
> >
> > Dear all,
> > I have a question regarding standard state conversion when comput= ing
> > free energies.
> > As far as I understand, if I compute a free energy with e.g. DFT = (in
> > gas phase or also using PCM), the energy will be a standard state=
> > free
> > energy at 1 atm. If I wish to convert to a solution reaction, i.e= . a
> > 1
> > M standard state, a correction term has to be added to each speci= es
> > amounting to +1.89 kcal/mol at 298 K. If the number of moles rema= ins
> > the same during the reaction, this correction cancels out, but if= I
> > have a reaction of the type:
> > =C2=A0A + B -> C
> > the correction term will not cancel out and the overall reaction<= br> > > energy will in this case be lowered by 1.89 kcal/mol (compared to= the
> > computed value).
> >
> > I have the following question: =C2=A0What if the reacting species= have
> > different standard states? E.g. if A is a gas (such as H2) reacti= ng
> > with B, which is dissolved in a solvent, to form complex C (also<= br> > > dissolved):
> > A(g) + B(aq) -> C(aq)
> > If I compute the free energies for the species in this reaction w= ith
> > DFT (all in 1 atm standard state) and I wish to do a standard sta= te
> > conversion to obtain the free energy for this reaction in solutio= n,
> > would the correction term of 1.89 kcal/mol be applied to A, the g= as?
> > I appreciate your thoughts on this.
> >
> > best regards
> > Kathrin H. Hopmann
> > CTCC, University of Troms, Norway
> > kathrin.hopmann^uit.n= o
> >
> >
> >
> > -=3D This is automatically added to each message by the mailing s= cript
> > =3D-
> > To recover the email address of the author of the message, please=
> > change> Conferences:
> > http://server.ccl.net/chemistry/announcements/confe= rences/
>



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