Hi Ambrish,

The lines yo= u see in structural formulas and 3D representations may or may not represen= t shared electron density. The lines are not used by quantum chem programs = to optimize geometry or calculate other properties: they are qualitative to= ols applied by the visualization software.

To illustrate the arbitrary nature of bond lines, I optimized the SO2= -NH3 complex using Hyperchem and the PM3 method. I drew 6, or 5, or 3 bond = lines. The result? three identical geometries all with PM3 energy of -525.2= 84126 kcal/mol and 1.9154 Ang N--S distance. The bond order for the N--S &q= uot;bond" is 0.405. So drawing a bond line between N and S is up to yo= u! The other bond orders are what you would expect, about 1 to 1.2 so "= ;single lines" are appropriate in a graphical representation of the mo= lecular portions of the complex.

John Keller

Dept of Chemistry and Biochemistry

Univ= of Alaska Fairbanks

<= /div>

On Sat, Feb 9, 2013 at 12:21 PM, Ambrish K. Srivastava ambrishphysicsa/gmail.com <owner-chemistry(!)ccl.net&= gt; wrote:

Sent to CCL by: "Ambrish K. Srivastava" [ambrishphysics|*|gmail.com]
Dear all,
I had tried to optimize the geometry of dimeric complex of a cluster X by i= ntroducing a single bond i.e. X-X. I got all real frequencies but confused = with optimized geometry. The trouble is that : when i visualize .log file, = i see that bond between X is removed but .chk file shows X-X bond. I am una= ble to conclude whether two X will be bonded or not.

Can anybody please suggest what to do and how to do? which one is reliable?= Why this happened?

Million thanks in advance!

Ambrish K Srivastava

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--047d7b15aedbc6a43e04d558c729-- From owner-chemistry@ccl.net Sun Feb 10 09:12:01 2013 From: "Mehdi Esrafili m_esrafili~!~yahoo.com" To: CCL Subject: CCL:G: Extract NMR data from Gaussian output Message-Id: <-48212-130210012447-3803-FAuvLxUTZjyho1/Dvhd6yA(!)server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="406169123-469081985-1360477480=:87406" Date: Sat, 9 Feb 2013 22:24:40 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili * yahoo.com] --406169123-469081985-1360477480=:87406 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear=0ADenis:=0AIn the output file, find " SCF GIAO Magnetic shielding tens= or=0A(ppm):" line. For each nucleus, there are isotropic (=CF=83iso), aniso= tropic (=CE=94=CF=83), chemical=0Ashielding tensor components ( as XX, XY, = XZ, YX, YY, YZ, ZX, ZY and ZZ) and=0Achemical shielding tensor principal co= mponents (given as Eigenvalues). The=0Achemical shielding isotropy (=CF=83i= so) and anisotropy (=CE=94=CF=83)=0Aare defined as:=0A=CF=83iso=3D (=CF=831= 1+ =CF=8322 + =CF=8333) / 3=0A=CE=94=CF=83=3D=CF=8333-(=CF=8311+ =CF=8322)/= 2=0Awhere =CF=83iiis referred to chemical shielding=0Atensor principal comp= onents, where. =C2=A0=0AIf you want to=0Acompute chemical shift (=CE=B4)rat= her than chemical shielding, use =0A=CE=B4=3D=CF=83iso,ref-=CF=83iso,cal=C2= =A0=C2=A0 =0Awhere =CF=83iso,refrefers to the absolute=0Achemical shielding= isotropy of reference compound (e.g. TMS for 13C=0Anuclei) and =CF=83iso,c= alcorresponds to the chemical=0Ashielding isotropy of the nucleus of intere= st.=0ASincerely=0AMehdi=0A=C2=A0=0A=C2=A0=0A-------------------------------= ---------------------------------------------------------------------------= --------------------=C2=A0=C2=A0=0A`The man who makes no mistakes does not = usually make anything.'=0A=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= Edward John Phelps (1822-1900)=0A-----------------------------------------= ---------------------------------------------------------------------------= ---------- =0AMehdi D. Esrafili, Ph.D.=0AAssistant Professor of Physical Ch= emistry=C2=A0=0ACurrent address:=C2=A0Department of Chemistry, =0AFaculty o= f Basic Sciences,University of=0AMaragheh, Iran. =0AE-mail 1:m_esrafili#%#yah= oo.com=0AE-mail 2: esrafili#%#maragheh.ac.ir=0A------------------------------= ---------------------------------------------------------------------------= --------------------- =0A=0A=0A________________________________=0A From: De= nis Kazakiewicz d.kazakiewicz###gmail.com =0ATo: "= Esrafili, Mehdi D " =0ASent: Sunday, Februar= y 10, 2013 12:38 AM=0ASubject: CCL:G: Extract NMR data from Gaussian output= =0A =0A=0ASent to CCL by: "Denis=C2=A0 Kazakiewicz" [d.kazakiewicz^_^gmail.= com]=0AHello=0AWould you please tell how to extract NMR data from gaussian = .log output?=0ADesirably, it should be something like 'NMR summary' at Gaus= sView. Unfortunately don't have access to GaussView=0ADenis=0A=0A=0A=0A-=3D= This is automatically added to each message by the mailing script =3D-=0AT= o recover the email address of the author of the message, please change=0At= he strange characters on the top line to the #%# sign. You can also=0Alook up= the X-Original-From: line in the mail header.=0A=0AE-mail to subscribers: = CHEMISTRY#%#ccl.net or use:=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin= /ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST#%#ccl.= net or use=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_m= essage=0A=0A=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.n= et/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: http:= //www.ccl.net=0A=0A=0AConferences: http://serv= er.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messages: http:= //www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces fro= m CCL with 5.7.1 error, check:=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/sp= ammers.txt=0A=0A--406169123-469081985-1360477480=:87406 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

=0A=0A

Dear=0ADenis:

=0A=0A

In the output file, find " SCF G= IAO Magnetic shielding tensor=0A(ppm):" line. For each nucleus, there are i= sotropic (= =CF=83_iso), anisotropic (=CE=94=CF=83), chemical=0Ashielding tensor components ( as XX, XY, XZ, YX, YY, YZ, = ZX, ZY and ZZ) and=0Achemical shielding tensor principal components (given = as Eigenvalues). The=0Achemical shielding isotropy (=CF=83_iso) and anisotropy (=CE=94=CF=83)=0Aare defined as:=0A=0A

=CF=83_iso<=
/span> =3D (=CF=83₁₁<= span style=3D"font-size:12.0pt;line-height:150%;font-family:"Times New= Roman","serif";=0Amso-ascii-theme-font:major-bidi;mso-farea= st-font-family:"Times New Roman";=0Amso-hansi-theme-font:major-bi= di;mso-bidi-theme-font:major-bidi;color:black;=0Amso-fareast-language:AR-SA= ">+ =CF=83₂₂+ =CF=83₃₃) / 3

=0A=0A

=CE=94=CF=83=3D = =CF=83₃₃-(=CF= =83₁₁+ =CF=83= ₂₂)/2

=0A=0A

where =CF=83_ii is referred to chemical shielding=0Atensor prin= cipal components, where

=0A=0A

If you want to=0Acompute chemical shi= ft (=CE=B4)=0Arather than chemical shielding, use

=0A=0A

=CE=B4=3D = =CF=83_iso,ref -=CF=83= _=
iso,cal

=0A=0A

where =CF=83_{<=
span style=3D"font-family:"Times New Roman","serif";mso=
-ascii-theme-font:major-bidi;=0Amso-hansi-theme-font:major-bidi;mso-bidi-th=
eme-font:major-bidi;color:black;=0Amso-fareast-language:AR-SA">iso,ref} refers to the a= bsolute=0Achemical shielding isotropy of reference compound (e.g. TMS for <= sup>13C=0Anuclei) and =CF=83_iso,cal corresponds to the chemical=0Ashielding isotropy of the nucleus of interest.=0A=0A

Sincerely

=0A=0A

Mehdi

=0A=0A

-----------------------------------------= ---------------------------------------------------------------------------= ----------

`The man who makes no mistakes does not usua= lly make anything.'

= ; &n= bsp; = ; Edward John Phelps (1822-1900)

----------------------------------= ---------------------------------------------------------------------------= -----------------
Mehdi D. Esrafili, Ph.D.

Assistant Prof= essor of Physical Chemistry
Current address: Departmen= t of Chemistry,

Faculty of Basic Sciences,University of

Ma= ragheh, Iran.

E-mail 1: m_esrafili#%#yahoo.com E-mail 2: esrafili#%#maragheh.ac.ir

-------------------------------------------------------------------= ----------------------------------------------------------- <= /font>

From: Denis Kazakiewicz d.kazakiewicz###gmail.com <= owner-chemistry#%#ccl.net>
To: "Esrafili, Mehdi D " <m_esrafili#%#yahoo.com>
Sent: Sunday, February 10, 2= 013 12:38 AM
Subject: = CCL:G: Extract NMR data from Gaussian output

=0A
= Sent to CCL by: "Denis Kazakiewicz" [d.kazakiewicz^_^gmail.com]
He= llo
Would you please tell how to extract NMR data from gaussian .log out= put?
Desirably, it should be something like 'NMR summary' at GaussView. = Unfortunately don't have access to GaussView
Denis

-=3D T= his is automatically added to each message by the mailing script =3D-
To= recover the email address of the author of the message, please change
t= he strange characters on the top line to the #%# sign. You can also
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E-mail to subscriber= s: CHEMISTRY#%#ccl.net or use:
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If your mail bounces from CCL with 5.7.1 = error, check:

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