From owner-chemistry@ccl.net Tue Jul 23 05:09:01 2013 From: "Cina Foroutan-Nejad canyslopus|,|yahoo.co.uk" To: CCL Subject: CCL:G: What settings should I use in G09W to prevent the breaking of a bond? Message-Id: <-48990-130723050749-12987-HOOBU2q5+Jpmx7aTq4cD2A(0)server.ccl.net> X-Original-From: Cina Foroutan-Nejad Content-Type: multipart/alternative; boundary="-1712059246-1916292686-1374570461=:4033" Date: Tue, 23 Jul 2013 10:07:41 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Cina Foroutan-Nejad [canyslopus**yahoo.co.uk] ---1712059246-1916292686-1374570461=:4033 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Gabriela,=0A=0AHow you conclude that "the bond between the thiol group= and the adjacent carbon is broken"? I guess when you opened the output fil= e of your optimization, you realized that there is no "bond" between sulfur= and the neighboring carbon. If it is the case I should say do not worry! I= n each viewer program bond length has a particular definition; for instance= in your viewer software a "single" S-C bond has a particular definition, e= .g. 1.7 to 1.87 A. If the S-C "distance" increases more than 1.87 A then yo= u will see no "line" between S and C. However, it does not necessarily mean= that there is no bond between S and C. Chemical bond has no quantum mechan= ical operator so you cannot simply state that there is no bond between S an= d C based on a simple DFT computation. Measure the distance between S and C= and if you find it in an acceptable range then go ahead and do not worry f= or the absence of so-called "bond". If the distance between C and S is unus= ual, i.e. more than 2.5 A, then repeat your computations on a different workstation = or different version of program. Because, there might be some problem with = your software/hardware.=0AChemical bond is one of the most troublesome conc= epts in chemistry but not in such simple molecule!=0A=0AGood luck,=0ACina F= oroutan-Nejad=0A=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=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=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=3D= =3D=0ACina Foroutan-Nejad, Ph.D.=0Ahttp://muni.academia.edu/CinaForoutanNej= ad=0A=0A=0A=0A=0A________________________________=0A From: Gabriela Arias g= abriela.ariasdelarosa ~~ gmail.com =0ATo: "Forouta= n-Nejad, Cina " =0ASent: Tuesday, 23 July = 2013, 2:02=0ASubject: CCL:G: What settings should I use in G09W to prevent = the breaking of a bond?=0A =0A=0A=0ASent to CCL by: "Gabriela=A0 Arias" [ga= briela.ariasdelarosa[-]gmail.com]=0AHello everyone:=0A=0AI am doing an opti= mization and frequency calculation in Gaussian09 to obtain the Raman and In= frared spectra of cysteine. In the output, the bond between the thiol group= and the adjacent carbon is broken, which is wrong. What can I do to preven= t this bond from breaking? These are the settings that I am using:=0A=0A%np= rocshared=3D2=0A# opt=3Dtight freq=3Draman b3lyp/6-311+g geom=3Dconnectivit= y=0A=0ATitle Card Required=0A=0A-1 1=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2= .18907515=A0 =A0 2.08528252=A0 -2.35362466=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 -2.51526953=A0 =A0 1.22134909=A0 -1.12122202=0AO=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 -2.82257852=A0 =A0 1.77040643=A0 -0.03142030=0AN=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 -0.74900832=A0 =A0 2.37936285=A0 -2.37861038=0AH=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 -0.23470752=A0 =A0 1.52307575=A0 -2.42622442= =0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -0.53719378=A0 =A0 2.94035858=A0 -3.1= 7887183=0AO=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.46894955=A0 -0.20480359=A0 = -1.21525919=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.57949898=A0 =A0 1.32244= 966=A0 -3.63317742=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.02919712=A0 =A0 = 0.40622247=A0 -3.68412445=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.35285743= =A0 =A0 1.92271509=A0 -4.48945717=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.7= 3937700=A0 =A0 3.00150971=A0 -2.30267762=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 -4.08814042=A0 =A0 1.01436550=A0 -3.60700190=0AH=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 -4.35940892=A0 =A0 0.48434527=A0 -4.49604181=0AH=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 -4.63844227=A0 =A0 1.93059270=A0 -3.55605487=0AS=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 -4.46517029=A0 =A0 0.01579310=A0 -2.18253651= =0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -5.74849515=A0 -0.24627848=A0 -2.160= 27033=0A=0A1 2 1.0 4 1.0 8 1.0 11 1.0=0A2 3 2.0 7 1.0=0A3=0A4 5 1.0 6 1.0= =0A5=0A6=0A7=0A8 9 1.0 10 1.0 12 1.0=0A9=0A10=0A11=0A12 13 1.0 14 1.0 15 1.= 0=0A13=0A=0ABest regards and thanks for your help,=0A=0AGabriela=0A=0A=0A= =0A-=3D This is automatically added to each message by the mailing script = =3D-=0ATo recover the email address of the author of the message, please ch= ange=0A= =0A=0A=0AE-mail to sub= scribers: CHEMISTRY=ccl.net or use:=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bi= n/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST=ccl= .net or use=0A=A0 =A0 =A0= =0A=0A=0A=A0 =A0 =A0 http://www.ccl.net/chemistry/su= b_unsub.shtml=0A=0A= =0A=0A=0AConferences: http://server.ccl.net/ch= emistry/announcements/conferences/=0A=0ASearch Messages: http://www.ccl.net= /chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from CCL with 5.= 7.1 error, check:=0A=A0 =A0 =A0=0A=0ARTFI: = http://www.ccl.net/chemistry/aboutccl/instructions/ ---1712059246-1916292686-1374570461=:4033 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Gab= riela,

How y= ou conclude that "the bond between the thiol group and the adjacent carbon = is broken"? I guess when you opened the output file of your optimization, y= ou realized that there is no "bond" between sulfur and the neighboring carb= on. If it is the case I should say do not worry! In each viewer program bon= d length has a particular definition; for instance in your viewer software = a "single" S-C bond has a particular definition, e.g. 1.7 to 1.87 A. If the S-C "distance" increases more than 1.87 A then you will see no "line" = between S and C. However, it does not necessarily mean that there is no bon= d between S and C. Chemical bond has no quantum mechanical operator so you = cannot simply state that there is no bond between S and C based on a simple= DFT computation. Measure the distance between S and C and if you find it i= n an acceptable range then go ahead and do not worry for the absence of so-= called "bond". If the distance between C and S is unusual, i.e. more than 2= .5 A, then repeat your computations on a different workstation or different= version of program. Because, there might be some problem with your softwar= e/hardware.
Chemical bond is one of the most troublesome= concepts in chemistry but not in such simple molecule!

Good luck,
Cina Forout= an-Nejad
=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=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=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=3D=3D
Cina Foroutan-Nejad, Ph.D.
http://muni.academia.edu/CinaForoutanNejad


<= span style=3D"font-weight:bold;">From: Gabriela Arias gabriela.a= riasdelarosa ~~ gmail.com <owner-chemistry=ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus=yahoo.co.uk>
= Sent: Tuesday, 23 July 2013, 2:02
Subject: CCL:G: What settings should I use in G09W t= o prevent the breaking of a bond?


Sent to CCL by: "Gabriela  Arias" [gabriela.ariasdela= rosa[-]gmail.com]
Hello everyone:

I am doing an optimization and = frequency calculation in Gaussian09 to obtain the Raman and Infrared spectr= a of cysteine. In the output, the bond between the thiol group and the adja= cent carbon is broken, which is wrong. What can I do to prevent this bond f= rom breaking? These are the settings that I am using:

%nprocshared= =3D2
# opt=3Dtight freq=3Draman b3lyp/6-311+g geom=3Dconnectivity
Title Card Required

-1 1
C          &n= bsp;     -2.18907515    2.08528252  -2.35362466<= br> C                -2.51526953 = ;   1.22134909  -1.12122202
O        &nb= sp;       -2.82257852    1.77040643  -0.031= 42030
N                -0.7490= 0832    2.37936285  -2.37861038
H      &= nbsp;         -0.23470752    1.52307575 = ; -2.42622442
H               = -0.53719378    2.94035858  -3.17887183
O   =             -2.46894955  -0.20480359&= nbsp; -1.21525919
C              &n= bsp; -2.57949898    1.32244966  -3.63317742
H  &n= bsp;             -2.02919712    0.= 40622247  -3.68412445
H                -2.35285743    1.92271509  -4.489457= 17
H                -2.7393770= 0    3.00150971  -2.30267762
C      &nbs= p;         -4.08814042    1.01436550  = -3.60700190
H                -= 4.35940892    0.48434527  -4.49604181
H    &n= bsp;           -4.63844227    1.9305927= 0  -3.55605487
S              =   -4.46517029    0.01579310  -2.18253651
H  =               -5.74849515  -0.246= 27848  -2.16027033

1 2 1.0 4 1.0 8 1.0 11 1.0
2 3 2.0 7 1= .0
3
4 5 1.0 6 1.0
5
6
7
8 9 1.0 10 1.0 12 1.0
= 9
10
11
12 13 1.0 14 1.0 15 1.0
13

Best regards and thanks for your help,

Gabriela



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---1712059246-1916292686-1374570461=:4033-- From owner-chemistry@ccl.net Tue Jul 23 12:37:00 2013 From: "Susi Lehtola susi.lehtola]_[alumni.helsinki.fi" To: CCL Subject: CCL:G: Orbital plotting tools Message-Id: <-48991-130723101852-12899-No4elLgUDRgLzjLKqbqcbg-*-server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Tue, 23 Jul 2013 17:18:40 +0300 Mime-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi] Hi, I'm looking for a decent software that is able to produce orbital plots > from Gaussian-style formatted checkpoint or cube files. Moreover, I'm interested in software that can be scripted, so that manual labor involved in plotting hundreds of orbitals can be avoided. I've already had a look at Avogadro and IQmol, which don't support scripting. -- --------------------------------------------------------------- Mr. Susi Lehtola, PhD Postdoctoral researcher susi.lehtola\a/alumni.helsinki.fi Department of Applied Physics http://www.helsinki.fi/~jzlehtol Aalto University Finland --------------------------------------------------------------- Susi Lehtola, FT Tutkijatohtori susi.lehtola\a/alumni.helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Aalto-yliopisto --------------------------------------------------------------- From owner-chemistry@ccl.net Tue Jul 23 14:16:00 2013 From: "Dr. Vitaly Chaban vvchaban__gmail.com" To: CCL Subject: CCL:G: What settings should I use in G09W to prevent the breaking of a bond? Message-Id: <-48992-130723121310-31971-nahKVnt8BIuUngbHtCQGCQ|-|server.ccl.net> X-Original-From: "Dr. Vitaly Chaban" Content-Type: multipart/alternative; boundary=001a11c22ac035fd0304e2301182 Date: Tue, 23 Jul 2013 18:12:21 +0200 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly Chaban" [vvchaban|gmail.com] --001a11c22ac035fd0304e2301182 Content-Type: text/plain; charset=ISO-8859-1 If bonds breaks, this means that your method is not perfect for your task. My first step would be to change the method / increase basis set. If B3LYP cannot predict right geometry, how can you be sure that it produces right frequencies and orbital energies? Gaussian can impose certain constraints during optimization, see "freeze" in the manual: http://www.gaussian.com/g_tech/g_ur/k_opt.htm Good luck! Dr. Vitaly V. Chaban On Tue, Jul 23, 2013 at 2:02 AM, Gabriela Arias gabriela.ariasdelarosa ~~ gmail.com wrote: > > Sent to CCL by: "Gabriela Arias" [gabriela.ariasdelarosa[-]gmail.com] > Hello everyone: > > I am doing an optimization and frequency calculation in Gaussian09 to > obtain the Raman and Infrared spectra of cysteine. In the output, the bond > between the thiol group and the adjacent carbon is broken, which is wrong. > What can I do to prevent this bond from breaking? These are the settings > that I am using: > > %nprocshared=2 > # opt=tight freq=raman b3lyp/6-311+g geom=connectivity > > Title Card Required > > -1 1 > C -2.18907515 2.08528252 -2.35362466 > C -2.51526953 1.22134909 -1.12122202 > O -2.82257852 1.77040643 -0.03142030 > N -0.74900832 2.37936285 -2.37861038 > H -0.23470752 1.52307575 -2.42622442 > H -0.53719378 2.94035858 -3.17887183 > O -2.46894955 -0.20480359 -1.21525919 > C -2.57949898 1.32244966 -3.63317742 > H -2.02919712 0.40622247 -3.68412445 > H -2.35285743 1.92271509 -4.48945717 > H -2.73937700 3.00150971 -2.30267762 > C -4.08814042 1.01436550 -3.60700190 > H -4.35940892 0.48434527 -4.49604181 > H -4.63844227 1.93059270 -3.55605487 > S -4.46517029 0.01579310 -2.18253651 > H -5.74849515 -0.24627848 -2.16027033 > > 1 2 1.0 4 1.0 8 1.0 11 1.0 > 2 3 2.0 7 1.0 > 3 > 4 5 1.0 6 1.0 > 5 > 6 > 7 > 8 9 1.0 10 1.0 12 1.0 > 9 > 10 > 11 > 12 13 1.0 14 1.0 15 1.0 > 13 > > Best regards and thanks for your help, > > Gabriela> > > --001a11c22ac035fd0304e2301182 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
If bonds breaks, this means that your method is not perfec= t for your task. My first step would be to change the method / increase bas= is set. If B3LYP cannot predict right geometry, how can you be sure that it= produces right frequencies and orbital energies?

Gaussian can impose certain constraints during optimization, see &= quot;freeze" in the manual:=A0http://www.gaussian.com/g_tech/g_ur/k_opt.htm

Good luck!

Dr. Vitaly V. Chaban
=


<= div class=3D"gmail_extra">


On Tue, Jul 23, 2013 at 2:02 AM, Gabriela = Arias gabriela.ariasdelarosa ~~ gmail.com = <owner-chemistry!A!ccl.net> wrote:

Sent to CCL by: "Gabriela =A0Arias" [gabriela.ariasdelarosa[-]gmail.com]
Hello everyone:

I am doing an optimization and frequency calculation in Gaussian09 to obtai= n the Raman and Infrared spectra of cysteine. In the output, the bond betwe= en the thiol group and the adjacent carbon is broken, which is wrong. What = can I do to prevent this bond from breaking? These are the settings that I = am using:

%nprocshared=3D2
# opt=3Dtight freq=3Draman b3lyp/6-311+g geom=3Dconnectivity

Title Card Required

-1 1
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.18907515 =A0 =A02.08528252 =A0 -2.3= 5362466
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.51526953 =A0 =A01.22134909 =A0 -1.1= 2122202
=A0O =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.82257852 =A0 =A01.77040643 =A0 -0.0= 3142030
=A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -0.74900832 =A0 =A02.37936285 =A0 -2.3= 7861038
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -0.23470752 =A0 =A01.52307575 =A0 -2.4= 2622442
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -0.53719378 =A0 =A02.94035858 =A0 -3.1= 7887183
=A0O =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.46894955 =A0 -0.20480359 =A0 -1.215= 25919
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.57949898 =A0 =A01.32244966 =A0 -3.6= 3317742
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.02919712 =A0 =A00.40622247 =A0 -3.6= 8412445
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.35285743 =A0 =A01.92271509 =A0 -4.4= 8945717
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -2.73937700 =A0 =A03.00150971 =A0 -2.3= 0267762
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -4.08814042 =A0 =A01.01436550 =A0 -3.6= 0700190
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -4.35940892 =A0 =A00.48434527 =A0 -4.4= 9604181
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -4.63844227 =A0 =A01.93059270 =A0 -3.5= 5605487
=A0S =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -4.46517029 =A0 =A00.01579310 =A0 -2.1= 8253651
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -5.74849515 =A0 -0.24627848 =A0 -2.160= 27033

=A01 2 1.0 4 1.0 8 1.0 11 1.0
=A02 3 2.0 7 1.0
=A03
=A04 5 1.0 6 1.0
=A05
=A06
=A07
=A08 9 1.0 10 1.0 12 1.0
=A09
=A010
=A011
=A012 13 1.0 14 1.0 15 1.0
=A013

Best regards and thanks for your help,

Gabriela



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--001a11c22ac035fd0304e2301182-- From owner-chemistry@ccl.net Tue Jul 23 14:51:00 2013 From: "Domenico Quartarolo quartarolo*unical.it" To: CCL Subject: CCL: Stacking interaction Message-Id: <-48993-130723141951-24225-3TgYo+kO+o25EP5vBSGDhA]~[server.ccl.net> X-Original-From: "Domenico Quartarolo" Date: Tue, 23 Jul 2013 14:19:49 -0400 Sent to CCL by: "Domenico Quartarolo" [quartarolo : unical.it] Dear CClers, I have two questions (experimental and theoretical) about the binding energy for the complex formation of a molecule of 88 atoms. The resulting interaction, from quantum-mechanical simulation, between the two starting fragments is mixed (stacking and hydrogen bonding). The first question regards the experimental data: the water solution enthalpy energy derived from spectrophotometry is -55 kJ/mol, on the other side the value from spectrofluorimetric measurements is -12 kJ/mol. Does anyone have experience about the difference between these two methodologies for evaluating thermodynamic parameters? The theoretical question is about the best approach to calculate the binding energy. The TZVP/MP2 and TZVP/DFT-D3 binding energies, that I found, are generally close to the spectrophotometric data, while the SCS-MP2, which should be better than MP2 for non-covalent interactions, is close to the spectrophotometric value. How to explain these results? Could I consider the SCS-MP2 as the reference method? Thanks for your help Quartarolo Domenico From owner-chemistry@ccl.net Tue Jul 23 15:25:00 2013 From: "Adam Tenderholt atenderholt() gmail.com" To: CCL Subject: CCL:G: Orbital plotting tools Message-Id: <-48994-130723145434-10799-ZWjn3nWCETWbgD3NUZv58w:server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=089e011616da6c3e1d04e232525a Date: Tue, 23 Jul 2013 11:54:05 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt]=[gmail.com] --089e011616da6c3e1d04e232525a Content-Type: text/plain; charset=ISO-8859-1 If are using using a 64-bit Mac, take a look at LUMO in the App Store which was written by a former colleague of mine. If you're using Windows or Linux, my approach in grad school was a script to generate POVRAY files using molden and another script to render these to PNG files. The downside to this approach was the POVRAY files often needed to rotated and translated, which I did with a graphical POVRAY editor (kpovmodeler, now defunct as far as I know) and sed. If you want help with this approach, please email me directly so I can send you the scripts. Adam On Tue, Jul 23, 2013 at 7:18 AM, Susi Lehtola susi.lehtola]_[ alumni.helsinki.fi wrote: > > Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi] > Hi, > > > I'm looking for a decent software that is able to produce orbital plots > > from Gaussian-style formatted checkpoint or cube files. Moreover, I'm > interested in software that can be scripted, so that manual labor > involved in plotting hundreds of orbitals can be avoided. > > I've already had a look at Avogadro and IQmol, which don't support > scripting. > -- > --089e011616da6c3e1d04e232525a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 
If are using using a 64-bi=
t Mac, take a look at LUMO in the App Store which
was written by a former colleague of mine.

If you're using Windows or Linux, my approach in grad school was a scri=
pt
to generate POVRAY files using molden and another script to render these to
PNG files. The downside to this approach was the POVRAY files often needed
to rotated and translated, which I did with a graphical POVRAY editor
(kpovmodeler, now defunct as far as I know) and sed. If you want help with
this approach, please email me directly so I can send you the scripts.

Adam


On = Tue, Jul 23, 2013 at 7:18 AM, Susi Lehtola susi.lehtola]_[alumni.helsinki.fi <owner-chemistry:-:ccl.n= et> wrote:

Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi]
Hi,


I'm looking for a decent software that is able to produce orbital plots=
> from Gaussian-style formatted checkpoint or cube files. Moreover, I= 9;m
interested in software that can be scripted, so that manual labor
involved in plotting hundreds of orbitals can be avoided.

I've already had a look at Avogadro and IQmol, which don't support<= br> scripting.
--
--089e011616da6c3e1d04e232525a-- From owner-chemistry@ccl.net Tue Jul 23 16:00:00 2013 From: "kalyan onekalyan^-^yahoo.com" To: CCL Subject: CCL:G: What settings should I use in G09W to prevent the breaking of a bond? Message-Id: <-48995-130723151511-28780-+TjqmewJBQNzeb9ynCiOgQ * server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="_2F565D1F-A33D-5DC1-6418-8D029B007CAA_" Date: Tue, 23 Jul 2013 21:15:00 +0200 MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan.:.yahoo.com] --_2F565D1F-A33D-5DC1-6418-8D029B007CAA_ Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Just use b3lyp/6-311+g(d,p) nosym opt freq pop=3Dfull gfprint . Hope it work.=20 Best Regards=20 Kalyan -----Original Message----- > From: Dr. Vitaly Chaban vvchaban__gmail.com Sent: 23/07/2013 21:06 To: Dhar, Kalyan kumar Subject: CCL:G: What settings should I use in G09W to prevent the breaking = of a bond? If bonds breaks, this means that your method is not perfect for your task. = My first step would be to change the method / increase basis set. If B3LYP = cannot predict right geometry, how can you be sure that it produces right f= requencies and orbital energies? Gaussian can impose certain constraints during optimization, see "freeze" i= n the manual: http://www.gaussian.com/g_tech/g_ur/k_opt.htm Good luck! Dr. Vitaly V. Chaban =20 On Tue, Jul 23, 2013 at 2:02 AM, Gabriela Arias gabriela.ariasdelarosa ~~ g= mail.com wrote: Sent to CCL by: "Gabriela Arias" [gabriela.ariasdelarosa[-]gmail.com] Hello everyone: =20 I am doing an optimization and frequency calculation in Gaussian09 to obtai= n the Raman and Infrared spectra of cysteine. In the output, the bond betwe= en the thiol group and the adjacent carbon is broken, which is wrong. What = can I do to prevent this bond from breaking? These are the settings that I = am using: %nprocshared=3D2 # opt=3Dtight freq=3Draman b3lyp/6-311+g geom=3Dconnectivity =20 Title Card Required =20 -1 1 C -2.18907515 2.08528252 -2.35362466 C -2.51526953 1.22134909 -1.12122202 O -2.82257852 1.77040643 -0.03142030 N -0.74900832 2.37936285 -2.37861038 H -0.23470752 1.52307575 -2.42622442 H -0.53719378 2.94035858 -3.17887183 O -2.46894955 -0.20480359 -1.21525919 C -2.57949898 1.32244966 -3.63317742 H -2.02919712 0.40622247 -3.68412445 H -2.35285743 1.92271509 -4.48945717 H -2.73937700 3.00150971 -2.30267762 C -4.08814042 1.01436550 -3.60700190 H -4.35940892 0.48434527 -4.49604181 H -4.63844227 1.93059270 -3.55605487 S -4.46517029 0.01579310 -2.18253651 H -5.74849515 -0.24627848 -2.16027033 =20 1 2 1.0 4 1.0 8 1.0 11 1.0 2 3 2.0 7 1.0 3 4 5 1.0 6 1.0 5 6 7 8 9 1.0 10 1.0 12 1.0 9 10 11 12 13 1.0 14 1.0 15 1.0 13 =20 Best regards and thanks for your help, =20 Gabriela =20 -=3D This is automatically added to each message by the mailing script =3D-= =20 E-mail to subscribers: CHEMISTRY ~ ccl.net or use:=20 E-mail to administrators: CHEMISTRY-REQUEST ~ ccl.net or use=20http://www.ccl.net/chemistry/sub_unsub.shtml =20=20=20http://www.ccl.net/spammers.txt =20= --_2F565D1F-A33D-5DC1-6418-8D029B007CAA_ Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="iso-8859-1"
Just use b3lyp/6-311+g(d,p) nosym opt freq pop=3Dful= l gfprint .
Hope it work.

Best Regards
Kalyan
From: Dr. Vitaly Chaban vvchaban__gmail.com
S= ent: To: Dhar, Kalyan kumar Subject: CCL:G: What settings should I use in G09W to prevent the b= reaking of a bond?

If bonds breaks, this mea= ns that your method is not perfect for your task. My first step would be to= change the method / increase basis set. If B3LYP cannot predict right geom= etry, how can you be sure that it produces right frequencies and orbital en= ergies?
=0A= =0A=
Gaussian can impose certain constraints during optimization, see "= freeze" in the manual: http://www.gaussian.com/g_tech/g_ur/k_opt.htm
=0A= =0A=
Good luck!

Dr. Vitaly V. Chaban
=
=0A=


<= div class=3D"gmail_extra">


On Tue, Jul 23, 2013 at 2:02 AM, Gabriela = Arias gabriela.ariasdelarosa ~~ gmail.com = <owner-chemistry ~ ccl.net> wrote:
=0A= =0A=

=0A= Sent to CCL by: "Gabriela  Arias" [gabriela.ariasdelarosa[-]gmail.com]
=0A= Hello everyone:
=0A=
=0A= I am doing an optimization and frequency calculation in Gaussian09 to obtai= n the Raman and Infrared spectra of cysteine. In the output, the bond betwe= en the thiol group and the adjacent carbon is broken, which is wrong. What = can I do to prevent this bond from breaking? These are the settings that I = am using:
=0A= =0A= =0A=
=0A= %nprocshared=3D2
=0A= # opt=3Dtight freq=3Draman b3lyp/6-311+g geom=3Dconnectivity
=0A=
=0A= Title Card Required
=0A=
=0A= -1 1
=0A=  C                 -2.18907515=    2.08528252   -2.35362466
=0A=  C                 -2.51526953=    1.22134909   -1.12122202
=0A=  O                 -2.82257852=    1.77040643   -0.03142030
=0A=  N                 -0.74900832=    2.37936285   -2.37861038
=0A=  H                 -0.23470752=    1.52307575   -2.42622442
=0A=  H                 -0.53719378=    2.94035858   -3.17887183
=0A=  O                 -2.46894955=   -0.20480359   -1.21525919
=0A=  C                 -2.57949898=    1.32244966   -3.63317742
=0A=  H                 -2.02919712=    0.40622247   -3.68412445
=0A=  H                 -2.35285743=    1.92271509   -4.48945717
=0A=  H                 -2.73937700=    3.00150971   -2.30267762
=0A=  C                 -4.08814042=    1.01436550   -3.60700190
=0A=  H                 -4.35940892=    0.48434527   -4.49604181
=0A=  H                 -4.63844227=    1.93059270   -3.55605487
=0A=  S                 -4.46517029=    0.01579310   -2.18253651
=0A=  H                 -5.74849515=   -0.24627848   -2.16027033
=0A=
=0A=  1 2 1.0 4 1.0 8 1.0 11 1.0
=0A=  2 3 2.0 7 1.0
=0A=  3
=0A=  4 5 1.0 6 1.0
=0A=  5
=0A=  6
=0A=  7
=0A=  8 9 1.0 10 1.0 12 1.0
=0A=  9
=0A=  10
=0A=  11
=0A=  12 13 1.0 14 1.0 15 1.0
=0A=  13
=0A=
=0A= Best regards and thanks for your help,
=0A=
=0A= Gabriela
=0A=
=0A=
=0A=
=0A= -=3D This is automatically added to each message by the mailing script =3D-= =0A=
=0A= E-mail to subscribers: CHEMISTRY ~ c= cl.net or use:
=0A=       http://www.ccl.net/cgi-bin/ccl/send_ccl_message=
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=0A= Job: http://www.ccl.n= et/jobs
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=0A= = --_2F565D1F-A33D-5DC1-6418-8D029B007CAA_-- From owner-chemistry@ccl.net Tue Jul 23 23:53:00 2013 From: "Bradley Welch bwelch5:_:slu.edu" To: CCL Subject: CCL: Single Point Calculation Not Converging Message-Id: <-48996-130723235223-29726-mx7/zdeHAjw+cfpaSTCQpQ[*]server.ccl.net> X-Original-From: "Bradley Welch" Date: Tue, 23 Jul 2013 23:52:22 -0400 Sent to CCL by: "Bradley Welch" [bwelch5^slu.edu] Dear All, I am attempting to do a single point calculation on the experimental configuration of a dimer from the crystal structure. I first attempted to use a small basis set, and the pure functional BLYP. I used lanl2dz on the Co,N, H, C, and O, and 6-31G* on the Cl. This calculation failed. I then scaled up to QZVP since my first thought was those small basis sets were not flexible enough for the problem. This calculation failed as well. I also ran it without density fitting, but that seems to have not helped at all. Besides using the QC algorithm in G09, what other options do I have available to get this to converge? Would some sort of building up scheme be the best option? I have no expectation any one will attempt to run this through your own computers, but here is the geometry for reference, and the settings I used. #P BLYP/QZVP/QZVP scf=(conver=6) experimental geometry 0 1 27 5.002085847 5.527639519 3.769636231 17 2.775981352 5.742824793 3.450911304 17 5.546753961 3.315125693 3.901329243 7 5.924033679 6.059375512 2.056774986 7 7.367285171 7.017739534 0.538552372 7 5.329847859 6.600279690 5.476159302 7 5.628916118 8.190682272 6.981718950 8 7.992410500 6.757762124 4.087383042 8 7.220472773 9.928071865 0.016751237 8 5.882736218 10.116709493 4.825129579 8 7.549278914 9.813545786 9.131690524 6 5.540311097 5.774325339 0.711331232 6 4.473410144 4.979811059 0.381835999 1 3.859126438 4.546902992 1.015732800 6 4.246513234 4.796851429 -1.007364206 1 3.527710954 4.249846257 -1.320888541 6 5.129536800 5.327712653 -1.918643862 1 4.976995945 5.140184441 -2.876428185 6 6.212200256 6.141215741 -1.566836291 1 6.795373031 6.518924731 -2.189646747 6 6.379741752 6.271667542 -0.159858692 6 7.062037912 6.924128185 1.797355812 6 7.855453225 7.488696470 2.876591627 6 8.408420196 8.653596538 3.066796656 1 8.476585953 9.339403196 2.490968423 6 9.036221671 8.638557761 4.323484816 1 9.578333942 9.315788022 4.764173567 6 8.797552510 7.455617781 4.935914205 6 9.114843207 6.838967224 6.282960453 1 9.640525734 7.427288969 6.723441028 1 9.617140474 6.063666005 6.113289936 1 8.320796846 6.635830003 6.723346510 6 8.443256052 7.758533777 -0.099336545 1 8.878214897 7.254709403 -0.798582485 1 9.134483581 8.017438368 0.636198222 6 7.991736354 9.063272518 -0.716794079 6 8.123463108 9.526253294 -1.931202696 1 8.601822942 9.113404964 -2.673626264 6 7.463396364 10.840068634 -1.913221842 1 7.392018278 11.446942470 -2.698319207 6 7.006514398 10.984022095 -0.744299342 6 6.076473429 12.059683829 -0.186844583 1 5.940562627 12.790816725 -0.747644153 1 6.508438605 12.393163095 0.645607847 1 5.293794132 11.649869317 0.120246634 6 5.477736092 6.011069398 6.726417264 6 5.478849464 4.677047884 7.148806369 1 5.436191064 3.962625722 6.608309113 6 5.677829464 4.335773695 8.507904704 1 5.654313312 3.458777704 8.790046029 6 5.750707559 5.439454187 9.440596345 1 5.890759969 5.189993974 10.383390984 6 5.814237718 6.751734681 9.082420310 1 5.933671202 7.458874795 9.721758410 6 5.682694713 6.981782150 7.731808973 6 5.419022403 7.894567699 5.697568848 6 5.195478578 8.861443412 4.667418699 6 4.498452769 8.933642581 3.493283303 1 3.929991077 8.260361931 3.243455039 6 4.645736250 10.200269116 2.925951823 1 4.278773756 10.506328025 2.107154476 6 5.538905685 10.844249658 3.775817889 6 6.111700614 12.283006626 3.690195386 1 5.897147563 12.709706680 2.950172085 1 7.116130616 12.139044805 3.684531374 1 5.902181139 12.766313588 4.474706074 6 5.674480281 9.542153156 7.660702360 1 5.192471789 10.125687167 7.023651283 1 5.216127277 9.541459686 8.487633745 6 7.145210290 9.987642162 7.838999763 6 8.028668417 10.552104249 7.083290724 1 7.922985320 10.868278474 6.233110557 6 9.221774683 10.754249594 7.965688270 1 10.031752812 11.131834119 7.662147491 6 8.902972867 10.351545018 9.119819534 6 9.642903903 10.254134645 10.424869646 1 10.537195137 10.599571129 10.309738383 1 9.761768034 9.294885842 10.739370881 1 9.162129307 10.677801631 11.134509494 27 2.877414389 7.598002607 12.260829584 17 5.076996807 7.424383099 12.516765924 17 2.281502170 9.796256518 12.094466462 7 1.952797307 6.953534573 13.943619270 7 0.525865321 6.045931131 15.504106500 7 2.550167703 6.501577388 10.477582499 7 2.291295147 4.916333272 8.989998318 8 -0.134789408 6.386924003 11.970589278 8 0.591908871 3.157716510 15.962595004 8 1.962654620 2.978953678 11.178389063 8 0.194237522 3.275420766 6.863509088 6 2.306366041 7.388901708 15.250844444 6 3.413458621 8.155646453 15.651447671 1 4.010956547 8.562586504 14.975538228 6 3.612633001 8.333547764 16.940881809 1 4.309938891 8.853312146 17.328905422 6 2.761562682 7.774519705 17.966472115 1 2.841856052 7.976868162 18.831452782 6 1.622343042 6.993885174 17.545296100 1 1.088412665 6.593336084 18.111711793 6 1.456504667 6.801973874 16.148733162 6 0.830395129 6.254180958 14.158715927 6 -0.021812943 5.651391048 13.025286191 6 -0.620235679 4.421606331 12.976813723 1 -0.638085005 3.669896993 13.486953612 6 -1.170851985 4.472630296 11.636591740 1 -1.713443293 3.792468062 11.267257298 6 -0.892543886 5.646539067 11.104327598 6 -1.275391950 6.306419281 9.773947095 1 -1.787872517 5.729962116 9.274471352 1 -1.679213207 7.140530959 9.908860837 1 -0.440979317 6.457092259 9.277623117 6 -0.639069324 5.319034642 16.094740524 1 -0.989950910 5.862226174 16.752918343 1 -1.234994765 5.078858456 15.403253987 6 -0.064617146 4.093908675 16.716790370 6 -0.220772479 3.544304370 18.012050641 1 -0.733055092 3.986570661 18.616283855 6 0.425821649 2.258182130 17.922435093 1 0.471244655 1.654574994 18.662621366 6 0.893695721 2.108356575 16.796684152 6 1.728583214 1.096985675 16.170343932 1 1.895416019 0.382305766 16.758195416 1 1.354395066 0.650640505 15.352506543 1 2.628371432 1.471616836 15.868729962 6 2.357656655 7.104492030 9.289366565 6 2.366439959 8.426015676 8.838112721 1 2.470425971 9.122988904 9.449136744 6 2.181450698 8.689088557 7.454493003 1 2.218549373 9.584447907 7.148028971 6 2.007827071 7.628363483 6.590550216 1 1.968561839 7.933270679 5.654382158 6 2.044282172 6.353490560 6.943303150 1 1.876694612 5.672839855 6.356636578 6 2.191853895 6.123360881 8.318243329 6 2.456106617 5.213530597 10.310445730 6 2.669990175 4.194002381 11.340552735 6 3.377823281 4.215711635 12.477358237 1 3.924207954 4.815916857 12.820795833 6 3.203492349 2.886398776 13.047974548 1 3.615024603 2.572002796 13.878331158 6 2.354981994 2.216217400 12.259920146 6 1.646921395 0.866559886 12.258584813 1 2.026313010 0.411722858 13.143856688 1 0.781277169 0.950827057 12.306177086 1 1.935590075 0.433359728 11.510914001 6 2.147219720 3.523211592 8.349471974 1 2.661708055 2.926859771 8.937550033 1 2.584773502 3.592651357 7.551331747 6 0.734961031 3.098741994 8.109218860 6 -0.201240890 2.513278379 8.862315795 1 -0.042523805 2.243205588 9.809955560 6 -1.327777425 2.343464001 8.118178819 1 -2.091174002 2.013287589 8.359381223 6 -1.030184150 2.787991531 6.909908034 6 -1.792097118 2.922813975 5.619415598 1 -2.701670008 2.502836806 5.692255413 1 -1.820195348 3.802383476 5.315545842 1 -1.275371663 2.375694279 4.910314058 Bradley Welch