From owner-chemistry@ccl.net Tue Sep 8 07:50:01 2015 From: "Sara Tortorella sara::chemiome.chm.unipg.it" To: CCL Subject: CCL:G: Electronic potential g09 output Message-Id: <-51672-150908063303-20745-UEV7XlG0nNEERBhDeWTEiQ[A]server.ccl.net> X-Original-From: "Sara Tortorella" Date: Tue, 8 Sep 2015 06:33:02 -0400 Sent to CCL by: "Sara Tortorella" [sara{}chemiome.chm.unipg.it] Hi everyone, I'm new to this forum (...and also to computational chemistry!), so I'm wondering if you could help me in clarifying the electrostatic properties section of gaussian 09 output. In particular, I'm performing B3LYP/6-31g* Pop=MK or Pop=CHelpG in order to obtain an estimation of atomic charges. Below you can see the output I get. The question is: how is the electric potential reported below the charges (from '1 Atom -14.652466' to the end) exactly calculated? It is the same I could get with the cubegen potential utility (but in different units)? Is it the potential the MK or CHelpG charges are trying to fit? Any references will be appreciated! Fitting point charges to electrostatic potential Charges from ESP fit, RMS= 0.00190 RRMS= 0.07922: Charge= 0.00000 Dipole= 3.5674 -6.6676 -2.0973 Tot= 7.8474 1 1 C -0.041036 2 C 0.100413 3 N 0.080397 4 C 0.104730 5 N -0.419796 6 C -0.228373 7 S -0.123685 8 C 0.369090 9 N -0.595642 10 C 0.472394 11 N -0.666989 12 C 0.639533 13 N -0.603091 14 H 0.419839 15 C 0.259744 16 N -0.485481 17 C 0.047084 18 N 0.863622 19 O -0.420014 20 O -0.442699 21 H 0.137993 22 H 0.113894 23 H 0.117979 24 H 0.094647 25 H 0.076982 26 H 0.128461 ----------------------------------------------------------------- Electrostatic Properties (Atomic Units) ----------------------------------------------------------------- Center Electric -------- Electric Field -------- Potential X Y Z ----------------------------------------------------------------- 1 Atom -14.652466 2 Atom -14.647722 3 Atom -18.250028 4 Atom -14.649824 5 Atom -18.341442 6 Atom -14.659441 7 Atom -59.145459 8 Atom -14.643023 9 Atom -18.341917 10 Atom -14.653606 11 Atom -18.337872 12 Atom -14.633363 13 Atom -18.255162 14 Atom -0.954134 15 Atom -14.632556 16 Atom -18.337428 17 Atom -14.679161 18 Atom -18.117945 19 Atom -22.308685 20 Atom -22.308127 21 Atom -1.047777 22 Atom -1.070324 23 Atom -1.061627 24 Atom -1.067950 25 Atom -1.092820 26 Atom -1.041033 ----------------------------------------------------------------- Thank you in advance for your precious help! Sara sara],[chemiome.chm.unipg.it From owner-chemistry@ccl.net Tue Sep 8 09:05:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor===fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: Electronic potential g09 output Message-Id: <-51673-150908090322-25106-g4o7he2DueXu++LGDBCL2w],[server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Tue, 08 Sep 2015 14:46:52 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor**fluor.quimica.uniovi.es] On Tue, Sep 08, 2015 at 06:33:02AM -0400, Sara Tortorella sara::chemiome.chm.unipg.it wrote: > > Sent to CCL by: "Sara Tortorella" [sara{}chemiome.chm.unipg.it] > Hi everyone, > I'm new to this forum (...and also to computational chemistry!), so I'm wondering if you could help me in clarifying the electrostatic properties section of gaussian 09 output. > In particular, I'm performing B3LYP/6-31g* Pop=MK or Pop=CHelpG in order to obtain an estimation of atomic charges. Below you can see the output I get. > The question is: how is the electric potential reported below the charges (from '1 Atom -14.652466' to the end) exactly calculated? It is the same I could get with the cubegen potential utility (but in different units)? Is it the potential the MK or CHelpG charges are trying to fit? > Any references will be appreciated! Sara, Obtaing the electrostatic potential from the charges is an awful approach. The electrostatic potencial is $ \int \frac{D(r') dr'}{\abs{r-r}} $ where D(r') is the total charge density (i.e. electronic plus nuclear). You can approach the potential by a multipolar dixtribution, but that includes terms from 0-poles (charges), 2-poles (dipoles), 4-poles, and all the collection of 2^L poles up to the desired accuracy. The cubegen utility provides you the Molecular electrostatic potential, and it is given in atomic units (electrons per cube bohr). That can be depicted with codes like vmd, and analyzed with tools like critic2. There are many others. The electron density and the EP are related through the Poisson equation, and solving it is another way for obtaing the EP. A book on the subject is book{QCB-MurraySen1996, editor = "Murray, J. S. and Sen, K.", title = "Molecular electrostatic potentials", serie = "Theoretical and computational chemistry", volume = 3, publisher = "Elsevier", pages = 661, isbn = "0444823530", } Peter Politzer and Jane S. Murray have been working on the molecular EP for *many* years. Best regards, Dr. Víctor Luaña -- . . "In science a person can be convinced by a good argument. / `' \ That is almost impossible in politics or religion" /(o)(o)\ (Adapted from Carl Sagan) /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero también es peor / '`'` \ que lo malo, porque la mediocridad no es un grado, es una | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 | |'`'`| | (Mediocre is worse than good, but it is also worse than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==================================+========================= ! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems, ! Departamento de Química Física y Analítica ! the urgent and the important. ! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important, ! e-mail: victor]_[fluor.quimica.uniovi.es ! and the important are never ! phone: +34-985-103491 fax: +34-985-103125 ! urgent. +--------------------------------------------+ (Dwight D. Eisenhower) GroupPage : http://azufre.quimica.uniovi.es/ From owner-chemistry@ccl.net Tue Sep 8 13:02:01 2015 From: "Ayyaz Mahmmod ayyazcmc^^gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51674-150908122936-28391-4PzlZAuaHsQwQECSAKDaxA[#]server.ccl.net> X-Original-From: Ayyaz Mahmmod Content-Type: multipart/alternative; boundary=f46d0445182fce73c6051f3edec6 Date: Tue, 8 Sep 2015 13:29:10 -0300 MIME-Version: 1.0 Sent to CCL by: Ayyaz Mahmmod [ayyazcmc ~~ gmail.com] --f46d0445182fce73c6051f3edec6 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi, Have a look on a recently published work of mine, "Understanding the Reactivity and Regioselectivity of Methylation of Nitronates [R1R2CNO2]=E2= =88=92 by CH3I in the Gas Phase =E2=80=8B" using ab initio quantum chemical methods. ( =E2=80=8B http://pubs.acs.org/doi/abs/10.1021/acs.joc.5b01273 =E2=80=8B)=E2=80=8B =E2=80=8B =E2=80=8B =E2=80=8B. Hope it would be helping. =E2=80=8BBest.=E2=80=8B =E2=80=8B On Mon, Sep 7, 2015 at 2:23 PM, Bashford, Don Don.Bashford ~ stjude.org < owner-chemistry!A!ccl.net> wrote: > > Sent to CCL by: "Bashford, Don" [Don.Bashford^_^stjude.org] > Hi Peter, > > I have a case in which QM calculations by me (Bashford) predicted a > meta-stable carbocation intermediate following the elimination of > pyrophosphate from dihydropterin-PP in the mechanism of Dihydropteroate > synthase (DHPS), and this intermediate was seen in a subsequent X-ray > structure. The in-crystal experiment also supported the SN1-like mechanis= m > that the calculation suggested (Yun et al., 2012, Science 335: 1110-1114)= . > > This enzyme is an important anti-bacterial target, as it is now known to > be the target of the sulfa-drugs. It is part of the bacterial > folate-synthesis pathway, which higher animals do not have. Sulfa-drug > resistance has come about through mutations of DHPS. > > Don Bashford > > -----Original Message----- > > From: owner-chemistry+don.bashford=3D=3Dstjude.org]-[ccl.net [mailto: > owner-chemistry+don.bashford=3D=3Dstjude.org]-[ccl.net] On Behalf Of Pete= r > Damian Jarowski peterjarowski[-]gmail.com > Sent: Monday, September 07, 2015 2:40 AM > To: Bashford, Don > Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity > > > Sent to CCL by: "Peter Damian Jarowski" [peterjarowski : gmail.com] Dear > All: > > I am looking to collect case studies of how computational chemistry > (specifically QM) has been able to predict or refine/optimize chemical > reactions, especially cases where experimental work has followed this > theoretical work up to achieve higher yields or selectivity. Any referenc= es > or descriptions would be much appreciated and I would use them to build a= n > argument for QM. I would of course give references and credit and then I > will share a report here. > > A good example would be my own work where we were able to predict the > existence of an isolable intermediate and then prove this with experiment > and XRD: > > Wu, Y.-L.; Jarowski, P. D.; Schweizer, W. B.; Diederich, F. "Mechanistic > Investigation of the Formal [2+2] Cycloaddition-Cycloreversion Reaction > between 4-(N,N-Dimethylamino)phenylacetylene and Arylated 1,1-Dicyanoviny= l > Derivatives to Form Intramolecular Charge-Transfer Chromophores." Chem. > Eur. J. 2009, 16, 202-211. > > However, I am looking for industry relevant examples. I would love to hea= r > from the community about this and I think it would benefit everyone to ha= ve > at hand such examples. > > Best Regards, > > Peterhttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_= unsub.shtmlhttp://www.ccl.net/spammers.txt > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 *Ayyaz Mahmood* *Laboratory of Theoretical and Computational ChemistryFundamental Chemistry Department - Federal University of Pernambuco, Recife, Brazil.Cell: +55 81 9920 0049 / / Tel: +55 81 2126 5007 / / Fax: +55 81 2126 8442* --f46d0445182fce73c6051f3edec6 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,=C2=A0

Have a look on a recently published = work of mine, "Understanding the Reactivity and Regioselectivity of Methy= lation of Nitronates [R1R2CNO2]=E2=88=92=C2=A0by CH3I in the Gas Phase
=E2=80=8B" using ab initio quantum che= mical methods. (
=E2=80=8B=
http://pubs.acs.org/doi/abs/10.1021/acs.joc.5b01= 273
=E2=80=8B)=E2= =80=8B
=E2=80=8B
=E2=80=8B
=E2=80=8B.=C2=A0
Hope it would be helping.=C2=A0

=E2=80=8B= Best.=E2=80=8B
=E2=80=8B


On Mon, Sep 7, 2015 at 2:23 PM, Ba= shford, Don Don.Bashford ~ stjude.org <owner-chemistry!A!ccl.net> wrote:

Sent to CCL by: "Bashford, Don" [Don.Bashford^_^stjude.org]
Hi Peter,

I have a case in which QM calculations by me (Bashford) predicted a meta-st= able carbocation intermediate following the elimination of pyrophosphate fr= om dihydropterin-PP in the mechanism of Dihydropteroate synthase (DHPS), an= d this intermediate was seen in a subsequent X-ray structure. The in-crysta= l experiment also supported the SN1-like mechanism that the calculation sug= gested (Yun et al., 2012, Science 335: 1110-1114).

This enzyme is an important anti-bacterial target, as it is now known to be= the target of the sulfa-drugs. It is part of the bacterial folate-synthesi= s pathway, which higher animals do not have. Sulfa-drug resistance has come= about through mutations of DHPS.

Don Bashford

-----Original Message-----
> From: owner-chemistry+don.bashford=3D=3Dstjude.org]-[ccl.net [mailto:owner-chemistry+don.bashford=3D= =3Dstjud= e.org]-[ccl.net] On Behalf Of Peter Damian Jarowski peterjarowski[-]gmail.com
Sent: Monday, September 07, 2015 2:40 AM
To: Bashford, Don
Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity


Sent to CCL by: "Peter Damian Jarowski" [peterjarowski : gmail.com] D= ear All:

I am looking to collect case studies of how computational chemistry (specif= ically QM) has been able to predict or refine/optimize chemical reactions, = especially cases where experimental work has followed this theoretical work= up to achieve higher yields or selectivity. Any references or descriptions= would be much appreciated and I would use them to build an argument for QM= . I would of course give references and credit and then I will share a repo= rt here.

A good example would be my own work where we were able to predict the exist= ence of an isolable intermediate and then prove this with experiment and XR= D:

Wu, Y.-L.; Jarowski, P. D.; Schweizer, W. B.; Diederich, F. "Mechanist= ic Investigation of the Formal [2+2] Cycloaddition-Cycloreversion Reaction = between 4-(N,N-Dimethylamino)phenylacetylene and Arylated 1,1-Dicyanovinyl = Derivatives to Form Intramolecular Charge-Transfer Chromophores." Chem= . Eur. J. 2009, 16, 202-211.

However, I am looking for industry relevant examples. I would love to hear = > from the community about this and I think it would benefit everyone to have= at hand such examples.

Best Regards,

Peterhttp://www.ccl.net/cgi-bin/ccl/send_ccl_m= essagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spamme= rs.txt


-=3D This is automatically added to each message by the mailing script =3D-=
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--
=
=
Ayyaz = Mahmood
Laboratory of Theoretical and Computati= onal Chemistry
Fundamental Chemistry Department - Federal University of = Pernambuco, Recife, Brazil.
Cell: +55 81 9920 0049 / / Tel: +55 81 2126 = 5007 / / Fax: +55 81 2126 8442
--f46d0445182fce73c6051f3edec6-- From owner-chemistry@ccl.net Tue Sep 8 23:37:00 2015 From: "Susi Lehtola susi.lehtola a alumni.helsinki.fi" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51675-150908170220-8551-lAYADWMKX57yRq13EUle9A ~~ server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 8 Sep 2015 14:02:08 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola.],[.alumni.helsinki.fi] On 09/07/2015 12:39 AM, Peter Damian Jarowski peterjarowski[-]gmail.com wrote: > I am looking to collect case studies of how computational chemistry (specifically QM) has been able to predict or refine/optimize chemical reactions, especially cases where experimental work has followed this theoretical work up to achieve higher yields or selectivity. Any references or descriptions would be much appreciated and I would use them to build an argument for QM. I would of course give references and credit and then I will share a report here. > > A good example would be my own work where we were able to predict the existence of an isolable intermediate and then prove this with experiment and XRD: > > Wu, Y.-L.; Jarowski, P. D.; Schweizer, W. B.; Diederich, F. "Mechanistic Investigation of the Formal [2+2] Cycloaddition-Cycloreversion Reaction between 4-(N,N-Dimethylamino)phenylacetylene and Arylated 1,1-Dicyanovinyl Derivatives to Form Intramolecular Charge-Transfer Chromophores." Chem. Eur. J. 2009, 16, 202-211. > > However, I am looking for industry relevant examples. I would love to hear from the community about this and I think it would benefit everyone to have at hand such examples. > from the abstract: "have been studied experimentally by the method of initial rates and computationally at the unrestricted B3LYP/6-31G(d) level." What is this, the 1990s? :P -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola],[alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA -----------------------------------------------------------------------