From owner-chemistry@ccl.net Tue Nov 29 05:57:01 2016 From: "Reza Shojaei shojaei81|a|gmail.com" To: CCL Subject: CCL: SIESTA's scan option Message-Id: <-52531-161129055527-1961-bQ7aGHtH7XKnTa6M1EqfFQ[-]server.ccl.net> X-Original-From: "Reza Shojaei" Date: Tue, 29 Nov 2016 05:55:26 -0500 Sent to CCL by: "Reza Shojaei" [shojaei81=gmail.com] Dear CCL users, Would you please comment on how to use scan option in SIESTA. I want to apply a voltage on a crystal in z direction in steps of 0.5 starting from 0 to 3. Regards, Reza From owner-chemistry@ccl.net Tue Nov 29 11:31:00 2016 From: "Timur Madzhidov tmadzhidov^gmail.com" To: CCL Subject: CCL:G: AIM Message-Id: <-52532-161129091326-10510-IH+vapOhCu6OTPSzpaz0Xg _ server.ccl.net> X-Original-From: Timur Madzhidov Content-Type: multipart/alternative; boundary=f403045ea36a7fce1f054271305b Date: Tue, 29 Nov 2016 14:13:05 +0000 MIME-Version: 1.0 Sent to CCL by: Timur Madzhidov [tmadzhidov=gmail.com] --f403045ea36a7fce1f054271305b Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable There is other very good and free code AIMAll http://aim.tkgristmill.com/. Standard version is free, professional that is good due to visualization capabilities is paid. But for getting numbers but pictures AIMAll is excellent. Best regards, Timur Madzhidov =D0=B2=D1=81, 27 =D0=BD=D0=BE=D1=8F=D0=B1. 2016 =D0=B3. =D0=B2 9:24, V=C3= =ADctor Lua=C3=B1a Cabal victor() fluor.quimica.uniovi.es : > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor= =3D=3D=3D > fluor.quimica.uniovi.es] > On Sun, Nov 27, 2016 at 08:55:09AM +0800, =E9=83=AD=E5=BB=BA=E4=B8=9C guo= jiandong13() > mails.ucas.ac.cn wrote: > > > > Dear Prof. V=C3=ADctor Lua=C3=B1a > > I am a beginner of computational chemistry. I have little > > knowledge of AIM. I did not try whether the AIM can be performed on > > Gaussuan 09. > > =C2=BFAre you asking why not using the AIM facility internal to g09? > Dont! The AIM algorithms within g09 fails in too many occasions and they > are not useful, in general. In fact, failures in the g09 aim algorithm > have always been a source of concern for the people doing QTAIM work. > > Use an independent code. The original AIMPAC from the Bader's > group is still available (1), but newer codes have improved > characteristics. Directly from Bader's students you have: aim2000 > and aimall. > > (1) > > My group, that went to study with Bader's group after we had created > independently codes to to do AIM studies on solid state problems, > published critic as an open source code. The original critic was intended > to analyse the electron density and its laplacian in solids. It was > heavily improved in critic2, also open source, that works both on > crystals and molecules and implements a special computational langage > to create new tasks not hard coded in the critic2 source. > > There are also excellent QTAIM codes by PLA. Popelier, from Manchester > University but I'm not currently sure how they can be obtained. You must > explore that if you want. Popelier has written that QCT (quantum chemistr= y > topology of topography) is a better name that QTAIM. The reason is that > QTAIM analysis can be extended to other scalar properties within the > electron density basins. > > There is also a chinese code, multiwfn, but the algorithms implemented > there prefer que quantity of doing many things to que quality of doing > them well. > > So, my advise is: do not use the g09 internal aim task! Use aimall > or critic2 to analyse the g09 WFX file that g09 produces. NOtice that > WFX improves on the WFN format that g03 (surely even previous gaussian > versions) started to produce to give AIMPAC programs the wavefunction > to explore. Most Bader's articles were done that way. > > If you need to study what is the AIM analysis you should read Bader's > book: Bader, Richard (1994). Atoms in Molecules: A Quantum Theory. USA: > Oxford University Press. ISBN 978-0-19-855865-1. > > I started to write this message without realizing that you were using the > CCL list. Maybe this is a too personal opinion for a Universal audience, > but I do not regret having strong opinions and showing them clearly. > > Enjoy, > Dr. V=C3=ADctor Lua=C3=B1a > -- > . . "De la cuna a la tumba es una escuela, por eso lo que llamas > / `' \ problemas son lecciones." > /(o)(o)\ (From the cradle to the grave life is a school, ...) > /`. \/ .'\ -- Facundo Cabral, Cuna > / '`'` \ > | \'`'`/ | "When are we ready to learn something? Motivation is the > | |'`'`| | Motivation is the most important step in education." > \/`'`'`'\/ -- adapted from Adam Steltzner, 2016 (ElPa=C3=ADs) > =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=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 > ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. ! > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: ! > ! phone: +34-985-103491 <+34%20985%2010%2034%2091> fax: +34-985-103125 > <+34%20985%2010%2031%2025> ! > +--------------------------------------------+ > GroupPage: > Articles: > git-hub: > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > -- Best regards, Timur Madzhidov (sent from telephone) ***************************************************************************= *********************************** Dr. Timur I. Madzhidov (PhD in Organic Chemistry) Senior Researcher of Laboratory of Chemoinformatics and Molecular Modeling Senior Lecturer of Department of Organic Chemistry Responsible for Education at Master Program on Chemoinformatics and Molecular Modeling A.M. Butlerov Institute of Chemistry, Kazan Federal University E-mails: Timur.Madzhidov]![kpfu.ru, tmadzhidov]![gmail.com, madzhidov]![mail.ru Web-page: http://kpfu.ru/Timur.Madzhidov ***************************************************************************= *********************************** --f403045ea36a7fce1f054271305b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
There is other very good and free code AIMAll=C2=A0
http://aim.tkgristmill.com/.=C2= =A0

Standard version is free, professional that is= good due to visualization capabilities is paid. But for getting numbers bu= t pictures AIMAll is excellent.

Best regards,
= Timur Madzhidov




=D0=B2=D1=81, 27 =D0= =BD=D0=BE=D1=8F=D0=B1. 2016 =D0=B3. =D0=B2 9:24, V=C3=ADctor Lua=C3=B1a Cab= al victor()fluor.quimica.uniovi.= es <owner-chemistry]![ccl.n= et>:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor=3D= =3D=3Dfluor.quimica.uniovi.es]
On Sun, Nov 27, 2016 at 08:55:09AM +0800, =E9=83=AD=E5=BB=BA=E4=B8=9C guoji= andong13() mails.ucas.ac.cn wrote:
>
> Dear Prof. V=C3=ADctor Lua=C3=B1a
>=C2=A0 =C2=A0 =C2=A0 =C2=A0I am a beginner of computational chemistry. = I have little
> knowledge of AIM. I did not try=C2=A0 whether the AIM can be performed= on
> Gaussuan 09.

=C2=BFAre you asking why not using the AIM facility internal to g09?
Dont! The AIM algorithms within g09 fails in too many occasions and they are not useful, in general. In fact, failures in the g09 aim algorithm
have always been a source of concern for the people doing QTAIM work.

Use an independent code. The original AIMPAC from the Bader's
group is still available (1), but newer codes have improved
characteristics. Directly from Bader's students you have: aim2000
and aimall.

(1) <http://www.= chemistry.mcmaster.ca/aimpac/imagemap/imagemap.htm>

My group, that went to study with Bader's group after we had created independently codes to to do AIM studies on solid state problems,
published critic as an open source code. The original critic was intended to analyse the electron density and its laplacian in solids. It was
heavily improved in critic2, also open source, that works both on
crystals and molecules and implements a special computational langage
to create new tasks not hard coded in the critic2 source.

There are also excellent QTAIM codes by PLA. Popelier, from Manchester
University but I'm not currently sure how they can be obtained. You mus= t
explore that if you want. Popelier has written that QCT (quantum chemistry<= br class=3D"gmail_msg"> topology of topography) is a better name that QTAIM. The reason is that
QTAIM analysis can be extended to other scalar properties within the
electron density basins.

There is also a chinese code, multiwfn, but the algorithms implemented
there prefer que quantity of doing many things to que quality of doing
them well.

So, my advise is: do not use the g09 internal aim task! Use aimall
or critic2 to analyse the g09 WFX file that g09 produces. NOtice that
WFX improves on the WFN format that g03 (surely even previous gaussian
versions) started to produce to give AIMPAC programs the wavefunction
to explore. Most Bader's articles were done that way.

If you need to study what is the AIM analysis you should read Bader's book:=C2=A0 Bader, Richard (1994). Atoms in Molecules: A Quantum Theory. US= A:
Oxford University Press. ISBN 978-0-19-855865-1.

I started to write this message without realizing that you were using the CCL list. Maybe this is a too personal opinion for a Universal audience, but I do not regret having strong opinions and showing them clearly.

Enjoy,
=C2=A0 =C2=A0 =C2=A0 Dr. V=C3=ADctor Lua=C3=B1a
--
=C2=A0 =C2=A0 .=C2=A0 .=C2=A0 =C2=A0 "De la cuna a la tumba es una esc= uela, por eso lo que llamas
=C2=A0 =C2=A0/ `' \=C2=A0 =C2=A0 problemas son lecciones."
=C2=A0 /(o)(o)\=C2=A0 =C2=A0(From the cradle to the grave life is a school,= ...)
=C2=A0/`. \/ .'\=C2=A0 -- Facundo Cabral, Cuna
/=C2=A0 =C2=A0'`'`=C2=A0 =C2=A0\
|=C2=A0 \'`'`/=C2=A0 | "When are we ready to learn something? = Motivation is the
|=C2=A0 |'`'`|=C2=A0 | Motivation is the most important step in edu= cation."
=C2=A0\/`'`'`'\/=C2=A0 -- adapted from Adam Steltzner, 2016 (El= Pa=C3=ADs)
=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=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
! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:=C2=A0 <victor:fluor.quimica.uniovi.= es>=C2=A0 !
! phone: +34-985-103491=C2=A0 fax: +34-985-103125 !
+--------------------------------------------+
=C2=A0GroupPage: <http://azufre.quimica.uniov= i.es/>
=C2=A0Articles:=C2=A0 <http://scholar.google.com/citations?user=3DIbl1BWAAAAAJ&hl= =3Des>
=C2=A0git-hub:=C2=A0 =C2=A0<https://github.c= om/aoterodelaroza>



-=3D This is automatically added to each message by the mailing script =3D-=

E-mail to subscribers: CHEMISTRY]![ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.c= cl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST]![ccl.net or use
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Before posting, check wait time at: http://www.ccl.net

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=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.= txt

RTFI: http://www.ccl.net/ch= emistry/aboutccl/instructions/


--

Best regards,
Timur Madzhidov

(sent from telephone)

************************************************************= **************************************************
Dr. Timur I. Madzhidov (PhD in Organic Chemistry)
Senior Researcher of Laboratory of Chemoinformatics and Molecular Modeling<= br> Senior Lecturer of Department of Organic Chemistry
Responsible for Education at Master Program on Chemoinformatics and Molecul= ar Modeling
A.M. Butlerov Institute of Chemistry, Kazan Federal University
E-mails: Timur.Madzhidov]![kpfu.ru= , tmadzhidov]![gmail.com, madzhidov]![mail.ru
Web-page: http://kpfu.ru/Timur.M= adzhidov
***************************************************************************= ***********************************

--f403045ea36a7fce1f054271305b-- From owner-chemistry@ccl.net Tue Nov 29 12:06:01 2016 From: "Andre Schleife schleife-,-illinois.edu" To: CCL Subject: CCL: APS March Meeting: Tutorial on "Electron Phonon Interactions" Message-Id: <-52533-161129120302-32335-ycqO2wT5vcc0PZbs5dROOQ[a]server.ccl.net> X-Original-From: "Andre Schleife" Date: Tue, 29 Nov 2016 12:03:01 -0500 Sent to CCL by: "Andre Schleife" [schleife###illinois.edu] Hello everyone, Before you finalize booking your trip to the APS March Meeting in New Orleans, we would like to bring the tutorial on "Electron Phonon Interactions", organized by Emmanouil Kioupakis and myself, to your attention: https://www.aps.org/meetings/march/events/tutorials.cfm#t2 This tutorial is scheduled for Sunday, March 12, 8:30 a.m. - 12:30 p.m, and it aims at graduate students, post-docs, and other scientists interested in learning about first-principles numerical techniques to describe electron-phonon interactions. Recent advances in the theoretical description and computational methodology have made harmonic and an-harmonic electron-phonon effects amenable to detailed investigations. While the underlying techniques are currently not standard and are oftentimes computationally expensive, the availability of modern high-performance computing enabled fantastic progress, e.g. for electron-phonon effects on band structures, optical absorption, recombination, and transport. In the near future it is expected that not only will the existing techniques be improved, but also become crucial for progress in many areas of materials research and condensed matter physics. This tutorial bridges the gap of introducing the underlying theories, explaining practical calculations using modern software packages, and understanding exciting physics for real-world applications. The latter comprises studies of material systems e.g. in the realm of semiconductor optics or thermo-electrics. The tutorial will be interesting for computational materials scientists and physicists who contemplate investigating electron-phonon effects in their research but also for experimentalists who want to connect closer with computational materials science. We are happy to have four excellent speakers * Feliciano Giustino, Oxford University * Chris G. Van de Walle, University of California, Santa Barbara * Carsten Ullrich, University of Missouri * Mark van Schilfgaarde, Kings College Their talks will be very pedagogical in describing the theoretical foundations as well as computational approaches used in practice. Latest developments and open questions will naturally be integrated into all topics. We're looking forward to seeing many of you on March 12! All the best, Andre Schleife and Emmanouil Kioupakis From owner-chemistry@ccl.net Tue Nov 29 12:41:01 2016 From: "Tobias Kraemer t.kraemer ~ hw.ac.uk" To: CCL Subject: CCL: 2J NMR spin-spin coupling involving P and H Message-Id: <-52534-161129123522-18140-1XBgQ1P4ALSzCYXs1TVovg:server.ccl.net> X-Original-From: "Tobias Kraemer" Date: Tue, 29 Nov 2016 12:35:21 -0500 Sent to CCL by: "Tobias Kraemer" [t.kraemer=-=hw.ac.uk] Dear colleagues, I am currently working on a problem related to indirect NMR spin-spin coupling within a bis-ortho-carborane phosphine compound. More precisely, the compound is (bis-o-CB)P-CH2CH3, containing an ethyl group bonded to the P atom. Now, what is interesting about this compound is that in the experimental 1H NMR spectrum the coupling between the CH2 (methylene) protons and P is absent (or very small and beyond instrument sensitivity) while the coupling to the CH3 (methyl) protons is clearly seen. Hence, the CH3 peak is split into a doublet of triplets due to 3J(PH) and 3J(HH) coupling, while the peak for CH2 is a regular quartet from 3J(HH) coupling. For such systems empirical Karplus-type relationships have been published in the literature (e.g. Gagnaire et al., Chem. Commun. 1968, 1469), relating the P(lonepair)-P-C-H dihedral angle to the 2J(PH) coupling constant. In the present case I find very good agreement between the experimental structure and the DFT-optimised structure including, importantly, the orientation of the Et group. According to Gagnaires work, in this orientation there are two lp-P-C-H torsion angles, 83 and 162 deg, both of which would be expected to result in near-zero 2J(PH) couplings (as observed experimentally). Whilst the 3J(PH) and 3J(HH) coupling constants are reproduced within 1 Hz by my DFT calculations (B3LYP/aug-cc-pVTZ-J [coupling atoms]/cc-pVDZ), the average 2J(PH) coupling constant is notably overestimated (~6 Hz). The individual computed 2J(PH) coupling constants are 1.5 and 10.9 Hz, respectively. Hence, the average value should be around 6.2 Hz, based on the fact that the (partial) rotation around the PC(H2) vector is not hindered, rendering these two methylene protons equivalent (very much like the 3 protons in the methyl group). Things are further complicated by the fact that the experimental 2J(PH) coupling is restored (~10 Hz) when additional atoms are bonded to the P atom (such as Se), which clearly points to an involvement of the lonepair (change of hybridisation). There is a possibility of the involvement of the lonepair in through-space coupling. We have also considered the idea of direct dipolar coupling, but I am not convinced by this argument. I wonder if anyone has dealt with similar systems and seen comparable effects (P lonepair...)? How realistic is it to think that I can capture this effect in the DFT calculations? I would appreciate any ideas, before I embark on method testing. The overall agreement of other individual PH coupling constants is reassuring, when compared with results I have seen in the literature for e.g. (tert-butyl)PCl2. I am somewhat puzzled by the above result. Thanks for your help Regards Tobias Dr. Tobias Kraemer MRSC Research Associate Institute of Chemical Sciences School of Engineering & Physical Sciences Heriot-Watt University Edinburgh EH14 4AS United Kingdom email: t.kraemer|hw.ac.uk phone: +44 (0)131 451 3259 From owner-chemistry@ccl.net Tue Nov 29 14:07:01 2016 From: "Peer Scientist peerscientist()gmail.com" To: CCL Subject: CCL: PeerScientist-Of the Scientists,for the Scientists & by the Scientists Message-Id: <-52535-161129130620-11668-CMGcOcsWundp9yrs2HKt4g]~[server.ccl.net> X-Original-From: "Peer Scientist" Date: Tue, 29 Nov 2016 13:06:19 -0500 Sent to CCL by: "Peer Scientist" [peerscientist[]gmail.com] Dear Researcher, Greetings for the day! We are hereby writing this to personally inform you about the launch of first of its kind networking platform for active researchers PeerScientist.com . Its a dedicated platform with useful tools for active researchers like literature search, project management, research papers sharing etc., Here are top 10 reasons why all active researchers should Use PeerScientist.com: https://www.peerscientist.com/10-reasons-why-all-active-researchers-should-use-peerscientist/ Below is a link for video demonstrating the features of PeerScientist.com: https://www.youtube.com/watch?v=CPxz1gKq46I Note: This message is personally sent with a genuine belief that it would be beneficial for you in some or the other way, if you wish not to receive any messages regarding the same, then please accept our sincere apologies for the inconvenience caused and "unsubscribe" below so that we won't send you any further information related to the same. Thank you, PeerScientist Team. From owner-chemistry@ccl.net Tue Nov 29 23:16:00 2016 From: "=?GBK?B?ufm9qLar?= guojiandong13]|[mails.ucas.ac.cn" To: CCL Subject: CCL: Thank you Message-Id: <-52536-161129204925-21818-iISZevllvk+yX9Trnayj4w!A!server.ccl.net> X-Original-From: =?GBK?B?ufm9qLar?= Content-Type: multipart/alternative; boundary="----=_Part_104833_3338822.1480470549176" Date: Wed, 30 Nov 2016 09:49:09 +0800 (GMT+08:00) MIME-Version: 1.0 Sent to CCL by: =?GBK?B?ufm9qLar?= [guojiandong13__mails.ucas.ac.cn] ------=_Part_104833_3338822.1480470549176 Content-Type: text/plain; charset=GBK Content-Transfer-Encoding: 7bit Dear Prof. Timur Madzhidov Thank you for your kind suggestion. Jiandong Best regards ------=_Part_104833_3338822.1480470549176 Content-Type: text/html; charset=GBK Content-Transfer-Encoding: 7bit Dear Prof. Timur Madzhidov

Thank you for your kind suggestion.

Jiandong

Best regards



------=_Part_104833_3338822.1480470549176-- From owner-chemistry@ccl.net Tue Nov 29 23:57:00 2016 From: "=?UTF-8?B?6YOt5bu65Lic?= guojiandong13%x%mails.ucas.ac.cn" To: CCL Subject: CCL: Thank you Message-Id: <-52537-161129204551-21434-6dtiy4uxCAkbua1JnR+NRg_-_server.ccl.net> X-Original-From: =?UTF-8?B?6YOt5bu65Lic?= Content-Type: multipart/alternative; boundary="----=_Part_104306_3053180.1480470335897" Date: Wed, 30 Nov 2016 09:45:35 +0800 (GMT+08:00) MIME-Version: 1.0 Sent to CCL by: =?UTF-8?B?6YOt5bu65Lic?= [guojiandong13 ~ mails.ucas.ac.cn] ------=_Part_104306_3053180.1480470335897 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: base64 CkRlYXIgUHJvZi4gLlbDrWN0b3IgTHVhw7FhCiAgICAgICBUaGFuayB5b3UgZm9yIHlvdXIgc3Vn Z2VzdGlvbnMuIEkgd2lsbCB0cnkgYWltYWxsIG9yIGNyaXRpYzIgdG8gY29uZHVjdCBwb3B1bGF0 aW9uIGFuYWx5c2lzLgoKCkppYW5kb25nIAoKCkJlc3QgcmVnYXJkcwoKDQoNCg0K ------=_Part_104306_3053180.1480470335897 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: base64 PGJyPkRlYXIgUHJvZi4mbmJzcDsuVsOtY3RvciBMdWHDsWE8ZGl2PiZuYnNwOyAmbmJzcDsgJm5i c3A7ICZuYnNwO1RoYW5rIHlvdSBmb3IgeW91ciBzdWdnZXN0aW9ucy4gSSB3aWxsIHRyeSZuYnNw O2FpbWFsbCBvciBjcml0aWMyIHRvIGNvbmR1Y3QgcG9wdWxhdGlvbiBhbmFseXNpcy48L2Rpdj48 ZGl2Pjxicj48L2Rpdj48ZGl2PkppYW5kb25nJm5ic3A7PC9kaXY+PGRpdj48YnI+PC9kaXY+PGRp dj5CZXN0IHJlZ2FyZHM8YnI+PGJyPjxzcGFuPjwvc3Bhbj48L2Rpdj48YnI+PGJyPjxicj4= ------=_Part_104306_3053180.1480470335897--