Natural Bond Orbitals (NBO) Visualization with Chemcraft

It=E2=80=99s been a long time since I last p= osted something and so many things have happened in our research group! I s= h...

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`The man who makes no mistakes does not usually make anything.'

= &nb= sp; = Edward John Phelps (1822-1= 900)

--------------------------------------------------------------= ----------------------------------------------------------------
Mehdi = D. Esrafili, Ph.D.

Associate Professor of Physical Chemistry <= br>Current address: Department of Chemistry,

= Faculty o= f Basic Sciences,University of

Maragheh, Iran.

E-mail 1: m_esrafili]^[yahoo.com<= /font>
E-mail 2: e= srafili]^[maragheh.ac.ir

-----------------------------------------------------------------= -------------------------------------------------------------

On Friday, May 6, 2016 10:32 PM, Partha Sengupta anapspsmo{:}gmail.com = <owner-chemistry]^[ccl.net> wrote:

Frien= ds, I am using Gaussian 09w. I want to draw NBOs with the help of Chemcraft= . How can I proceed.

Partha

--
=

Dr. Partha Sarathi Sengupta
Associ= ate Professor
Vivekananda Mahavidyalaya, Burdwan

<= /html> ------=_Part_551003_1702392585.1462692220663-- From owner-chemistry@ccl.net Sun May 8 20:59:01 2016 From: "David Shobe avidshobe|a|yahoo.com" To: CCL Subject: CCL:G: About phosphorus-carbon double bond vibrational-frequency(ies) Message-Id: <-52184-160508205659-657-ARmof1Uer7tYW3WEbq6v/g*server.ccl.net> X-Original-From: David Shobe Content-Type: multipart/alternative; boundary="----=_Part_668200_166460360.1462755339092" Date: Mon, 9 May 2016 00:55:39 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: David Shobe [avidshobe(a)yahoo.com] ------=_Part_668200_166460360.1462755339092 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Daniel, It may indeed be easier to look at the Gaussian text output. =C2=A0I'm assu= ming you have some idea of the frequency value for the C=3DP stretch. =C2= =A0(if not, a quick calculation of CH2=3DPH or CH2=3DP-CH3 might help). =C2= =A0Gaussian prints the vibrational data in frequency order, so note those v= ibrational modes that are near the expected frequency, and animate those vi= brational nodes individually (as opposed to plotting the entire IR spectrum= , which it sounds like you are doing). =C2=A0If you're lucky, there won't b= e too many vibrational nodes with frequencies in your range, and you can pi= ck out the C=3DP stretch from watching the animation. If you are unlucky, there will be several other vibrational nodes with simi= lar frequencies, and every one of those modes will be a mixed mode that has= only some C=3DP stretching character. I write about C=3DP stretching, but the same is true for the C=3DP twist on= ly my guess is that you will be less likely to be "lucky" with the twist. --David On Saturday, May 7, 2016 5:34 PM, Daniel Salazar danielmoralessalazar91= :+:gmail.com wrote: =20 =20 Sent to CCL by: "Daniel=C2=A0 Salazar" [danielmoralessalazar91]=3D[gmail.co= m] Hello, I am using B3LYP on Gaussian 09. I used it to obtain the vibrational=20 frequencies of a molecule (C39H41PS2) containing one phosphorus carbon=20 double bond by using the keyword "freq". I used Molden to visualize the=20 calculated IR Spectrum. Since there are a lot of frequencies and the=20 phosphorus carbon double bond may have a low intensity, I am having a hard= =20 time finding its frequency on the "Molden Frequency Select" panel. I wonder= =20 if there is any way to obtain this information in other ways, such as from= =20 the text output file, and if there is, how can I do it? Thank you very=20 much. Sincerely, Daniel Morales Salazar -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0------=_Part_668200_166460360.1462755339092 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Daniel,

It may indeed be easier to look at the Gaussian text output. &nb= sp;I'm assuming you have some idea of the frequency value for the C=3DP str= etch. (if not, a quick calculation of CH2=3DPH or CH2=3DP-CH3 might h= elp). Gaussian prints the vibrational data in frequency order, so not= e those vibrational modes that are near the expected frequency, and animate= those vibrational nodes individually (as opposed to plotting the entire IR= spectrum, which it sounds like you are doing). If you're lucky, ther= e won't be too many vibrational nodes with frequencies in your range, and y= ou can pick out the C=3DP stretch from watching the animation.

If you are unlucky, t= here will be several other vibrational nodes with similar frequencies, and = every one of those modes will be a mixed mode that has only some C=3DP stre= tching character.

I write about C=3DP stretching, but the same is true for the C=3DP t= wist only my guess is that you will be less likely to be "lucky" with the t= wist.

--Dav= id

<= /div>

On Saturday, May 7, 2016 5:34 PM, Daniel Salazar danielm= oralessalazar91:+:gmail.com <owner-chemistry||ccl.net> wrote:

Sent to CCL by: "Dani= el Salazar" [danielmoralessalazar91]=3D[gmail.com]
Hello,

I= am using B3LYP on Gaussian 09. I used it to obtain the vibrational
fre= quencies of a molecule (C39H41PS2) containing one phosphorus carbon
dou= ble bond by using the keyword "freq". I used Molden to visualize the
ca= lculated IR Spectrum. Since there are a lot of frequencies and the
phos= phorus carbon double bond may have a low intensity, I am having a hard
= time finding its frequency on the "Molden Frequency Select" panel. I wonder=
if there is any way to obtain this information in other ways, such as = > from
the text output file, and if there is, how can I do it? Thank you = very
much.
Sincerely,
Daniel Morales Salazar

-=3D = This is automatically added to each message by the mailing script =3D-
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