: >> >>> >>> Sent to CCL by: >>> =3D?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic= =3D?=3D >>> [hayak|ariel.ac.il] >>> I had calculated this molecule and everything was o.k. >>> Please try to change your initial configuration. >>> Haya >>> >>> >>> >>> >>> -----Original Message----- >>> > From: owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net [mailto: >>> owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net] On Behalf Of Ayesha Ina= yat >>> ayeshainayat9898++gmail.com >>> Sent: Tuesday, July 19, 2016 11:36 AM >>> To: =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5= - =D7=93=D7=A8/Haya Kornweitz - Dr' >>> Subject: CCL:G: DFT studies of H2O2 >>> >>> >>> Sent to CCL by: "Ayesha Inayat" [ayeshainayat9898#gmail.com] Dear CCL >>> members I am doing DFT calculation of H2O2(Hydrogen per oxide) at GAUSS= IAN >>> 09 software with various hybrid functions, After optimization the struc= ture >>> in an output file shows that the single bond between two oxygens in H2O= 2 is >>> missing. >>> Would any one please guide me why its happening???http://www.ccl.net/chemi= stry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt >>> >>> >>> -=3D This is automatically added to each message by the mailing script = =3D- >>> E-mail to subscribers: CHEMISTRY{}ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net or use>>> >>> >>> >> > > > -- > > > --001a114b18ba752bc105381f58be Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear Paco:

Thank you for helping me out.

I w= ant to ask that If I rebond the 2 oxygens in the output file, Can I use tha= t image for further calculation.

Here are some of the =C2=A0detai= ls about calculations.

Software: GUASSIAN 09

Theory : D= FT

Hybrid Function: B3LYP

Basis Set: 631-G

Gu= ass View used for visualizing the output file

On Tue, Jul 19, 2016 at 10:35 PM, F= rancisco Partal Ure=C3=B1a fpartal . ujaen.es <owner-chemistry*ccl.net> wrote:

Dear Ayesha: I guess you are using GaussV= iew. If so, there is no problem with your calculations, it is only that the= O-O bond lengths obtained in them are higher than a single O-O bond for Ga= ussView cutoffs. As Victor says is a visualization artifact. Just rebond us= ing the 'bond definition' icon. If you are using another visualizat= ion software then use the proper way to do that.

Best re= gards,

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Paco

2016-0= 7-19 17:43 GMT+02:00 Victor Rosas Garcia rosas.victor,gmail.com <owner-chemistry{}ccl.n= et>:
=
It could be a visualization artifact, but it would be necessary t= o know how you found out that the bond is "missing". Did you use = some visualization package? did you read a bond order from a text output fi= le? did you do some kind of critical point analysis that shows no critical = point between the oxygen atoms?

Without this information, it i= s hard to help you.

Best regards

Victor
=

2016-07-19 8:09 G= MT-05:00 =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7= =A5 - =D7=93=D7=A8/Haya Kornweitz - Dr' hayak ~~ ariel.ac.il <owner-chemistry{}cc= l.net>:

Sent to CCL by: =3D?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2Vp= dHogLSBEcic=3D?=3D
=C2=A0 =C2=A0 =C2=A0 =C2=A0 [hayak|ariel.ac.il]
I had calculated this molecule and everything was o.k.
Please try to change your initial configuration.
Haya

-----Original Message-----
> From: owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net [mailto:owner-chemistry+hayak=3D=3D= ariel.ac.il:ccl.net] On Behalf Of Ayesha Inayat ayeshainayat9898++gmail.com
Sent: Tuesday, July 19, 2016 11:36 AM
To: =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 - = =D7=93=D7=A8/Haya Kornweitz - Dr'
Subject: CCL:G: DFT studies of H2O2

Sent to CCL by: "Ayesha=C2=A0 Inayat" [ayeshainayat9898#gmail.com] D= ear CCL members I am doing DFT calculation of H2O2(Hydrogen per oxide) at G= AUSSIAN 09 software with various hybrid functions, After optimization the s= tructure in an output file shows that the single bond between two oxygens i= n H2O2 is missing.
Would any one please guide me why its happening???http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemi= stry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY{}ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/

--
=

<= /div>

--001a114b18ba752bc105381f58be-- From owner-chemistry@ccl.net Thu Jul 21 04:16:01 2016 From: "=?UTF-8?Q?Francisco_Partal_Ure=C3=B1a?= fpartal-.-ujaen.es" To: CCL Subject: CCL: DFT studies of H2O2 Message-Id: <-52321-160721040229-18046-NS2kL+OTxMDFI+qm4z+jIg]^[server.ccl.net> X-Original-From: =?UTF-8?Q?Francisco_Partal_Ure=C3=B1a?= Content-Type: multipart/alternative; boundary=001a113f399aa62cd8053820bca4 Date: Thu, 21 Jul 2016 10:02:17 +0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Francisco_Partal_Ure=C3=B1a?= [fpartal,ujaen.es] --001a113f399aa62cd8053820bca4 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Ayesha: You are going to manually draw a single bond between the two oxygen atoms, without changing bond length. The molecular structure will not vary and you can use it in a further calculation. Best regards, Paco 2016-07-21 8:22 GMT+02:00 ayesha inayat ayeshainayat9898.|a|.gmail.com < owner-chemistry|a|ccl.net>: > Dear Paco: > Thank you for helping me out. > I want to ask that If I rebond the 2 oxygens in the output file, Can I us= e > that image for further calculation. > Here are some of the details about calculations. > Software: GUASSIAN 09 > Theory : DFT > Hybrid Function: B3LYP > Basis Set: 631-G > Guass View used for visualizing the output file > > On Tue, Jul 19, 2016 at 10:35 PM, Francisco Partal Ure=C3=B1a fpartal . > ujaen.es wrote: > >> Dear Ayesha: I guess you are using GaussView. If so, there is no problem >> with your calculations, it is only that the O-O bond lengths obtained in >> them are higher than a single O-O bond for GaussView cutoffs. As Victor >> says is a visualization artifact. Just rebond using the 'bond definition= ' >> icon. If you are using another visualization software then use the prope= r >> way to do that. >> >> Best regards, >> >> Paco >> >> >> 2016-07-19 17:43 GMT+02:00 Victor Rosas Garcia rosas.victor,gmail.com < >> owner-chemistry{}ccl.net>: >> >>> It could be a visualization artifact, but it would be necessary to know >>> how you found out that the bond is "missing". Did you use some >>> visualization package? did you read a bond order from a text output fil= e? >>> did you do some kind of critical point analysis that shows no critical >>> point between the oxygen atoms? >>> >>> Without this information, it is hard to help you. >>> >>> Best regards >>> >>> Victor >>> >>> 2016-07-19 8:09 GMT-05:00 =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0= =D7=95=D7=95=D7=99=D7=A5 - =D7=93=D7=A8/Haya Kornweitz - Dr' hayak >>> ~~ ariel.ac.il : >>> >>>> >>>> Sent to CCL by: >>>> =3D?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic= =3D?=3D >>>> [hayak|ariel.ac.il] >>>> I had calculated this molecule and everything was o.k. >>>> Please try to change your initial configuration. >>>> Haya >>>> >>>> >>>> >>>> >>>> -----Original Message----- >>>> > From: owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net [mailto: >>>> owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net] On Behalf Of Ayesha In= ayat >>>> ayeshainayat9898++gmail.com >>>> Sent: Tuesday, July 19, 2016 11:36 AM >>>> To: =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7= =A5 - =D7=93=D7=A8/Haya Kornweitz - Dr' >>>> Subject: CCL:G: DFT studies of H2O2 >>>> >>>> >>>> Sent to CCL by: "Ayesha Inayat" [ayeshainayat9898#gmail.com] Dear CCL >>>> members I am doing DFT calculation of H2O2(Hydrogen per oxide) at GAUS= SIAN >>>> 09 software with various hybrid functions, After optimization the stru= cture >>>> in an output file shows that the single bond between two oxygens in H2= O2 is >>>> missing. >>>> Would any one please guide me why its happening???http://www.ccl.net/chem= istry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt >>>> >>>> >>>> -=3D This is automatically added to each message by the mailing script= =3D- >>>> E-mail to subscribers: CHEMISTRY{}ccl.net or use:>>>> >>>> E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net or use>>>> Conferences: http://server.ccl.net/chemistry/announcements/conferences= />>>> >>>> >>>> >>> >> >> >> -- >> >> >> > -- --001a113f399aa62cd8053820bca4 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

=C2=A0=C2=A0=C2=A0=C2=A0 Dear Ayesha: You are going t= o manually draw a single bond between the two oxygen atoms, without changin= g bond length.=C2=A0The molecular structure will not vary and you can use i= t=C2=A0in a further calculation.

=C2=A0=C2=A0=C2= =A0=C2=A0 Best regards,

=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Paco

2016-07-21 8:22 GMT+0= 2:00 ayesha inayat ayeshainayat9898.|a|.gmail.co= m <owner-chemistry|a|ccl.net>:

=
Dear Paco:
Thank you for helping me out.
I w= ant to ask that If I rebond the 2 oxygens in the output file, Can I use tha= t image for further calculation.
Here are some of the =C2=A0detai= ls about calculations.
Software: GUASSIAN 09
Theory : D= FT
Hybrid Function: B3LYP
Basis Set: 631-G
Gu= ass View used for visualizing the output file

On Tue, Jul 19, 2016 at 10:35 PM, F= rancisco Partal Ure=C3=B1a fpartal . ujaen.es <owner-chemistry]*[ccl.net> wro= te:
Dear Ayesha: I guess you are using= GaussView. If so, there is no problem with your calculations, it is only t= hat the O-O bond lengths obtained in them are higher than a single O-O bond= for GaussView cutoffs. As Victor says is a visualization artifact. Just re= bond using the 'bond definition' icon. If you are using another vis= ualization software then use the proper way to do that.

= Best regards,

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 P= aco

2016-07-19 17:43 GMT+02:00 Victor Rosas Garcia rosas.victor,gmail.com <owner-chemistry= {}ccl.net>:
It could be a visualization artifact, but it would be necessary to know = how you found out that the bond is "missing". Did you use some vi= sualization package? did you read a bond order from a text output file? did= you do some kind of critical point analysis that shows no critical point b= etween the oxygen atoms?

Without this information, it is hard = to help you.

Best regards

Victor

2016-07-19 8:09 GMT-05:0= 0 =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 - =D7= =93=D7=A8/Haya Kornweitz - Dr' hayak ~~ ariel.ac.il <owner-chemistry{}ccl.net= >:

Sent to CCL by: =3D?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2Vp= dHogLSBEcic=3D?=3D
=C2=A0 =C2=A0 =C2=A0 =C2=A0 [hayak|ariel.ac.il]
I had calculated this molecule and everything was o.k.
Please try to change your initial configuration.
Haya

-----Original Message-----
> From: owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net [mailto:owner-chemistry+hayak=3D=3D= ariel.ac.il:ccl.net] On Behalf Of Ayesha Inayat ayeshainayat9898++gmail.com
Sent: Tuesday, July 19, 2016 11:36 AM
To: =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 - = =D7=93=D7=A8/Haya Kornweitz - Dr'
Subject: CCL:G: DFT studies of H2O2

Sent to CCL by: "Ayesha=C2=A0 Inayat" [ayeshainayat9898#gmail.com] D= ear CCL members I am doing DFT calculation of H2O2(Hydrogen per oxide) at G= AUSSIAN 09 software with various hybrid functions, After optimization the s= tructure in an output file shows that the single bond between two oxygens i= n H2O2 is missing.
Would any one please guide me why its happening???http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemi= stry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY{}ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instr= uctions/

-- =
=

=

--001a113f399aa62cd8053820bca4-- From owner-chemistry@ccl.net Thu Jul 21 05:21:01 2016 From: "Ramon Crehuet rcsqtc-,-iqac.csic.es" To: CCL Subject: CCL: DFT studies of H2O2 Message-Id: <-52322-160721052016-11544-cj9X1MRkMVAZGFxIFBODbw]|[server.ccl.net> X-Original-From: "Ramon Crehuet" Date: Thu, 21 Jul 2016 05:20:15 -0400 Sent to CCL by: "Ramon Crehuet" [rcsqtc_-_iqac.csic.es] Dear Ayesha, I am afraid you are not understanding the calculations you are doing. Unfortunately, you cannot learn quantum chemistry by just asking some questions here. I really encourage you to ask your tutor/teacher/supervisor to lecture you on what you are doing. I know that if I tell you to read some textbooks such as Jensen's or Cramer's will sound as a lot of work, but otherwise running calculations is pointless. To answer your questions (and to show you that you need to understand what your are doing): 1. You cannot rebond two atoms. The bonds are formed by the electrons governed by the Schdinger equation. If what you mean is to generate a new input putting those atoms at a shorter distance, that can be done. After you optimize the geometry you will recover the same structure you had with the atoms not bonded... 2. An image cannot be used for further calculation. You probably mean the modified geometry (after the optimisation), which, as I said, will be the same as your first structure. Of course, you can always use any geometry for further calculation: optimized or not. It depends on what you are studying and why you do it. From a quantum chemical viewpoint, minima are not different from any other geometry. They are relevant because of statistical mechanics (and the harmonic approximation). Yours, Ramon From owner-chemistry@ccl.net Thu Jul 21 09:23:00 2016 From: "Jim Kress jimkress35 _ gmail.com" To: CCL Subject: CCL:G: DFT studies of H2O2 Message-Id: <-52323-160721091731-7935-Pv2s5/tNSEHoneQ/KsNqdw{=}server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0060_01D1E330.B0663A40" Date: Thu, 21 Jul 2016 09:17:21 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35+*+gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_0060_01D1E330.B0663A40 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable What is the distance between the two oxygen atoms before and after = optimization? =20 Jim =20 > From: owner-chemistry+jimkress35=3D=3Dgmail.com]*[ccl.net = [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com]*[ccl.net] On Behalf Of = ayesha inayat ayeshainayat9898.]*[.gmail.com Sent: Thursday, July 21, 2016 2:23 AM To: Kress, Jim Subject: CCL: DFT studies of H2O2 =20 Dear Paco: Thank you for helping me out. I want to ask that If I rebond the 2 oxygens in the output file, Can I = use that image for further calculation. Here are some of the details about calculations. Software: GUASSIAN 09 Theory : DFT Hybrid Function: B3LYP Basis Set: 631-G Guass View used for visualizing the output file =20 On Tue, Jul 19, 2016 at 10:35 PM, Francisco Partal Ure=C3=B1a fpartal . = ujaen.es

> wrote: Dear Ayesha: I guess you are using GaussView. If so, there is no problem = with your calculations, it is only that the O-O bond lengths obtained in = them are higher than a single O-O bond for GaussView cutoffs. As Victor = says is a visualization artifact. Just rebond using the 'bond = definition' icon. If you are using another visualization software then = use the proper way to do that. =20 Best regards, =20 Paco =20 =20 2016-07-19 17:43 GMT+02:00 Victor Rosas Garcia rosas.victor,gmail.com =

>: It could be a visualization artifact, but it would be necessary to know = how you found out that the bond is "missing". Did you use some = visualization package? did you read a bond order from a text output = file? did you do some kind of critical point analysis that shows no = critical point between the oxygen atoms? Without this information, it is hard to help you. Best regards Victor =20 2016-07-19 8:09 GMT-05:00 =D7=97=D7=99=D7=94 = =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 - =D7=93=D7=A8/Haya = Kornweitz - Dr' hayak ~~ ariel.ac.il = >: Sent to CCL by: = =3D?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic=3D= ?=3D [hayak|ariel.ac.il ] I had calculated this molecule and everything was o.k. Please try to change your initial configuration. Haya -----Original Message----- > From: owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net = [mailto:owner-chemistry+hayak = =3D=3Dariel.ac.il:ccl.net ] On Behalf Of Ayesha Inayat = ayeshainayat9898++gmail.com =20 Sent: Tuesday, July 19, 2016 11:36 AM To: =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 = - =D7=93=D7=A8/Haya Kornweitz - Dr' Subject: CCL:G: DFT studies of H2O2 Sent to CCL by: "Ayesha Inayat" [ayeshainayat9898#gmail.com = ] Dear CCL members I am doing DFT calculation of = H2O2(Hydrogen per oxide) at GAUSSIAN 09 software with various hybrid = functions, After optimization the structure in an output file shows that = the single bond between two oxygens in H2O2 is missing. Would any one please guide me why its = happening???http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl= .net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt = =20 -=3D This is automatically added to each message by the mailing script = =3D-=20 E-mail to subscribers: CHEMISTRY{}ccl.net = or use:E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net = or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt=20 =20 --=20 =20 =20 ------=_NextPart_000_0060_01D1E330.B0663A40 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable

What is the = distance between the two oxygen atoms before and after = optimization?

Jim

From:<= /b> = owner-chemistry+jimkress35=3D=3Dgmail.com]*[ccl.net = [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com]*[ccl.net] On Behalf = Of ayesha inayat ayeshainayat9898.]*[.gmail.com
Sent: = Thursday, July 21, 2016 2:23 AM
To: Kress, Jim = <jimkress35]*[gmail.com>
Subject: CCL: DFT studies of = H2O2

Dear = Paco:

Thank you for helping me = out.

I want to ask that If = I rebond the 2 oxygens in the output file, Can I use that image for = further calculation.

Here = are some of the details about = calculations.

Software: = GUASSIAN 09

Theory : = DFT

Hybrid Function: = B3LYP

Basis Set: = 631-G

Guass View used for = visualizing the output file

On Tue, = Jul 19, 2016 at 10:35 PM, Francisco Partal Ure=C3=B1a fpartal . ujaen.es <owner-chemistry]*[ccl.net> = wrote:

Dear = Ayesha: I guess you are using GaussView. If so, there is no problem with = your calculations, it is only that the O-O bond lengths obtained in them = are higher than a single O-O bond for GaussView cutoffs. As Victor says = is a visualization artifact. Just rebond using the 'bond definition' = icon. If you are using another visualization software then use the = proper way to do that.

Best regards,

= Paco

2016-07-19 17:43 GMT+02:00 Victor Rosas Garcia = rosas.victor,gmail.com <owner-chemistry{}ccl.net>:
It could be a = visualization artifact, but it would be necessary to know how you found = out that the bond is "missing". Did you use some visualization = package? did you read a bond order from a text output file? did you do = some kind of critical point analysis that shows no critical point = between the oxygen atoms?
Without this information, it is hard to = help you.
Best regards
Victor

2016-07-19 8:09 GMT-05:00 =D7=97=D7=99=D7=94 = =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 - =D7=93=D7=A8/Haya = Kornweitz - Dr' hayak ~~ ariel.ac.il <owner-chemistry{}ccl.net>:

Sent to CCL by: = =3D?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic=3D= ?=3D
[hayak|ariel.ac.il]
I had = calculated this molecule and everything was o.k.
Please try to change = your initial configuration.
Haya

-----Original = Message-----
> From: owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net [mailto:owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net] On Behalf Of Ayesha = Inayat ayeshainayat9898++gmail.com
Sent: Tuesday, July 19, 2016 11:36 = AM
To: =D7=97=D7=99=D7=94 = =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 - =D7=93=D7=A8/Haya = Kornweitz - Dr'
Subject: CCL:G: DFT studies of H2O2

Sent = to CCL by: "Ayesha Inayat" [ayeshainayat9898#gmail.com] Dear CCL = members I am doing DFT calculation of H2O2(Hydrogen per oxide) at = GAUSSIAN 09 software with various hybrid functions, After optimization = the structure in an output file shows that the single bond between two = oxygens in H2O2 is missing.
Would any one please guide me why its = happening???http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://w= ww.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

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------=_NextPart_000_0060_01D1E330.B0663A40-- From owner-chemistry@ccl.net Thu Jul 21 15:52:01 2016 From: "Indrajit Deb biky2004indra(a)gmail.com" To: CCL Subject: CCL:G: Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL Message-Id: <-52324-160721155005-16047-RVlRAt0zcyeFo2uBfJ3XHQ-.-server.ccl.net> X-Original-From: Indrajit Deb Content-Type: multipart/alternative; boundary=001a114dad407e0b9705382a9f29 Date: Thu, 21 Jul 2016 21:49:19 +0200 MIME-Version: 1.0 Sent to CCL by: Indrajit Deb [biky2004indra*o*gmail.com] --001a114dad407e0b9705382a9f29 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Pezhman and Swetanshu, Thanks to you both for replying. Finally I solved the problem. And fortunately the problem was with the input file. I am trying to explain. May be it will help others. 1. I was running both Optimization and SP calculation with the same B97D/def2TZVPPD external basis set (downloaded from EMSL). 2. In the Optimization calculation there was two blank lines at the end of the external basis set file (as it was downloaded) and one blank line at end of Gaussian09 input file. It was running successfully. 3. So, I decided to use same strategy of blank lines during the SP calculation. But It was crashing. 4. Solve: I removed all the blank lines from the end of the external basis set file, but kept one blank line at end of Gaussian09 input file (as a general rule). Its running. 5. Another point to be noted----do not keep any blank lines at the beginning of the external basis set file. *But now I have one more problem.* The SP calculation with B97D/def2TZVPPD basis set is not converging. My system has four nucleic acid base rings --all are optimized with the B97D/def2TZVPPD basis set. They are oriented in the space in a specific manner which I can not alter. Because these orientations are from MD simulations. Is there any way to use loose convergence criteria in this DFT calculation. For information, the calculations are converging with B97D/def2TZVPP basis set (without diffuse function). I want to use the diffuse function. I am very new in this calculations. Any help will be useful. Thank you, ----indrajit ---------------------------------------------------------------------------= ----------------------------------- *Indrajit Deb* alternate emails: indrajitdeb81%%gmail.com, idbmbg_s%%caluniv.ac.in *Present Position* International Centre for Genetic Engineering and Biotechnology (ICGEB, Italy) SMART Fellow, Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry (IBCh), Polish Academy of Sciences (PAS). European Center for Bioinformatics and Genomics (ECBiG) Campus ( R oom: 2.6.28 ). Z. Noskowskiego Str. 12/14. Poznan 61-704, Poland=E2=80=8B. Phone: +48616653042, =E2=80=8BPersonal Mobile: +48662513522=E2=80=8B =E2=80=8B *Previous Position*=E2=80=8B Ph.D Student, Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta (CU), 92 APC Road, Kolkata - 700009, India. Phone: +91332350838= 6 (extn. 329, 321), Fax: +913323519755. Personal Mobile: +919239202278 On Thu, Jul 14, 2016 at 8:23 PM, Tandon Swetanshu tandons|tcd.ie < owner-chemistry%%ccl.net> wrote: > Hi Indrajit, > > I think you need to copy the whole basis set from EMSL website def2TZVPPD > for each atom and stick it in your input file. So, in the end your input > file will look something like: > > #P B97D/Gen SP NoSymm > > ***system definition (coordinates of atoms)*** > > C 0 > copy the basis set for carbon as given on the website > **** > H 0 > copy the basis set for hydrogen as given on the website > **** > Similariliy define the basis set for each atom. > The calculation should work then. > > Hope that helps, > Swetanshu. > > On 14 July 2016 at 16:53, Indrajit Deb biky2004indra---gmail.com < > owner-chemistry:_:ccl.net> wrote: > >> >> Sent to CCL by: "Indrajit Deb" [biky2004indra_-_gmail.com] >> Hi, >> >> I am facing some problems with G09. >> >> My objective is to calculate the interaction energy between RNA bases fo= r >> the geometries extracted from MD simulation run in AMBER. >> >> My problem is as follows..... >> >> I am optimizing four individual nucleic acid bases with B97D/def2TZVPPD >> basis set. The def2TZVPPD basis set. I have downloaded it from EMSL >> website. >> Because G09 don't have this diffusion function and we have license for >> only >> G09. Anyway G09 have def2TZVPP without the diffuse function (D). >> >> I am using the following input....... >> >> #P B97D/Gen Opt(ModRedundant) NoSymm >> >> ------------------------------------------------------------ >> >> ++./Def2-TZVPPD >> >> There was nothing wrong with the optimization. >> >> But when I tried single point (SP) energy calculation with the same basi= s >> set and same geometry that I used during optimization, there are some >> errors >> and calculation is terminating. The input is as follows.......... >> >> #P B97D/Gen SP NoSymm >> >> ------------------------------------------------------------ >> >> ++./Def2-TZVPPD >> >> The errors are as follows........ >> >> (Enter /home/indra/g09/g09/l301.exe) >> General basis read from cards: (5D, 7F) >> Warning: center 1 has no basis functions! >> Warning: center 2 has no basis functions! >> Warning: center 3 has no basis functions! >> Warning: center 4 has no basis functions! >> Warning: center 5 has no basis functions! >> Warning: center 6 has no basis functions! >> Warning: center 7 has no basis functions! >> Warning: center 8 has no basis functions! >> Warning: center 9 has no basis functions! >> Warning: center 10 has no basis functions! >> Warning: center 11 has no basis functions! >> Warning: center 12 has no basis functions! >> Warning: center 13 has no basis functions! >> Warning: center 14 has no basis functions! >> Warning: center 15 has no basis functions! >> Ernie: Thresh=3D 0.10000D-02 Tol=3D 0.10000D-05 Strict=3DF. >> AO basis set in the form of general basis input (Overlap normalization): >> **** >> >> Bad length for file. >> FileIO: IOper=3D 1 IFilNo(1)=3D -582 Len=3D 0 IPos=3D 0 Q=3D 47472055144= 592 >> >> >> dumping /fiocom/, unit =3D 1 NFiles =3D 25 SizExt =3D 524288 WInBlk =3D = 512 >> defal =3D T LstWrd =3D 596480 FType=3D2 FMxFil=3D10000 >> >> >> ........................................................................= ... >> .................... >> >> >> ........................................................................= ... >> .................... >> >> >> ........................................................................= ... >> .................... >> >> Error termination in NtrErr: >> NtrErr Called from FileIO. >> >> Further, I took the geometries of the four optimized nucleic acid bases >> as a >> supramolecule and tried to calculate the single point energy with >> "Counterpoise=3D4". Then I found the same error as mentioned above. But = for >> this supramolecule Optmization calculation is running without any error. >> >> It seems that B97D/def2TZVPPD basis set with diffusion function (D) is >> not >> working for single point energy (SP) calculation. To verify this I tried >> both the optmization and single point energy calculation using >> B97D/def2TZVPP basis set (available in G09). Both the calculation >> completed >> successfully. >> >> I want to use B97D/def2TZVPP with the diffuse function (D) in my >> calculation >> because literature says that for pi-pi interaction it is important. Ther= e >> is >> a very recent publication few months before where they used B97D/def2TZV= PP >> basis set without the diffuse function. >> >> It will be really nice if anyone can help. Looking forward to some >> responses. I can attach the input files if anyone need. >> >> Thanking you, >> >> Indrajit Deb >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY:_:ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST:_:ccl.net or use>> >> >> > --001a114dad407e0b9705382a9f29 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi= Pezhman and Swetanshu,

Thanks to you both for replying. Finally I solved the problem. And fortuna= tely the problem was with the input file. I am trying to explain. May be it= will help others.

1. I= was running both Optimization and SP calculation with the same=C2=A0B97D/def2TZVPPD=C2=A0= external basis set (downloaded from EMSL).
2. In the Optimization calculation there was t= wo blank lines at the end of the external basis set file (as it was downloa= ded) and one blank line at end of Gaussian09 input file. It was running suc= cessfully.
3. = So, I decided to use same strategy of blank lines during the SP calculation= . But It was crashing.
4. Solve: I removed all the blank lines from the end of the extern= al basis set file, but kept one blank line at end of Gaussian09 input file = (as a general rule). Its running.
5. Another point to be noted----do not keep any blank= lines at the beginning of the external basis set file.

But now I have one more problem.

The SP calculation with= =C2=A0B97D/def2TZVPPD = basis set is not converging. My system has four nucleic acid base rings --a= ll are optimized with the=C2=A0B97D/def2TZVPPD basis set. They are oriented in the space i= n a specific manner which I can not alter. Because these orientations are f= rom MD simulations. Is there any way to use loose convergence criteria in t= his DFT calculation. For information, the calculations are converging with= =C2=A0B97D/def2= TZVPP basis set (without diffuse function). I want to use the diffuse funct= ion.

I am very new in this calculations. Any help wil= l be useful.

Thank you,

----ind= rajit=C2=A0
=C2=A0=C2=A0 =C2=A0

=

----------------= ---------------------------------------------------------------------------= -------------------
Indrajit= Deb
alternat= e emails: indr= ajitdeb81%%gmail.com,=C2=A0idbmbg_s%%caluniv.ac.in
Present Positi= on
International Centre for Genetic Engineering and Bi= otechnology (ICGEB, Italy) SMART Fellow,=C2=A0
Department of Structural Chemistry and Biology of Nucleic Acids,=C2= =A0
Institute of Bioorganic C= hemistry (IBCh),=C2=A0
Polish Academy of = Sciences (PAS).=C2=A0
European Center for Bioinformatics and Genomics (ECBiG) Campus (
= R
oom: 2.6.28
).=C2=A0=
Z. Noskowskiego Str. 12/14.=C2=A0Poznan 61-704,=C2=A0Poland=E2=80=8B.=C2=A0
Phone:=C2=A0+48616= 653042,=C2=A0=E2=80=8BPersonal= Mobile:=C2=A0+48662513522=E2=80=8B
=E2=80=8B
Previous Position<= span style=3D"color:rgb(0,0,0);font-family:'comic sans ms',sans-ser= if;font-size:12.8px">=E2=80=8B
Ph.D Student,=C2=A0
Department of Biophysics, Molecular Biology and Bioinformatics,=C2=A0<= /span>University of Calcutta (CU),=C2=A092 APC Road,= =C2=A0Kolkata - 700009, India.=C2=A0Phone: +913= 323508386 (extn. 329, 321),=C2=A0Fax: +913323519755.=C2=A0Personal Mobile: +919239202278=C2=A0

On Thu, Jul 14, 2016 at 8:23 PM, Tandon Swet= anshu tandons|tcd.ie <owner-chemistry%%ccl.net> wrote:
Hi Indrajit,

I think you need to copy the whole basis set from EMSL website def2TZVPPD = for each atom and stick it in your input file. So, in the end your input fi= le will look something like:

#P B97D/Gen SP NoSymm

***system definition (coordinates of atoms)***

C 0
= copy the basis set for carbon as given on the website
****
H 0= =C2=A0
copy the basis set for hydrogen as given on the website
****<= br>
Similariliy define the basis set for each atom.
The calculatio= n should work then.

Hope that helps,
Swetanshu.<= br>

On 14 July 2016 at 16:53, Indrajit Deb biky2004indra---gmail.com <owner-= chemistry:_:ccl.net> wrote:
=

Sent to CCL by: "Indrajit=C2=A0 Deb" [biky2004indra_-_gmai= l.com]
Hi,

I am facing some problems with G09.

My objective is to calculate the interaction energy between RNA bases for the geometries extracted from MD simulation run in AMBER.

My problem is as follows.....

I am optimizing four individual nucleic acid bases with B97D/def2TZVPPD
basis set. The def2TZVPPD basis set. I have downloaded it from EMSL website= .
Because G09 don't have this diffusion function and we have license for = only
G09. Anyway G09 have def2TZVPP without the diffuse function (D).

I am using the following input.......

#P B97D/Gen Opt(ModRedundant) NoSymm

------------------------------------------------------------

++./Def2-TZVPPD

There was nothing wrong with the optimization.

But when I tried single point (SP) energy calculation with the same basis set and same geometry that I used during optimization, there are some error= s
and calculation is terminating. The input is as follows..........

#P B97D/Gen SP NoSymm

------------------------------------------------------------

++./Def2-TZVPPD

The errors are as follows........

(Enter /home/indra/g09/g09/l301.exe)
General basis read from cards: (5D, 7F)
Warning: center 1 has no basis functions!
Warning: center 2 has no basis functions!
Warning: center 3 has no basis functions!
Warning: center 4 has no basis functions!
Warning: center 5 has no basis functions!
Warning: center 6 has no basis functions!
Warning: center 7 has no basis functions!
Warning: center 8 has no basis functions!
Warning: center 9 has no basis functions!
Warning: center 10 has no basis functions!
Warning: center 11 has no basis functions!
Warning: center 12 has no basis functions!
Warning: center 13 has no basis functions!
Warning: center 14 has no basis functions!
Warning: center 15 has no basis functions!
Ernie: Thresh=3D 0.10000D-02 Tol=3D 0.10000D-05 Strict=3DF.
AO basis set in the form of general basis input (Overlap normalization): ****

Bad length for file.
FileIO: IOper=3D 1 IFilNo(1)=3D -582 Len=3D 0 IPos=3D 0 Q=3D 47472055144592=

dumping /fiocom/, unit =3D 1 NFiles =3D 25 SizExt =3D 524288 WInBlk =3D 512=
defal =3D T LstWrd =3D 596480 FType=3D2 FMxFil=3D10000

...........................................................................=
....................

...........................................................................=
....................

...........................................................................=
....................

Error termination in NtrErr:
NtrErr Called from FileIO.

Further, I took the geometries of the four optimized nucleic acid bases as = a
supramolecule and tried to calculate the single point energy with
"Counterpoise=3D4". Then I found the same error as mentioned abov= e. But for
this supramolecule Optmization calculation is running without any error.
It seems that=C2=A0 B97D/def2TZVPPD basis set with diffusion function (D) i= s not
working for single point energy (SP) calculation. To verify this I tried both the optmization and single point energy calculation using
B97D/def2TZVPP basis set (available in G09). Both the calculation completed=
successfully.

I want to use B97D/def2TZVPP with the diffuse function (D) in my calculatio= n
because literature says that for pi-pi interaction it is important. There i= s
a very recent publication few months before where they used B97D/def2TZVPP<= br> basis set without the diffuse function.

It will be really nice if anyone can help. Looking forward to some
responses. I can attach the input files if anyone need.

Thanking you,

Indrajit Deb

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--001a114dad407e0b9705382a9f29-- From owner-chemistry@ccl.net Thu Jul 21 19:22:01 2016 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor[-]fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL Message-Id: <-52325-160721192023-28316-PmD0VH1UuQOKOEvAnlRHfA%a%server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 22 Jul 2016 01:01:32 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor*|*fluor.quimica.uniovi.es] On Thu, Jul 21, 2016 at 09:49:19PM +0200, Indrajit Deb biky2004indra(a)gmail.com wrote: > Finally I solved the problem. And fortunately the problem was with > the input file. I am trying to explain. May be it will help others. Indrajit, An excellent iniciative that was common years ago but it is disappearing in our days. I hope other follow this path. > 4. Solve: I removed all the blank lines from the end of the external basis > set file, but kept one blank line at end of Gaussian09 input file (as a > general rule). Its running. > 5. Another point to be noted----do not keep any blank lines at the > beginning of the external basis set file. There are many differences in the mode programs get their input data > from the external file. Gaussian keeps a very old format since the very beginnings, and it is very important to examine carefully the rules in the manual, which can be a bit obscure at some times. There are many different traditions in this respect. One that comes from the tradition of compilers is using keywords to document the meaning of each input line. This is a format that is gaining impetus: see the format for nwchem: title "Nitrogen cc-pvdz SCF geometry optimization" geometry n 0 0 0 n 0 0 1.08 end basis n library cc-pvdz end task scf optimize Something even a non expert with some knowledge of the field can read as a text. This format must be parsed and executed by the software. Creating this type of soft requires some knowledge on lexical analysis and parsing, but today is relatively simple to use a scripting language (oldies: bash, perl, awk, ...; modern: python, php, lua, ...) for driving the interpreting part and let fortran, c or any compiled language to do the numerical part. Orca, also a relatively recent code, follow gaussian tradition, but includes significant goodies in the format: # Comment lines can be added if the line begins with a #. ! BP86 def2-SVP Opt # BP86 is here the method (DFT functional), def2-SVP the basis set and Opt is the jobtype (geometry optimization). # Order of the keywords is not important. *xyz 0 1 H 0.0 0.0 0.0 H 0.0 0.0 1.0 * Lesson to take home: Be very careful with the input of gaussian. You can use a modeller to create the input or a first version for it (gaussvies, avogadro, ...). And finally: there are many more q-chem codes apart > from gaussian. It is a good practice to get used to several of them > from the beginning. In fact, we theoretitians should check that a particular result can be reproduced on more than a code to avoid disturbing mistakes. Thanks for your summary of your experiences, V�ctor -- . . "Patriotism is the last refuge of a scoundrel." / `' \ -- Samuel Johnson (UK, 1755) /(o)(o)\ /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero tambi�n es peor / '`'` \ que lo malo, porque la mediocridad no es un grado, es una | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 | |'`'`| | (Mediocre is worse than good, but it is also worse than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==================================+========================= ! Dr.V�ctor Lua�a, in silico chemist & prof. ! ! Departamento de Qu�mica F�sica y Anal�tica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: ! ! phone: +34-985-103491 fax: +34-985-103125 ! +--------------------------------------------+ GroupPage: Articles: git-hub: