Hi,

Maybe it may help

1. I am asking weather th= is order is correct or not?

you can put in any order freely

2. can I use a= solvent except solvents in gaussian09?

Yes, by specify the d= ielectric constant

http://www.gaussian.com/g_tech/g_ur/k_scrf.htm

<= div class=3D"" style=3D"">

Daniel
Universit=E9 de Gen=E8ve, Switzerland

On Wednesday, 10 Septemb= er 2014, 8:23, fateme sabzalizade fatemesabzalizade=3Dgmail.com <owner-c= hemistry_-_ccl.net> wrote:

=
Sent to CCL by: "fateme sabzalizade" [fatem= esabzalizade|gmail.com]
Hi friends
I am working on biomolecule intraction. I have optimized the stru= cture of two my compound in both vacuum as well as solvent(PCM and cpcm mod= el) using b3lyp/6-311++G** basis.for cpcm model I using syntax
# b3lyp/6-311++g** opt freq scrf=3D(cpcm,solvent=3DH2O)
I have several questions about using from Gaussian:
1. I am asking weather this order is correct or not?2. can I use a solvent except solvents in gaussian09?
3. How I can study biomol= ecule intraction in natural condition?
4. How I st= udy exchange structural?

please help me

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--813071025-1536046545-1410959532=:65621-- From owner-chemistry@ccl.net Wed Sep 17 10:05:00 2014 From: "Henrique Castro Silva Junior henriquecsj|,|gmail.com" To: CCL Subject: CCL:G: MOPAC - Problem with Iron complex and gradients Message-Id: <-50501-140917092627-9136-gETsetFQB3gEHbRIoIjnAw .. server.ccl.net> X-Original-From: "Henrique Castro Silva Junior" Date: Wed, 17 Sep 2014 09:26:25 -0400 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: * =============================== * Input file for Mopac * =============================== PM7 THERMO ROT=1 EPS=78.39 RSOLV=1.3 UHF CHARGE=2 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 = 298.62520 ** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED, (LIMIT=10) ** 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 = -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=78.39 RSOLV=1.3 UHF CHARGE=2 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. From owner-chemistry@ccl.net Wed Sep 17 15:02:00 2014 From: "John McKelvey jmmckel/./gmail.com" To: CCL Subject: CCL:G: runing in gaussian 09 Message-Id: <-50502-140917145939-4218-dpJHg0ljrDxetTGnjfjQHQ.:.server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001a11c251def9d97005034777f9 Date: Wed, 17 Sep 2014 14:59:33 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel]![gmail.com] --001a11c251def9d97005034777f9 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable How big is your system? 6-31G/++** seems like a whopping big basis set to me. Also for solvation studies one might first try 6-31G*, and add basis functions as seems appropriate. John On Wed, Sep 17, 2014 at 9:12 AM, Daniel daniel danielkimia2004*yahoo.com < owner-chemistry[A]ccl.net> wrote: > Hi, > > Maybe it may help > 1. I am asking weather this order is correct or not? > you can put in any order freely > 2. can I use a solvent except solvents in gaussian09? > Yes, by specify the dielectric constant > http://www.gaussian.com/g_tech/g_ur/k_scrf.htm > > > Daniel > Universit=C3=A9 de Gen=C3=A8ve, Switzerland > > > On Wednesday, 10 September 2014, 8:23, fateme sabzalizade > fatemesabzalizade=3Dgmail.com wrote: > > > > Sent to CCL by: "fateme sabzalizade" [fatemesabzalizade|gmail.com] > Hi friends > I am working on biomolecule intraction. I have optimized the structure of > two my compound in both vacuum as well as solvent(PCM and cpcm model) usi= ng > b3lyp/6-311++G** basis.for cpcm model I using syntax > # b3lyp/6-311++g** opt freq scrf=3D(cpcm,solvent=3DH2O) > I have several questions about using from Gaussian: > 1. I am asking weather this order is correct or not? > 2. can I use a solvent except solvents in gaussian09? > 3. How I can study biomolecule intraction in natural condition? > 4. How I study exchange structural? > > please help me > > > > -=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[A]gmail.com --001a11c251def9d97005034777f9 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

How big is your system?=C2=A0 6-31G/++** seems like a= whopping big basis set to me.=C2=A0 Also for solvation studies one might f= irst try 6-31G*, and add basis functions as seems appropriate.

John

O= n Wed, Sep 17, 2014 at 9:12 AM, Daniel daniel danielkimia2004*yahoo.com <owner-chemistry[A]ccl.net> wrote:

Hi= ,

Maybe it may help
1. I = am asking weather this order is correct or not?
you can put in any order fr= eely
2. can I use a solvent except sol= vents in gaussian09?
Yes, by specif= y the dielectric constant
http://www.gaussian.com/g_tech/g_ur= /k_scrf.htm

=C2=A0
Daniel
Universit=C3=A9 de Gen=C3=A8ve, Switzerlan= d

On Wednesday, 10 September 2014, 8:23, fateme sa= bzalizade fatemesabzalizade=3Dgmail.com <owner-chemistry%ccl.net> wrote:

Sent to = CCL by: "fateme=C2=A0 sabzalizade" [fatemesabzalizade|gmail.com]
Hi friends
I am wo= rking on biomolecule intraction. I have optimized the structure of two my c= ompound in both vacuum as well as solvent(PCM and cpcm model) using b3lyp/6= -311++G** basis.for cpcm model I using syntax
# b3lyp/6-311++g** opt fre= q scrf=3D(cpcm,solvent=3DH2O)
I have several questions about using from = Gaussian:
1. I am asking weather this order is correct or not?
2. can= I use a solvent except solvents in gaussian09?
3. How I can study biomolecule intraction in na= tural condition?
4. How I study exchange structural?

please help = me

-=3D This is automatically added to each message by the m= ailing script =3D-
To recover the email address of the author of the mes= sage, please change
the strange characters on the top line to the % sign= . You can also=
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--
John McKelvey10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel[A]gmail.com

--001a11c251def9d97005034777f9--