From owner-chemistry@ccl.net Sun Apr 1 02:31:01 2007 From: "Green Power powergreen^-^gmail.com" To: CCL Subject: CCL:G: ModRedundant question Message-Id: <-33942-070401022832-20493-Xepe/52SZEji7/uTnHkX+A]~[server.ccl.net> X-Original-From: "Green Power" 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

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-- From owner-chemistry@ccl.net Sun Apr 1 09:39:00 2007 From: "Jozsef Csontos jozsefcsontos#%#creighton.edu" To: CCL Subject: CCL:G: ModRedundant question Message-Id: <-33943-070401093240-16994-Z++xr5wxXGuuAN/ewEP52Q#%#server.ccl.net> X-Original-From: Jozsef Csontos 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" 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" 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" 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 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