id="yui_3_16_0_ym19_1_1462744162038_44235">Daniel,

id="yui_3_16_0_ym19_1_1462744162038_44235">

id="yui_3_16_0_ym19_1_1462744162038_44235">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.

id="yui_3_16_0_ym19_1_1462744162038_44235">

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.

id="yui_3_16_0_ym19_1_1462744162038_44235">

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.

id="yui_3_16_0_ym19_1_1462744162038_44235">

id="yui_3_16_0_ym19_1_1462744162038_44235">--David

id="yui_3_16_0_ym19_1_1462744162038_44235">

class="qtdSeparateBR">

style="display: block;">

style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida > Grande, sans-serif; font-size: 16px;">

face="Arial"> 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

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

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

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.=C2=A0 I'm = assuming 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=A0 Gaussian prints the vibrational data in frequency order, so note tho= se vibrational modes that are near the expected frequency, and animate thos= e vibrational nodes individually (as opposed to plotting the entire IR spec= trum, which it sounds like you are doing).=C2=A0 If you're lucky, there= won't be too many vibrational nodes with frequencies in your range, an= d you can pick 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 th= e twist.
--David

=C2=A0 =C2=A0 On Saturday, May 7, 2016 5:34 PM, Daniel Salazar danielmorale= ssalazar91:+:gmail.com <owner-chemistry_-_ccl.net> wrote:

Sent to CCL by: "Daniel=C2=A0 Salazar" [danielmoralessalazar91]= =3D[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 visuali= ze 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<= br> 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<= br> the text output file, and if there is, how can I do it? Thank you very
much.
Sincerely,
Daniel Morales Salazar

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<html><head></head><body><div style=3D"colo= r:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, H= elvetica, Arial, Lucida Grande, sans-serif;font-size:13px"><div = dir=3D"ltr" id=3D"yui_3_16_0_ym19_1_1462744162038_44235"= ;>Daniel,</div><div dir=3D"ltr" id=3D"yui_3_16_0= _ym19_1_1462744162038_44235"><br></div><div dir=3D&q= uot;ltr" id=3D"yui_3_16_0_ym19_1_1462744162038_44235">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=3DP stretch. =  (if not, a quick calculation of CH2=3DPH or CH2=3DP-CH3 might hel= p).  Gaussian prints the vibrational data in frequency order, so n= ote those vibrational modes that are near the expected frequency, and anima= te those vibrational nodes individually (as opposed to plotting the entire = IR spectrum, which it sounds like you are doing).  If you're l= ucky, there won't be too many vibrational nodes with frequencies in you= r range, and you can pick out the C=3DP stretch from watching the animation= .</div><div dir=3D"ltr" id=3D"yui_3_16_0_ym19_1_146= 2744162038_44235"><br></div><div dir=3D"ltr&quo= t; id=3D"yui_3_16_0_ym19_1_1462744162038_44235">If you are unl= ucky, there will be several other vibrational nodes with similar frequencie= s, and every one of those modes will be a mixed mode that has only some C= =3DP stretching character.</div><div dir=3D"ltr" id=3D&q= uot;yui_3_16_0_ym19_1_1462744162038_44235"><br></div>&l= t;div dir=3D"ltr" id=3D"yui_3_16_0_ym19_1_1462744162038_4423= 5">I write about C=3DP stretching, but the same is true for the C= =3DP twist only my guess is that you will be less likely to be "lucky&= quot; with the twist.</div><div dir=3D"ltr" id=3D"y= ui_3_16_0_ym19_1_1462744162038_44235"><br></div><div= dir=3D"ltr" id=3D"yui_3_16_0_ym19_1_1462744162038_44235&quo= t;>--David</div><div dir=3D"ltr" id=3D"yui_3_16_= 0_ym19_1_1462744162038_44235"><br></div><div dir=3D&= quot;ltr" id=3D"yui_3_16_0_ym19_1_1462744162038_44235">&l= t;br></div><div class=3D"qtdSeparateBR"><br>= <br></div><div class=3D"yahoo_quoted" style=3D&quo= t;display: block;"> <div style=3D"font-family: HelveticaNeu= e, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: = 13px;"> <div style=3D"font-family: HelveticaNeue, Helvetica= Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"&= gt; <div dir=3D"ltr"><font size=3D"2" face=3D&= quot;Arial"> On Saturday, May 7, 2016 5:34 PM, Daniel Salazar danie= lmoralessalazar91:+:gmail.com <owner-chemistry_-_ccl.net&= gt; wrote:<br></font></div>=C2=A0 <br><br> &l= t;div class=3D"y_msg_container"><br>Sent to CCL by: &quo= t;Daniel  Salazar" [danielmoralessalazar91]=3D[gmail.com]<br>= ;Hello,<br><br>I am using B3LYP on Gaussian 09. I used it to ob= tain the vibrational <br>frequencies of a molecule (C39H41PS2) contai= ning one phosphorus carbon <br>double bond by using the keyword "= ;freq". I used Molden to visualize the <br>calculated IR Spectru= m. 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 fi= nding its frequency on the "Molden Frequency Select" panel. I won= der <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>Danie= l Morales Salazar<br><br><br><br>-=3D This is autom= atically added to each message by the mailing script =3D-<br>To recov= er the email address of the author of the message, please change<br>= =3Dr><br><= br>E-mail to subscribers: <a ymailto=3D"mailto:CHEMISTRY_-_ccl.net" href=3D"mailto:CHEMISTRY_-_ccl.net">CHEMIS= TRY_-_ccl.net</a> or use:<br>      &= lt;a href=3D"http://www.ccl.net/cgi-bin/ccl/send= _ccl_message" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><= ;br>E-mail to administrators: <a ymailto=3D"mailto:CHEMISTRY-REQUEST_-_ccl.net" hre= f=3D"mailto:CHEMISTRY-R= EQUEST_-_ccl.net">CHEMISTRY-REQUEST_-_ccl.net</a> or use&= lt;br>      <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target=3D= "_blank">http://www.ccl.net/cgi-bin/ccl/= send_ccl_message</a><br><br>&l= t;br>      <a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtml" target=3D"_= blank">http://www.ccl.net/chemistry/sub_unsub.sh= tml</a><br><br>Before posting, check wait time at: &l= t;a href=3D"http://www.ccl.net/" target=3D"_blank">http://ww= w.ccl.net</a><br><br>Job: <a href=3D"http://ww= w.ccl.net/jobs" target=3D"_blank">http://www.ccl.net/jo= bs </a><br>Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/conferences/= " target=3D"_blank">= http://server.ccl.net/chemistry/announcements/conferences/</a><= ;br><br>Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.shtml" target=3D&q= uot;_blank">http://www.ccl.net/chemistry/s= earchccl/index.shtml</a><br><br>If your mail bounces = > from CCL with 5.7.1 error, check:<br>     = <a href=3D"http://www.ccl.net/spammers.txt" target= =3D"_blank">http://www.ccl.net/spammers.txt</a>= ;<br><br>RTFI: <a href=3D"htt= p://www.ccl.net/chemistry/aboutccl/instructions/" target=3D"_= blank">http://www.ccl.net/chemistry/about= ccl/instructions/</a><br><br><br><br><= br></div>=C2=A0 </div> </div>=C2=A0 </div></d= iv></body></html>