From owner-chemistry@ccl.net Sun Apr 1 02:31:01 2007
From: "Green Power powergreen^-^gmail.com" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL:G: ModRedundant question
Message-Id: <-33942-070401022832-20493-Xepe/52SZEji7/uTnHkX+A]~[server.ccl.net>
X-Original-From: "Green Power" <powergreen!A!gmail.com>
Content-Type: multipart/alternative;
boundary="----=_Part_92944_20485585.1175408895656"
Date: Sun, 1 Apr 2007 02:28:15 -0400
MIME-Version: 1.0
Sent to CCL by: "Green Power" [powergreen||gmail.com]
------=_Part_92944_20485585.1175408895656
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit
Content-Disposition: inline
*Dear CCLers*
*I am confused by the following example in Gaussian manual. * *What will be
the difference if Modredun option were not used. The manual explanation is
that a hydrogen bond was created between O3 and H8 by such redundant
coordinate definition. But I can not see say difference for the calculated
result if such redundant were not used. Any suggestion on this will be
appreciated.
*
*"Specifying Redundant Internal Coordinates*. The following input file
illustrates the method for specifying redundant internal coordinates within
an input file:
# HF/6-31G(d) Opt=ModRedun Test
Opt job
0,1
C1 0.000 0.000 0.000
C2 0.000 0.000 1.505
O3 1.047 0.000 -0.651
H4 -1.000 -0.006 -0.484
H5 -0.735 0.755 1.898
H6 -0.295 -1.024 1.866
O7 1.242 0.364 2.065
H8 1.938 -0.001 1.499
3 8
2 1 3
"
Y.Tian
------=_Part_92944_20485585.1175408895656
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline
<p><b><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;">Dear CCLers</span></span></span></span></b></p><p><b><span style="font-weight: bold;">
<span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;">I am confused by the following example in Gaussian manual. </span></span></span></span></span>
</b> <b><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;">What will be the difference if Modredun option were not used. The manual explanation is that a hydrogen bond was created between O3 and H8 by such redundant coordinate definition. But I can not see say difference for the calculated result if such redundant were not used. Any suggestion on this will be appreciated.
</span><br></span></span></span></span></b></p><p><b><span style="font-weight: bold;">"</span>Specifying
Redundant Internal Coordinates</b>. The following input file illustrates the method
for specifying redundant internal coordinates within an input file:</p>
<pre><font face="Courier New, Courier, mono"># HF/6-31G(d) Opt=ModRedun Test <br><br>Opt job <br><br>0,1 <br>C1 0.000 0.000 0.000 <br>C2 0.000 0.000 1.505 <br>O3 1.047 0.000 -0.651 <br>H4 -1.000 -0.006
-0.484 <br>H5 -0.735 0.755 1.898 <br>H6 -0.295 -1.024 1.866 <br>O7 1.242 0.364 2.065 <br>H8 1.938 -0.001 1.499 <br><br>3 8 <br>2 1 3 <br><br>"<br><br>Y.Tian<br></font></pre>
------=_Part_92944_20485585.1175408895656--
From owner-chemistry@ccl.net Sun Apr 1 09:39:00 2007
From: "Jozsef Csontos jozsefcsontos#%#creighton.edu" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL:G: ModRedundant question
Message-Id: <-33943-070401093240-16994-Z++xr5wxXGuuAN/ewEP52Q#%#server.ccl.net>
X-Original-From: Jozsef Csontos <jozsefcsontos]![creighton.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain
Date: Sun, 01 Apr 2007 08:32:23 -0500
Mime-Version: 1.0
Sent to CCL by: Jozsef Csontos [jozsefcsontos]=[creighton.edu]
Hi,
this kind of redundant coordinate specification is just for your
convenience. It means that your specified coordinates will be included
explicitly in the output file, so you can easily follow how they change,
for example, during an optimization process (Check the number of
internal coordinates in the output files (with and without the
modredundant specification). The results shouldn't depend on them unless
you constrain them too.
I hope this helps,
Jozsef
On Sun, 2007-04-01 at 02:28 -0400, Green Power powergreen^-^gmail.com
wrote:
> Dear CCLers
>
> I am confused by the following example in Gaussian manual. What will
> be the difference if Modredun option were not used. The manual
> explanation is that a hydrogen bond was created between O3 and H8 by
> such redundant coordinate definition. But I can not see say difference
> for the calculated result if such redundant were not used. Any
> suggestion on this will be appreciated.
>
>
> "Specifying Redundant Internal Coordinates. The following input file
> illustrates the method for specifying redundant internal coordinates
> within an input file:
>
> # HF/6-31G(d) Opt=ModRedun Test
>
> Opt job
>
> 0,1
> C1 0.000 0.000 0.000
> C2 0.000 0.000 1.505
> O3 1.047 0.000 -0.651
> H4 -1.000 -0.006
> -0.484
> H5 -0.735 0.755 1.898
> H6 -0.295 -1.024 1.866
> O7 1.242 0.364 2.065
> H8 1.938 -0.001 1.499
>
> 3 8
> 2 1 3
>
> "
>
> Y.Tian
--
Jozsef Csontos, Ph.D.
(jozsefcsontos_at_creighton.edu)
Department of Biomedical Sciences
Creighton University,
Omaha, NE
From owner-chemistry@ccl.net Sun Apr 1 10:14:01 2007
From: "Jonathan Kerr jorphancore^_^yahoo.com.cn" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL: Quintet State of Mo Atom and Its NBO analysis
Message-Id: <-33944-070401094210-18480-+HF+lwUIQ0EtVU2c9Zvxxw]![server.ccl.net>
X-Original-From: "Jonathan Kerr" <jorphancore ~ yahoo.com.cn>
Date: Sun, 1 Apr 2007 09:42:06 -0400
Sent to CCL by: "Jonathan Kerr" [jorphancore * yahoo.com.cn]
Dear ccl members
I have a question about the quintet Mo atom when doing NBO analysis.
After stable=opt, and the consequent SP calculation, i have found the stable wavefunction of the quintet Mo atom.
The Alpha Orbitals:
Occupied (A1G) (T1U) (T1U) (T1U) (T2G) (T2G) (T2G) (EG)
(EG)
The Beta Orbitals:
Occupied (A1G) (T1U) (T1U) (T1U) (A1G)
The electronic state of the quintet Mo atom is 5-A1G, that is, this quintet state has a 4d55s1 electron configuration with one 4d orbital that is doubly occupied.This is in agreement with the experimental result that the lowest quintet state of Mo has a 4d55s1 electron configuration.
However, when i ran the NBO analysis,
( uBHandHLYP/SDD pop=nbo geom=check guess=read)
the NAO results showed that
2 Mo 1 S Val( 5S) 1.00000
25 Mo 1 dxy Val( 4d) 1.00000
28 Mo 1 dxz Val( 4d) 1.00000
31 Mo 1 dyz Val( 4d) 1.00000
34 Mo 1 dx2y2 Val( 4d) 1.00000
37 Mo 1 dz2 Val( 4d) 1.00000
The obtained electron configuration was 4d55s1, but the multiplicity changed from quintet to septet.
If I used this input keywords ( uBHandHLYP/SDD pop=nbo geom=check)
the NAO results showed that
2 Mo 1 S Val( 5S) 1.97100
25 Mo 1 dxy Val( 4d) 0.99980
28 Mo 1 dxz Val( 4d) 1.00000
31 Mo 1 dyz Val( 4d) 1.00000
34 Mo 1 dx2y2 Val( 4d) 0.00000
37 Mo 1 dz2 Val( 4d) 1.02421
This time the Mo atom was quintet, but its electron configuration changed into 4d65s0
I can not get the right results when doing NBO analysis.
Any help will be appreciated.
Yours
Jonathan
From owner-chemistry@ccl.net Sun Apr 1 13:01:01 2007
From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas ~~ chem.elte.hu" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL:G: ModRedundant question
Message-Id: <-33945-070401125825-6481-T6e7N3FE/I0xmQSJ/bwuvg(-)server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas <farkas_._chem.elte.hu>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=UTF-8
Date: Sun, 01 Apr 2007 18:57:35 +0200
Mime-Version: 1.0
Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas..chem.elte.hu]
Hi,
Well, the example is not perfect but shows well how to use the
ModRedundant option. It add the bond 3-8 but the angle 2-1-3 should
appear in the list anyway. Many modification in the internal coordinate
definition does not affect the final result, except:
- Freezing some coordinates may lead to different results
- Making the coordinate system incomplete (removing coordinates which
are necessary for describing the geometry and geometry changes) may
cause job failure.
- Making the coordinate system complete (in rare cases it might happen
that the automatic coordinate definition does not produce a numerically
stable coordinate system) may fix previously failed job.
Adding H-bonds as explicite coordinates is in general a good idea and
usually improves optimization convergence. Sometimes changes in the
coordinate system may even cause convergence to a different critical
point of the potential energy surface due to the somewhat different
optimization path.
Best wishes,
Ödön
On Sun, 2007-04-01 at 02:28 -0400, Green Power powergreen^-^gmail.com
wrote:
> Dear CCLers
>
> I am confused by the following example in Gaussian manual. What will
> be the difference if Modredun option were not used. The manual
> explanation is that a hydrogen bond was created between O3 and H8 by
> such redundant coordinate definition. But I can not see say difference
> for the calculated result if such redundant were not used. Any
> suggestion on this will be appreciated.
>
>
> "Specifying Redundant Internal Coordinates. The following input file
> illustrates the method for specifying redundant internal coordinates
> within an input file:
>
> # HF/6-31G(d) Opt=ModRedun Test
>
> Opt job
>
> 0,1
> C1 0.000 0.000 0.000
> C2 0.000 0.000 1.505
> O3 1.047 0.000 -0.651
> H4 -1.000 -0.006
> -0.484
> H5 -0.735 0.755 1.898
> H6 -0.295 -1.024 1.866
> O7 1.242 0.364 2.065
> H8 1.938 -0.001 1.499
>
> 3 8
> 2 1 3
>
> "
>
> Y.Tian
--
Ödön Farkas
Associate professor
Deparment of Organic Chemistry and
Laboratory of Chemical Informatics,
Institute of Chemistry,
Eötvös Loránd University, Budapest
Address: 1/A Pázmány Péter sétány,
H-1117 Budapest, Hungary
Phone: +36-1-372-2570
Cell phone: +36-30-255-3111
Fax: +36-1-372-2620
URL: http://organ.elte.hu/farkas