From owner-chemistry ":at:" ccl.net Fri Sep 19 13:38:00 2014 From: "John McKelvey jmmckel:_:gmail.com" To: CCL Subject: CCL:G: MOPAC - Problem with Iron complex and gradients Message-Id: <-50518-140919100656-2761-ZY/7HEncFmbVLSTqt46L5Q[]server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001a11c1f546c6507d05036b9c9b Date: Fri, 19 Sep 2014 10:06:50 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel _ gmail.com] --001a11c1f546c6507d05036b9c9b Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable 1) First, optimize the geometry with xyz PM7 ef scfcrt=3D1.d-10 UHF CHARGE=3D2 Quintet BONDS AUX & gnorm=3D0.1 let ddmin=3D0. DUMMY line Note: be sure there are 3 lines of text before the 'Fe" card 2: Carve a new input from the associated ".arc" file 3: Add solvent parameters to second line and re-optimize. 4: Redo 2 and add thermo info to second line and remove "ef" from line 1. John On Fri, Sep 19, 2014 at 7:11 AM, Henrique C. S. Junior henriquecsj^^^ gmail.com wrote: > The same happens with ORCA as well. > > --- > *Henrique C. S. Junior* > Qu=C3=ADmica Industrial - UFRRJ > Centro de Processamento de Dados - PMP > > > On Wednesday, September 17, 2014 12:27 PM, "Henrique Castro Silva > Junior henriquecsj|,|gmail.com" wrote: > > > > Sent to CCL by: "Henrique Castro Silva Junior" [henriquecsj**gmail.com] > Hi, I am an undergraduate in Chemistry from Brazil, writing my thesis as > a requirement to receive my graduation. Im working in thermodynamic (and > MO) descriptions that takes place in [Fe(OH2)6]2+ --> [Fe(OH2)6]3+, > mostly using computational chemistry softwares. > I have decided to use MOPAC2012 and Gabedit (as a GUI), but Im having > problems in getting realistic values. Here is my input: > > * =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 > * Input file for Mopac > * =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 > PM7 THERMO ROT=3D1 EPS=3D78.39 RSOLV=3D1.3 UHF CHARGE=3D2 Quintet BONDS= AUX > Mopac file generated by Gabedit > Fe -0.1136 1 -0.9091 1 0.0000 1 > O -0.1136 1 0.9109 1 0.0000 1 > H 0.5055 1 1.2122 1 -0.7127 1 > O 1.7064 1 -0.9091 1 0.0000 1 > H 2.0628 1 -1.3124 1 0.8307 1 > O -0.1136 1 -0.9091 1 -1.8200 1 > H -0.4817 1 -1.7682 1 -2.1477 1 > O -0.1136 1 -2.7291 1 0.0000 1 > H -0.8413 1 -3.0457 1 0.5936 1 > O -1.9336 1 -0.9091 1 0.0000 1 > H -2.2569 1 -1.5900 1 -0.6429 1 > O -0.1136 1 -0.9091 1 1.8200 1 > H -1.0440 1 -0.9414 1 2.1566 1 > H -2.2613 1 -0.0487 1 -0.3649 1 > H 0.7122 1 -3.0886 1 0.4108 1 > H -0.7542 1 -0.2257 1 -2.1427 1 > H 2.0192 1 -1.5032 1 -0.7289 1 > H 0.3089 1 -1.7285 1 2.1807 1 > H 0.3233 1 1.2180 1 0.8341 1 > > The result is this: > > GRADIENT NORM =3D 298.62520 > ** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED, > (LIMIT=3D10) ** > EITHER ADD 'LET' OR REDUCE GRADIENT > USING 'TS' OR OTHER GEOMETRY OPTIMIZER > > If I add the keyword LET the calculation goes on, returning this: > HEAT OF FORMATION =3D -39.019942 KCALS/MOLE > > With bond distance of ~1,82 A (much less than what is expected, right?). > Then, I tried to perform an optimization first, to reduce the gradient > and do not use LET: > PM7 XYZ EPS=3D78.39 RSOLV=3D1.3 UHF CHARGE=3D2 Quintet BONDS AUX > > The result is a fragmentation, [Fe(OH)6] + 6H and the same result (the > fragmentation) goes with Gaussian09. > Any help will be very much appreciated and Im sorry if Im making some > obvious and stupid mistake here, but most of my knowledge on > computational chemistry Ive learned by myself. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> the strange characters on the top line to the * sign. You can also> > E-mail to subscribers: CHEMISTRY*ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use> > > > > --=20 John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel,+,gmail.com --001a11c1f546c6507d05036b9c9b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

1) First, optimize the geometry with
xyz PM7 ef scfcrt=3D1.d-10 UHF CHARGE=3D2 Quintet BONDS A= UX &
gnorm=3D0.1 let ddmin=3D0.
DUMMY lin= e

Note: be sure there are 3 lines of text before t= he 'Fe" card

2: Carve a new input from th= e associated ".arc" file

3: Add solvent = parameters to second line and re-optimize.

4: Redo= 2 and add thermo info to second line and remove "ef" from line 1= .



John

On Fri, Sep 19, 201= 4 at 7:11 AM, Henrique C. S. Junior henriquecsj^^^gmail.com <owner-chemistry,+,ccl.net> wrote:
=
The same happens with ORCA as well.
= =C2=A0
---
Henrique C. S. Junior
Qu=C3=ADmica Industrial = - UFRRJ
Centro de Processamento de Dados - PMP

On Wednesday, S= eptember 17, 2014 12:27 PM, "Henrique Castro Silva Junior henriquecsj|= ,|gmail.com" <ow= ner-chemistry*ccl.net> = wrote:



Sent to CCL by: "Henrique= Castro Silva Junior" [henriquecsj**gmail.com]
Hi, I am an undergraduate in Chemistry from = Brazil, writing my thesis as
a requirement to receive my graduation. Im= working in thermodynamic (and
MO) descriptions that takes place in [Fe= (OH2)6]2+ --> [Fe(OH2)6]3+,
mostly using computational chemistry sof= twares.
I have decided to use MOPAC2012 and Gabedit (as a GUI), but Im h= aving
problems in getting realistic values. Here is my input:

* = =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
* Input file for Mopac
* =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
PM= 7 THERMO ROT=3D1=C2=A0 EPS=3D78.39 RSOLV=3D1.3 UHF CHARGE=3D2 Quintet=C2=A0= BONDS AUX
Mopac file generated by Gabedit
Fe=C2=A0 -0.1136=C2=A0 1 = -0.9091=C2=A0 1 0.0000=C2=A0 1
O=C2=A0 -0.1136=C2=A0 1 0.9109=C2=A0 1 0.= 0000=C2=A0 1
H=C2=A0 0.5055=C2=A0 1 1.2122=C2=A0 1 -0.7127=C2=A0 1
O= =C2=A0 1.7064=C2=A0 1 -0.9091=C2=A0 1 0.0000=C2=A0 1
H=C2=A0 2.0628=C2=A0 1 -1.3124=C2=A0 1 0.8307=C2=A0 1
O=C2=A0 -0.1= 136=C2=A0 1 -0.9091=C2=A0 1 -1.8200=C2=A0 1
H=C2=A0 -0.4817=C2=A0 1 -1.7= 682=C2=A0 1 -2.1477=C2=A0 1
O=C2=A0 -0.1136=C2=A0 1 -2.7291=C2=A0 1 0.00= 00=C2=A0 1
H=C2=A0 -0.8413=C2=A0 1 -3.0457=C2=A0 1 0.5936=C2=A0 1
O= =C2=A0 -1.9336=C2=A0 1 -0.9091=C2=A0 1 0.0000=C2=A0 1
H=C2=A0 -2.2569=C2= =A0 1 -1.5900=C2=A0 1 -0.6429=C2=A0 1
O=C2=A0 -0.1136=C2=A0 1 -0.9091=C2= =A0 1 1.8200=C2=A0 1
H=C2=A0 -1.0440=C2=A0 1 -0.9414=C2=A0 1 2.1566=C2= =A0 1
H=C2=A0 -2.2613=C2=A0 1 -0.0487=C2=A0 1 -0.3649=C2=A0 1
H=C2=A0= 0.7122=C2=A0 1 -3.0886=C2=A0 1 0.4108=C2=A0 1
H=C2=A0 -0.7542=C2=A0 1 -= 0.2257=C2=A0 1 -2.1427=C2=A0 1
H=C2=A0 2.0192=C2=A0 1 -1.5032=C2=A0 1 -0= .7289=C2=A0 1
H=C2=A0 0.3089=C2=A0 1 -1.7285=C2=A0 1 2.1807=C2=A0 1
H= =C2=A0 0.3233=C2=A0 1 1.2180=C2=A0 1 0.8341=C2=A0 1

The result is th= is:

GRADIENT NORM =3D 298.62520
** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED,
(LIMIT=3D10) **
EITHER ADD &#= 39;LET' OR REDUCE GRADIENT
USING 'TS' OR OTHER GEOMETRY OPT= IMIZER

If I add the keyword LET the calculation goes on, returning t= his:
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 HEAT OF FORMATION =3D=C2=A0 =C2= =A0 -39.019942 KCALS/MOLE

With bond distance of ~1,82 A (much less = than what is expected, right?).
Then, I tried to perform an optimization= first, to reduce the gradient
and do not use LET:
PM7 XYZ=C2=A0 EPS= =3D78.39 RSOLV=3D1.3 UHF CHARGE=3D2 Quintet=C2=A0 BONDS AUX

The resu= lt is a fragmentation, [Fe(OH)6] + 6H and the same result (the
fragment= ation) goes with Gaussian09.
Any help will be very much appreciated and = Im sorry if Im making some
obvious and stupid mistake here, but most of= my knowledge on
computational chemistry Ive learned by myself.

=

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=



--
John McKelvey
10819 Middleford Pl
Ft W= ayne, IN 46818
260-489-2160
jmmc= kel,+,gmail.com --001a11c1f546c6507d05036b9c9b--