From owner-chemistry /at\ccl.net Mon Jul 7 13:09:00 2014 From: "Italo Anjos italocurvelo .. gmail.com" To: CCL Subject: CCL: Is there a good program to calculate ellipticity profiles? Message-Id: <-50308-140707123048-18305-txlF73cj5SwvjLAMwF/y7w[*]server.ccl.net> X-Original-From: Italo Anjos Content-Type: multipart/alternative; boundary=047d7b10ca01eec24404fd9cfef9 Date: Mon, 7 Jul 2014 13:30:40 -0300 MIME-Version: 1.0 Sent to CCL by: Italo Anjos [italocurvelo%%gmail.com] --047d7b10ca01eec24404fd9cfef9 Content-Type: text/plain; charset=UTF-8 Dear Tian Lu, I thank you for your quick tutorial. Actually I have already run a couple of calculations using Multiwfn before. I tried to generate ellipticity profiles using the "Output and plot a specific property in a line" and then I defined the line using the two nuclei involved. As the bond paths in the system I work with are approximately linear there was not much problem using that approach. But surely the way you described is more accurate and appropriate. The real issue is that the ellipticity by itself may not be enough to characterize the pi character of a given interaction as pointed out by Farrugia and Khalaji . We also need the angle between the molecular plane and the second eigenvector of the Hessian matrix (regarding the electron density). But I could not find a way to calculate it using Multiwfn. Does the program allow us to calculate and plot that angle or maybe the eigenvectors of the Hessian matrix? I thank you again for your help. Sincerely, Italo 2014-07-02 19:23 GMT-03:00 Tian Lu sobereva+/-sina.com < owner-chemistry]|[ccl.net>: > > Sent to CCL by: "Tian Lu" [sobereva%x%sina.com] > Dear Italo, > > You can use Multiwfn (http://multiwfn.codeplex.com) to do this. Below is > a simple example, we calculate and plot ellipicity of electron density > along bond path of C-F in C2H5F. > > After extract Multiwfn package, first open settings.ini file and change > "iuserfunc" parameter to 30 (The 30th user-defined function corresponds to > electron density ellipicity, see Section 2.7 of the manual for detail). > > Then boot up Multiwfn and input below commands: > examples\c2h5f.wfn > 2 // Topology analysis > 2 // Search NCP from nuclear positions > 3 // Search BCP from midpoint of atom pairs > 8 // Generate bond path > 0 // Enter GUI window to visualize result > In the GUI window, by using "Atom labels" and "Path labels" widgets at > right side, we find paths 9 and 10 collectively correspond to the bond path > of C-F. Clicking "RETURN" to close the window, and input > -5 > 7 // Calculate specific real space funtion along a path > 9,10 // The index of the paths > 100 // User-defined function, which corresponds to ellipicity of > electron density currently > > The curve of electron density ellipicity along the C-F bond path > immediately shows on the screen, the dash line denotes the position of BCP. > At the same time, the raw data of the curve are shown on the command-line > window and you may copy them out. > > For more information about the topology analysis module of Multiwfn you > can consult Section 3.14 of the manual and the examples in Section 4.2. > > PS: By using main functions 3 and 4 of Multiwfn, the electron density > ellipicity can also be easily plotted in a line or in a plane. > > Best wishes, > > Tian Lu > > Beijing Kein Research Center for Natural Sciences, Beijing, P. R. China > mailto: sobereva:+:sina.com > > > > ----- Original Message ----- > > From: "Italo Anjos italocurvelo/./gmail.com" > To: "Lu, Tian " > Subject: CCL: Is there a good program to calculate ellipticity profiles? > Date: 2014-07-03 00:43 > > > > Hi all, > > > I've been running some QTAIM calculations and I would like to calculate > ellipticity profiles along bond paths. Does anyone know a software which > can perform such calculations? > > > I usually make use of AIMAll package but the software seems unable to > calculate ellipticity profiles. > > > I appreciate any help. > > > With regards, > > > Italo> > > --047d7b10ca01eec24404fd9cfef9 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Tian Lu,

I thank you for your quic= k tutorial. Actually I have already run a couple of calculations using Mult= iwfn before. I tried to generate ellipticity profiles using the "Outpu= t and plot a specific property in a line" and then I defined the line = using the two nuclei involved. As the bond paths in the system I work with = are approximately linear there was not much problem using that approach. Bu= t surely the way you described is more accurate and appropriate.

The real issue is that the ellipticity by itself may no= t be enough to characterize the pi character of a given interaction as poin= ted out by Farrug= ia and Khalaji. We also need the angle between the molecular plane and = the second eigenvector of the Hessian matrix (regarding the electron densit= y). But I could not find a way to calculate it using Multiwfn. Does the pro= gram allow us to calculate and plot that angle or maybe the eigenvectors of= the Hessian matrix?

I thank you again for your help.

Sincerely,

Italo


2014-07-02 19:23 GMT-03:00 Tian = Lu sobereva+/-sina.com &l= t;owner-chemis= try]|[ccl.net>:

Sent to CCL by: "Tian =C2=A0Lu" [sobereva%x%sina.com]
Dear Italo,

You can use Multiwfn (http://multiwfn.codeplex.com) to do this. Below is a simple examp= le, we calculate and plot ellipicity of electron density along bond path of= C-F in C2H5F.

After extract Multiwfn package, first open settings.ini file and change &qu= ot;iuserfunc" parameter to 30 (The 30th user-defined function correspo= nds to electron density ellipicity, see Section 2.7 of the manual for detai= l).

Then boot up Multiwfn and input below commands:
examples\c2h5f.wfn
2 =C2=A0 // Topology analysis
2 =C2=A0 // Search NCP from nuclear positions
3 =C2=A0 // Search BCP from midpoint of atom pairs
8 =C2=A0 // Generate bond path
0 =C2=A0 // Enter GUI window to visualize result
In the GUI window, by using "Atom labels" and "Path labels&q= uot; widgets at right side, we find paths 9 and 10 collectively correspond = to the bond path of C-F. Clicking "RETURN" to close the window, a= nd input
-5
7 =C2=A0 // Calculate specific real space funtion along a path
9,10 =C2=A0// The index of the paths
100 =C2=A0 // User-defined function, which corresponds to ellipicity of ele= ctron density currently

The curve of electron density ellipicity along the C-F bond path immediatel= y shows on the screen, the dash line denotes the position of BCP. At the sa= me time, the raw data of the curve are shown on the command-line window and= you may copy them out.

For more information about the topology analysis module of Multiwfn you can= consult Section 3.14 of the manual and the examples in Section 4.2.

PS: By using main functions 3 and 4 of Multiwfn, the electron density ellip= icity can also be easily plotted in a line or in a plane.

Best wishes,

Tian Lu

Beijing Kein Research Center for Natural Sciences, Beijing, P. R. China
mailto: sobereva:+:sina.com



----- Original Message -----
> From: "Italo Anjos italocurvelo/./gmail.com" <owner-chemistry:+:ccl.net>
To: "Lu, Tian " <sobereva:+:sina.com>
Subject: CCL: Is there a good program to calculate ellipticity profiles? Date: 2014-07-03 00:43



Hi all,


I've been running some QTAIM calculations and I would like to calculate= ellipticity profiles along bond paths. Does anyone know a software which c= an perform such calculations?


I usually make use of AIMAll package but the software seems unable to calcu= late ellipticity profiles.


I appreciate any help.


With regards,


Italo



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