CCH is an overlay journal that identifies the most= important papers in computational and theoretical chemistry published in t= he last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists.&nbs= p;You can read more about it here.

Table of content for this issue features contr= ibutions from CCH editors David Bowler, Robert Paton and Steven Bachrach:

=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D= -=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D
Jan H. Jensen <= /span>Professor
Department of Chemistry jhjensen#,#chem.ku.dk **NEW*= *
University of Copenhagen Phone: +45 35 32 02 39
Universitetsparken 5 FAX: +45 35 32 02 14
2100 Copenhagen= Denmark
http://tinyurl.com/jhjensen
= http://molecularmodelingbasics.blogspot.com
http://proteinsandwavefunctions.blogspot.com/ <= br> http://compchemhighlights.org: A new kind of chemistry journal
=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D= -=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D

= --_000_C7750A7E669C4CA29ED089A524588103kudk_-- From owner-chemistry@ccl.net Thu May 1 12:28:00 2014 From: "Adam Tenderholt atenderholt[#]gmail.com" To: CCL Subject: CCL:G: cclib v1.2 released Message-Id: <-49968-140501112817-22669-643ytHOW4tC3a6kk8RD7ag#,#server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=90e6ba47673319bbfa04f85850f2 Date: Thu, 1 May 2014 08:27:51 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt * gmail.com] --90e6ba47673319bbfa04f85850f2 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable On behalf of the cclib development team, I am pleased to announce the release of cclib 1.2, which is now available for download from https://github.com/cclib/cclib/releases/tag/v1.2 and http://cclib.github.io. This version marks the first stable release to target Python 3, and includes several new features and bug fixes (see below). cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, Firefly, GAMESS (US), GAMESS-UK, Gaussian, Jaguar, Molpro and ORCA. Among other data, cclib extracts: * coordinates and energies * information about geometry optimization * atomic orbital information * molecular orbital information * information on vibrational modes * the results of a TD-DFT calculation (For a complete list see http://cclib.github.io/data.html). cclib also provides some calculation methods for interpreting the electronic properties of molecules using analyses such as: * Mulliken and Lowdin population analyses * Overlap population analysis * Calculation of Mayer's bond orders. (For a complete list see http://cclib.github.io/methods.html). For information on how to use cclib, see http://cclib.github.io/tutorial.html If you need help, find a bug, want new features or have any questions, please send an email to our mailing list: https://lists.sourceforge.net/lists/listinfo/cclib-users If your published work uses cclib, please support its development by citing the following article: N. M. O'Boyle, A. L. Tenderholt, K. M. Langner, cclib: a library for package-independent computational chemistry algorithms, J. Comp. Chem. 29 (5), 839-845 (2008) Regards, The cclib development team =E2=80=94=E2=80=94- Major changes since cclib 1.1: * Move project to github * Transition to Python 3 (Python 2.7 will still work) * Add a multifile mode to ccget script * Extract vibrational displacements for ORCA * Extract natural atom charges for Gaussian (Fedor Zhuravlev) * Updated test file versions to ADF2013.01, GAMESS-US 2012, Gaussian09, Molpro 2012 and ORCA 3.0.1 * Many bugfixes, thanks to Scott McKechnie, Tamilmani S, Melchor Sanchez, Clyde Fare, Julien Id=C3=A9 and Andrew Warden --90e6ba47673319bbfa04f85850f2 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

On behalf of the cclib development team, I am pleased =
to announce the release of cclib 1.2, which is now available for download f=
rom=C2=A0http=
s://github.com/cclib/cclib/releases/tag/v1.2 and http://cclib.github.io. This version marks the first s=
table release to target Python 3, and includes several new features and bug=
 fixes (see below).


cclib is an open source library, written in Python, for parsing and interpr=
eting the results of computational chemistry packages. It currently parses =
output files from ADF, Firefly, GAMESS (US), GAMESS-UK, Gaussian, Jaguar, M=
olpro and ORCA.

Among other data, cclib extracts:

    * coordinates and energies
    * information about geometry optimization
    * atomic orbital information
    * molecular orbital information
    * information on vibrational modes
    * the results of a TD-DFT calculation=20

(For a complete list see http:=
//cclib.github.io/data.html).

cclib also provides some calculation methods for interpreting the electroni=
c properties of molecules using analyses such as:

    * Mulliken and Lowdin population analyses
    * Overlap population analysis
    * Calculation of Mayer's bond orders.=20

(For a complete list see ht=
tp://cclib.github.io/methods.html).

For information on how to use cclib, see
      http://cclib.github.=
io/tutorial.html

If you need help, find a bug, want new features or have any questions, plea=
se send an email to our mailing list:
	https=
://lists.sourceforge.net/lists/listinfo/cclib-users

If your published work uses cclib, please support its development by citing=
 the following article:
    N. M. O'Boyle, A. L. Tenderholt, K. M. Langner, cclib: a library fo=
r package-independent computational chemistry algorithms, J. Comp. Chem. 29=
 (5), 839-845 (2008)

Regards,

 The cclib development team

=E2=80=94=E2=80=94-

Major changes since cclib 1.1:

    * Move project to github
    * Transition to Python 3 (Python 2.7 will still work)
    * Add a multifile mode to ccget script
    * Extract vibrational displacements for ORCA
    * Extract natural atom charges for Gaussian (Fedor Zhuravlev)
    * Updated test file versions to ADF2013.01, GAMESS-US 2012, Gaussian09,=
 Molpro 2012 and ORCA 3.0.1
    * Many bugfixes, thanks to Scott McKechnie, Tamilmani S, Melchor Sanche=
z, Clyde Fare, Julien Id=C3=A9 and Andrew Warden

--90e6ba47673319bbfa04f85850f2-- From owner-chemistry@ccl.net Thu May 1 15:10:01 2014 From: "Kathrin Helen Hopmann kathrin.hopmann(a)uit.no" To: CCL Subject: CCL: Standard state conversions Message-Id: <-49969-140501145323-18409-SESJElj9hfEjHMejwvoi2A|server.ccl.net> X-Original-From: "Kathrin Helen Hopmann" Date: Thu, 1 May 2014 14:53:21 -0400 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*o*uit.no From owner-chemistry@ccl.net Thu May 1 18:15:00 2014 From: "Christopher Cramer cramer]-[umn.edu" To: CCL Subject: CCL: Standard state conversions Message-Id: <-49970-140501181305-12778-GsHsO4tbpoyhlrEOqGZcxw%a%server.ccl.net> X-Original-From: Christopher Cramer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Thu, 1 May 2014 17:12:58 -0500 Mime-Version: 1.0 (Mac OS X Mail 7.2 \(1874\)) Sent to CCL by: Christopher Cramer [cramer#,#umn.edu] Kathrin, It is conventional to tabulate thermodynamic quantities with gases taken to be at a 1 bar standard state pressure and solutes at a 1 M standard state concentration, but there are many, many exceptions to be found in the literature, so in general one should simply be extremely careful to be specific about what one is doing (and about what one is comparing to). You�ve summarized the 1 bar �> 1 M free energy change nicely. Note that another key wrinkle is when one of the species in solution is buffered to a concentration other than 1 M (in which case the standard-state tabulation typically employs the buffer concentration � this is often true for electrochemical reactions that generate or consume ions, for example). And, there is the case where one of the solutes is also the SOLVENT (e.g., water is 55.6 M in water, not 1 M). The standard-state symbol can sometimes seem ambiguous, and ALWAYS merits close scrutiny with respect to its meaning. With apologies to Lewis Carroll, one should approach it bearing in mind: "When I use a [standard-state symbol]," Humpty Dumpty said, in rather a scornful tone, "it means just what I choose it to mean�neither more nor less.� Best regards, Chris On May 1, 2014, at 13:53, 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> > -- 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 Thu May 1 23:23:00 2014 From: "tarzan p tarzan11_11..yahoo.com" To: CCL Subject: CCL: Name of authors during review ...!!! Message-Id: <-49971-140501231902-12204-I7FamLqNVrMKDXxvZSjveg|,|server.ccl.net> X-Original-From: "tarzan p" Date: Thu, 1 May 2014 23:19:01 -0400 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 ....