CCL:G: About phosphorus-carbon double bond vibrational-frequency(ies)



Dear Daniel,
Provided that you have the chk file, you can "pick" vibrational modes that involve selected atoms using the freqchk utility.

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

That might help reduce the noise, if there are many modes in the same frequency range.

Regards,
Peter

On 9 May 2016 03:37, "David Shobe avidshobe|a|yahoo.com" <owner-chemistry a ccl.net> wrote:
Daniel,
It may indeed be easier to look at the Gaussian text output.  I'm assuming you have some idea of the frequency value for the C=P stretch.  (if not, a quick calculation of CH2=PH or CH2=P-CH3 might help).  Gaussian prints the vibrational data in frequency order, so note 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, there won't be too many vibrational nodes with frequencies in your range, and you can pick out the C=P stretch from watching the animation.
If you are unlucky, there 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=P stretching character.
I write about C=P stretching, but the same is true for the C=P twist only 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 <owner-chemistry_-_ccl.net> wrote:



Sent to CCL by: "Daniel  Salazar" [danielmoralessalazar91]=[gmail.com]
Hello,

I am using B3LYP on Gaussian 09. I used it to obtain the vibrational
frequencies of a molecule (C39H41PS2) containing one phosphorus carbon
double bond by using the keyword "freq". I used Molden to visualize the
calculated IR Spectrum. Since there are a lot of frequencies and the
phosphorus 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



-= This is automatically added to each message by the mailing script =-          Subscribe/Unsubscribe:
     Job: http://www.ccl.net/jobs      ------=art_668200_166460360.1462755339092
Content-Type: text/html; charset=F-8
Content-Transfer-Encoding: quoted-printable

<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:13px"><div dir="ltr" id="yui_3_16_0_ym19_1_1462744162038_44235">Daniel,</div><div dir="ltr" id="yui_3_16_0_ym19_1_1462744162038_44235"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1462744162038_44235">It may indeed be easier to look at the Gaussian text output. &nbsp;I'm assuming you have some idea of the frequency value for the C=P stretch. &nbsp;(if not, a quick calculation of CH2=PH or CH2=P-CH3 might help). &nbsp;Gaussian prints the vibrational data in frequency order, so note 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). &nbsp;If you're lucky, there won't be too many vibrational nodes with frequencies in your range, and you can pick out the C=P stretch from watching the animation.</div><div dir="ltr" id="yui_3_16_0_ym19_1_1462744162038_44235"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1462744162038_44235">If you are unlucky, there 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=P stretching character.</div><div dir="ltr" id="yui_3_16_0_ym19_1_1462744162038_44235"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1462744162038_44235">I write about C=P stretching, but the same is true for the C=P twist only my guess is that you will be less likely to be "lucky" with the twist.</div><div dir="ltr" id="yui_3_16_0_ym19_1_1462744162038_44235"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1462744162038_44235">--David</div><div dir="ltr" id="yui_3_16_0_ym19_1_1462744162038_44235"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1462744162038_44235"><br></div><div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 13px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font size="2" face="Arial"> On Saturday, May 7, 2016 5:34 PM, Daniel Salazar danielmoralessalazar91:+:gmail.com &lt;owner-chemistry_-_ccl.net&gt; wrote:<br></font></div>  <br><br> <div class="y_msg_container"><br>Sent to CCL by: "Daniel&nbsp; Salazar" [danielmoralessalazar91]=[gmail.com]<br>Hello,<br><br>I am using B3LYP on Gaussian 09. I used it to obtain the vibrational <br>frequencies of a molecule (C39H41PS2) containing one phosphorus carbon <br>double bond by using the keyword "freq". I used Molden to visualize the <br>calculated IR Spectrum. Since there are a lot of frequencies and the <br>phosphorus carbon double bond may have a low intensity, I am having a hard <br>time finding its frequency on the "Molden Frequency Select" panel. I wonder <br>if there is any way to obtain this information in other ways, such as > from <br>the text output file, and if there is, how can I do it? Thank you very <br>much.<br>Sincerely,<br>Daniel Morales Salazar<br><br><br><br>-= This is automatically added to each message by the mailing script =-<br>To recover the email address of the author of the message, please change<br>=r><br><br>E-mail to subscribers: <a ymailto="mailto:CHEMISTRY_-_ccl.net" href="" href="mailto:CHEMISTRY_-_ccl.net">CHEMISTRY_-_ccl.net">CHEMISTRY_-_ccl.net</a> or use:<br>&nbsp; &nbsp; &nbsp; <a href="" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message" rel="noreferrer" target="_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target="_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br>E-mail to administrators: <a ymailto="mailto:CHEMISTRY-REQUEST_-_ccl.net" href="" href="mailto:CHEMISTRY-REQUEST_-_ccl.net">CHEMISTRY-REQUEST_-_ccl.net">CHEMISTRY-REQUEST_-_ccl.net</a> or use<br>&nbsp; &nbsp; &nbsp; <a href="" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message" rel="noreferrer" target="_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target="_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br><br>&nbsp; &nbsp; &nbsp; <a href="" href="http://www.ccl.net/chemistry/sub_unsub.shtml" rel="noreferrer" target="_blank">http://www.ccl.net/chemistry/sub_unsub.shtml" target="_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br><br>Before posting, check wait time at: <a href="" href="http://www.ccl.net/" rel="noreferrer" target="_blank">http://www.ccl.net/" target="_blank">http://www.ccl.net</a><br><br>Job: <a href="" href="http://www.ccl.net/jobs" rel="noreferrer" target="_blank">http://www.ccl.net/jobs" target="_blank">http://www.ccl.net/jobs </a><br>Conferences: <a href="" href="http://server.ccl.net/chemistry/announcements/conferences/" rel="noreferrer" target="_blank">http://server.ccl.net/chemistry/announcements/conferences/" target="_blank">http://server.ccl.net/chemistry/announcements/conferences/</a><br><br>Search Messages: <a href="" href="http://www.ccl.net/chemistry/searchccl/index.shtml" rel="noreferrer" target="_blank">http://www.ccl.net/chemistry/searchccl/index.shtml" target="_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</a><br><br>If your mail bounces > from CCL with 5.7.1 error, check:<br>&nbsp; &nbsp; &nbsp; <a href="" href="http://www.ccl.net/spammers.txt" rel="noreferrer" target="_blank">http://www.ccl.net/spammers.txt" target="_blank">http://www.ccl.net/spammers.txt</a><br><br>RTFI: <a href="" href="http://www.ccl.net/chemistry/aboutccl/instructions/" rel="noreferrer" target="_blank">http://www.ccl.net/chemistry/aboutccl/instructions/" target="_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br><br><br><br><br></div>  </div> </div>  </div></div></body></html>