rega= rds

Abhinav Tathe | Researc= h Scholar | Dyestuff Tech.Dept, ICT,Mumbai.
| Mobile : +91 7666110210 | goldenabhi%%gmail.com

=A0

On Tue, Sep 4, 2012 at 10:31 PM, Steven = Trohalaki steven.trohalaki- -wpafb.af.mil <owner-chemistry%%ccl.net> wrote:

Sent to CCL by: "Steven =A0Trohalaki" [steven.trohalaki!=3D!wpafb.af.mil]

I downloaded the TINKER User Guide (Version 6.0, October 2011) as a PDF but= most of it is not searchable within Acrobat. =A0Is a searchable User Guide= available?

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--e89a8ff1c3889b9fde04c8e49239-- From owner-chemistry@ccl.net Wed Sep 5 09:00:00 2012 From: "Jens Spanget-Larsen spanget^^^ruc.dk" To: CCL Subject: CCL:G: Regarding the format of IR spectrum Message-Id: <-47533-120905033832-4593-ZThP2BQfYlJGtkpeJ/XzLA:+:server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_A94E15A372E6194CA8719D62642F6744C26DDBMBX4adrucdk_" Date: Wed, 5 Sep 2012 07:38:20 +0000 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget|ruc.dk] --_000_A94E15A372E6194CA8719D62642F6744C26DDBMBX4adrucdk_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hello again! The IR absorption intensity predicted and printed by Gaussian is in units o= f km/mol. It is directly related to the integrated absorption coefficient, = which is defined as an integral over the observed molar absorption coeffici= ent epsilon. This in turn is defined as epsilon =3D A/Cd, where A is the ab= sorbance (A =3D log(I0/I), C is the concentration (mol/L), and d is the pat= h length (cm). For a discussion of units, see this link: http://akira.ruc.dk/~spanget/IR_intensity_.pdf Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget###ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ > From: owner-chemistry+spanget=3D=3Druc.dk###ccl.net [mailto:owner-chemistry+s= panget=3D=3Druc.dk###ccl.net] On Behalf Of Flick Coleman wcoleman#wellesley.e= du Sent: 05 September 2012 01:42 To: Jens Spanget-Larsen Subject: CCL:G: Regarding the format of IR spectrum Ambrish, I believe that you are confusing the term intensity from Gaussian = calculations with that in Beer's Law. They are not the same. The intensit= ies in Beer's Law refer to the light intensity before and after the sample,= while those computed in Gaussian are based on the dipole derivatives - the= change in dipole moment on a particular vibration. These intensities are = far more closely related to the absorptivity in Beer's Law - a quantity tha= t relates back to the transition probability. My original answer stands - = you cannot calculate %transmittance from the intensities from a quantum mec= hanical calculation. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 On Tue, Sep 4, 2012 at 6:18 PM, Flick Coleman > wrote: My answer still holds - the vibrational intensities are proportional to cha= nges in dipole moment on vibration. Within a given molecule peak intensiti= es that are determined spectroscopically might mirror those that are calcul= ated, but an absolute number, such as %transmittance, cannot be calculated = . Using Beer's Law, both the spectral path length and molecule concentrati= on are needed, together with a quantity that will be proportional to the in= tensity, in order to compute absorbance or % transmittance. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 On Tue, Sep 4, 2012 at 4:26 PM, AMBRISH KUMAR SRIVASTAVA ambrishphysics*o*g= mail.com

> wrote: Sorry sir, According to Beer's law: A =3D a.L.C. here C is concentration and A =3D log10(1 / T) =3D -log10T =3D -log I/I0 So, how can we expect that only transmittance, but not intensity, is a func= tion of concentration. More ever, in the case of a mixture, various peaks may have different IR in= tensities because there are molecules present in different concentration. I just need an IR spectrum in %T vs wave number instead of Intensity vs wav= e number as obtained from gaussian program. What i want to know: Is there a= ny specific keyword in Gaussian to get it? and/or Is there any software program/utility/link to do the job? On Tue, Sep 4, 2012 at 11:16 PM, Flick Coleman wcoleman,,wellesley.edu

> wrote: Ambrish, the % transmittance is a function of concentration of a sample so = the calculation cannot give you that. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html www.flicksstuff.com/photos/pictures.html new galleries coming soon On Tue, Sep 4, 2012 at 6:44 AM, AMBRISH KUMAR SRIVASTAVA ambrishphysics---g= mail.com

> wrote: Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" [ambrishphysics[#]gmail.com] respected all, Is there any way to get IR spectrum with %Transmittance Vs wavenumber in Ga= ussian 03 w ? In fact, I already have that with intensity Vs wavenumber but= don't know how to convert it? is there any additional software to do this = job? Please help and suggest me. I am very sorry for this naive problem. Thanking you all! Ambrish K. Srivastava ambrishphysics^gmail.com -=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 usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Ambrish K. Srivastava CSIR Junior Research Fellow Department of Physics University of Lucknow Lucknow, India-226007 --_000_A94E15A372E6194CA8719D62642F6744C26DDBMBX4adrucdk_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello again!

The IR absorption intensity predicted and pr= inted by Gaussian is in units of km/mol. It is directly related to the inte= grated absorption coefficient, which is defined as an integral over the observed molar absorption coefficient epsilon. Thi= s in turn is defined as epsilon =3D A/Cd, where A is the absorbance (A =3D = log(I0/I), C is the concentration (mol/L), and d is the path length (cm). F= or a discussion of units, see this link:

http://akira.ruc.dk/~spanget/IR_intensity_.p= df

Yours, Jens >--<

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

JENS SPANGET-LARSEN = Office: +4= 5 4674 2710

Dept. of Science (18.1) &n= bsp; Fax: +45 467= 4 3011

Roskilde University = Mobile: +4= 5 2320 6246

P.O.Box 260 &n= bsp; E-Ma= il: spanget###ruc.dk

DK-4000 Roskilde, Denmark http://www= .ruc.dk/~spanget

------------------------------------------------------<= /o:p>

<= /p>

From: owner-chemistry+spanget=3D=3Druc.dk###ccl.net [mail= to:owner-chemistry+spanget=3D=3Druc.dk###ccl.net] On Behalf Of Flick Coleman wcoleman#wellesley.edu
Sent: 05 September 2012 01:42
To: Jens Spanget-Larsen
Subject: CCL:G: Regarding the format of IR spectrum

Ambrish, I = believe that you are confusing the term intensity from Gaussian calculation= s with that in Beer's Law. They are not the same. The intensiti= es in Beer's Law refer to the light intensity before and after the sample, wh= ile those computed in Gaussian are based on the dipole derivatives - the ch= ange in dipole moment on a particular vibration. These intensities ar= e far more closely related to the absorptivity in Beer's Law - a quantity that relates back to the transition probability= . My original answer stands - you cannot calculate %transmittance fro= m the intensities from a quantum mechanical calculation.

Cheers,

Flick

_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481

On Tue, Sep 4, 2012 at 6:18 PM, Flick Coleman <wcoleman= ++wellesley.edu> wrote:

My answer still holds - the vibrational in= tensities are proportional to changes in dipole moment on vibration. = Within a given molecule peak intensities that are determined spectroscopically might mirror those that are calculated, but an absolute = number, such as %transmittance, cannot be calculated . Using Beer's L= aw, both the spectral path length and molecule concentration are needed, to= gether with a quantity that will be proportional to the intensity, in order to compute absorbance or % transmittance.

Cheers,

Flick

_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481

On Tue, Sep 4, 2012 at 4:26 PM, AMBRISH KUMAR SRIVAS= TAVA ambrishphysics*o*gmail.= com <owner-chemistry++ccl.net> wrote:

Sorry sir,
According to Beer's law:
A =3D a.L.C. here C is concentration and
A =3D log10(1 / T) =3D –log10T =3D –log I/I0
So, how can we expect that only transmittance, but not intensity, is a func= tion of concentration.
More ever, in the case of a mixture, various peaks may have different IR in= tensities because there are molecules present in different concentration. I just need an IR spectrum in %T vs wave number instead of Intensity vs wav= e number as obtained from gaussian program. What i want to know: Is there a= ny specific keyword in Gaussian to get it?
and/or Is there any software program/utility/link to do the job?

On Tue, Sep 4, 2012 at 11:16 PM, Flick Coleman wcole= man,,wellesley.edu &= lt;owner-che= mistry-x-ccl.net> wrote:

Ambrish, th= e % transmittance is a function of concentration of a sample so the calcula= tion cannot give you that.

Cheers,

Flick

_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481

www.wellesley.edu/Chemistry/colemanw.html
www.flicksstuff.com/photos/pictures.html new galleries coming soon

On Tue, Sep 4, 2012 at 6:44 AM, AMBRISH KUMAR SRIVAS= TAVA ambrishphysics---gmail.com <owner-chemistry(!)ccl.net> wrote:<= /o:p>

Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" [ambrishphysics[#]gmail.com]
respected all,
Is there any way to get IR spectrum with %Transmittance Vs wavenumber in Ga= ussian 03 w ? In fact, I already have that with intensity Vs wavenumber but= don't know how to convert it? is there any additional software to do this = job? Please help and suggest me.
I am very sorry for this naive problem.
Thanking you all!
Ambrish K. Srivastava
ambrishphysics^gmail.c= om

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--
Ambrish K. Srivastava
CSIR Junior Research Fellow
Department of Physics
University of Lucknow
Lucknow, India-226007

--_000_A94E15A372E6194CA8719D62642F6744C26DDBMBX4adrucdk_-- From owner-chemistry@ccl.net Wed Sep 5 11:04:00 2012 From: "Arup Kumar Chakrabartty chakrabarttyarup.^^^.gmail.com" To: CCL Subject: CCL:G: Total partition functions Message-Id: <-47534-120905102129-5345-tbMh1eYYLKJJr8W22dUFcg^^^server.ccl.net> X-Original-From: "Arup Kumar Chakrabartty" Date: Wed, 5 Sep 2012 10:21:28 -0400 Sent to CCL by: "Arup Kumar Chakrabartty" [chakrabarttyarup.:.gmail.com] Dear all, I am trying to calculate rate constant using transition state theory from thermochemical output obtained by Gaussian09. The thermochemical output is given below Q Log10(Q) Ln(Q) Total Bot 0.101811D-15 -15.992205 -36.823412 Total V=0 0.125827D+19 18.099774 41.676269 Vib (Bot) 0.658774D-30 -30.181264 -69.494928 Vib (Bot) 1 0.627580D+01 0.797669 1.836701 Vib (Bot) 2 0.437441D+01 0.640919 1.475771 Vib (Bot) 3 0.381061D+01 0.580994 1.337789 Vib (Bot) 4 0.242888D+01 0.385406 0.887431 Vib (Bot) 5 0.138901D+01 0.142705 0.328591 Vib (Bot) 6 0.983124D+00 -0.007392 -0.017020 Vib (Bot) 7 0.798275D+00 -0.097848 -0.225303 Vib (Bot) 8 0.681738D+00 -0.166383 -0.383110 Vib (Bot) 9 0.571170D+00 -0.243235 -0.560068 Vib (Bot) 10 0.501433D+00 -0.299787 -0.690286 Vib (Bot) 11 0.431845D+00 -0.364672 -0.839689 Vib (Bot) 12 0.373929D+00 -0.427210 -0.983688 Vib (Bot) 13 0.304842D+00 -0.515925 -1.187961 Vib (Bot) 14 0.295855D+00 -0.528921 -1.217887 Vib (Bot) 15 0.280599D+00 -0.551913 -1.270828 Vib (Bot) 16 0.244908D+00 -0.610998 -1.406874 Vib (V=0) 0.814169D+04 3.910715 9.004753 Vib (V=0) 1 0.679569D+01 0.832233 1.916288 Vib (V=0) 2 0.490289D+01 0.690452 1.589825 Vib (V=0) 3 0.434327D+01 0.637817 1.468628 Vib (V=0) 4 0.297981D+01 0.474189 1.091860 Vib (V=0) 5 0.197626D+01 0.295844 0.681207 Vib (V=0) 6 0.160297D+01 0.204924 0.471855 Vib (V=0) 7 0.144194D+01 0.158946 0.365986 Vib (V=0) 8 0.134544D+01 0.128864 0.296720 Vib (V=0) 9 0.125910D+01 0.100061 0.230398 Vib (V=0) 10 0.120812D+01 0.082110 0.189066 Vib (V=0) 11 0.116067D+01 0.064710 0.149001 Vib (V=0) 12 0.112436D+01 0.050905 0.117212 Vib (V=0) 13 0.108560D+01 0.035670 0.082134 Vib (V=0) 14 0.108097D+01 0.033815 0.077862 Vib (V=0) 15 0.107336D+01 0.030743 0.070789 Vib (V=0) 16 0.105676D+01 0.023976 0.055206 Electronic 0.100000D+01 0.000000 0.000000 Translational 0.107851D+09 8.032826 18.496265 Rotational 0.143296D+07 6.156233 14.175251 I want to know the value of total partition functions for this molecule. Any help or suggestion is highly appreciated. With regards Arup Kumar Chakrabartty Research Scholar From owner-chemistry@ccl.net Wed Sep 5 11:39:00 2012 From: "Steve Williams willsd:_:appstate.edu" To: CCL Subject: CCL:G: Regarding the format of IR spectrum Message-Id: <-47535-120905104522-7358-JPYcouHcfoDsO0iPV6jDKg|-|server.ccl.net> X-Original-From: Steve Williams Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary=Apple-Mail-E05BCA79-B396-4DAE-BD83-7F9F38AC0105 Date: Wed, 5 Sep 2012 10:34:05 -0400 Mime-Version: 1.0 (1.0) Sent to CCL by: Steve Williams [willsd::appstate.edu] --Apple-Mail-E05BCA79-B396-4DAE-BD83-7F9F38AC0105 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Thanks, Jens. I've struggled with units for IR intensity several times, so I really apprec= iate your .pdf that puts this in such a clear light. Steve Williams Sent from my iPad On Sep 5, 2012, at 3:38 AM, "Jens Spanget-Larsen spanget^^^ruc.dk" wrote: > Hello again! > The IR absorption intensity predicted and printed by Gaussian is in units o= f km/mol. It is directly related to the integrated absorption coefficient, w= hich is defined as an integral over the observed molar absorption coefficien= t epsilon. This in turn is defined as epsilon =3D A/Cd, where A is the absor= bance (A =3D log(I0/I), C is the concentration (mol/L), and d is the path le= ngth (cm). For a discussion of units, see this link: > =20 > http://akira.ruc.dk/~spanget/IR_intensity_.pdf > =20 > Yours, Jens >--< > =20 > ------------------------------------------------------ > JENS SPANGET-LARSEN Office: +45 4674 2710 > Dept. of Science (18.1) Fax: +45 4674 3011 > Roskilde University Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget[#]ruc.dk > DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget > ------------------------------------------------------ > =20 > From: owner-chemistry+spanget=3D=3Druc.dk[#]ccl.net [mailto:owner-chemistr= y+spanget=3D=3Druc.dk[#]ccl.net] On Behalf Of Flick Coleman wcoleman#wellesl= ey.edu > Sent: 05 September 2012 01:42 > To: Jens Spanget-Larsen > Subject: CCL:G: Regarding the format of IR spectrum > =20 > Ambrish, I believe that you are confusing the term intensity from Gaussian= calculations with that in Beer's Law. They are not the same. The intensit= ies in Beer's Law refer to the light intensity before and after the sample, w= hile those computed in Gaussian are based on the dipole derivatives - the ch= ange in dipole moment on a particular vibration. These intensities are far m= ore closely related to the absorptivity in Beer's Law - a quantity that rela= tes back to the transition probability. My original answer stands - you can= not calculate %transmittance from the intensities from a quantum mechanical c= alculation. >=20 >=20 > Cheers, >=20 > Flick >=20 > _______________ > William F. Coleman > Professor of Chemistry > Wellesley College=20 > Wellesley MA 02481 >=20 >=20 >=20 >=20 >=20 >=20 > On Tue, Sep 4, 2012 at 6:18 PM, Flick Coleman wr= ote: > My answer still holds - the vibrational intensities are proportional to ch= anges in dipole moment on vibration. Within a given molecule peak intensiti= es that are determined spectroscopically might mirror those that are calcula= ted, but an absolute number, such as %transmittance, cannot be calculated . = Using Beer's Law, both the spectral path length and molecule concentration a= re needed, together with a quantity that will be proportional to the intensi= ty, in order to compute absorbance or % transmittance. >=20 >=20 > Cheers, >=20 > Flick >=20 > _______________ > William F. Coleman > Professor of Chemistry > Wellesley College=20 > Wellesley MA 02481 >=20 >=20 >=20 >=20 >=20 >=20 > On Tue, Sep 4, 2012 at 4:26 PM, AMBRISH KUMAR SRIVASTAVA ambrishphysics*o*= gmail.com wrote: > Sorry sir,=20 > According to Beer's law: > A =3D a.L.C. here C is concentration and=20 > A =3D log10(1 / T) =3D =E2=80=93log10T =3D =E2=80=93log I/I0 > So, how can we expect that only transmittance, but not intensity, is a fun= ction of concentration. > More ever, in the case of a mixture, various peaks may have different IR i= ntensities because there are molecules present in different concentration. > I just need an IR spectrum in %T vs wave number instead of Intensity vs wa= ve number as obtained from gaussian program. What i want to know: Is there a= ny specific keyword in Gaussian to get it? > and/or Is there any software program/utility/link to do the job? > =20 > On Tue, Sep 4, 2012 at 11:16 PM, Flick Coleman wcoleman,,wellesley.edu wrote: > Ambrish, the % transmittance is a function of concentration of a sample so= the calculation cannot give you that. >=20 > Cheers, >=20 > Flick >=20 > _______________ > William F. Coleman > Professor of Chemistry > Wellesley College=20 > Wellesley MA 02481 >=20 > www.wellesley.edu/Chemistry/colemanw.html > www.flicksstuff.com/photos/pictures.html new galleries coming soon >=20 >=20 >=20 >=20 > On Tue, Sep 4, 2012 at 6:44 AM, AMBRISH KUMAR SRIVASTAVA ambrishphysics---= gmail.com wrote: >=20 > Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" [ambrishphysics[#]gmail.com] > respected all, > Is there any way to get IR spectrum with %Transmittance Vs wavenumber in G= aussian 03 w ? In fact, I already have that with intensity Vs wavenumber but= don't know how to convert it? is there any additional software to do this j= ob? Please help and suggest me. > I am very sorry for this naive problem. > Thanking you all! > Ambrish K. Srivastava > ambrishphysics^gmail.com >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script =3D= - > E-mail to subscribers: CHEMISTRY(!)ccl.net or use:>=20 > E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net or use >=20>=20>=20>=20>=20> =20 >=20>=20 >=20 > =20 >=20 >=20 > --=20 > Ambrish K. Srivastava > CSIR Junior Research Fellow > Department of Physics=20 > University of Lucknow > Lucknow, India-226007 > =20 > =20 --Apple-Mail-E05BCA79-B396-4DAE-BD83-7F9F38AC0105 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8

Thanks, Jens.

I'= ve struggled with units for IR intensity several times, so I really apprecia= te your .pdf that puts this in such a clear light.

Steve Williams<= br>
Sent from my iPad

On Sep 5, 2012, at 3:38 AM, "Jens Spa= nget-Larsen spanget^^^ruc.dk" <owner-chemistry!=!ccl.net> wrote:

=

Hello again!

The IR absorption intensity predicted and prin= ted by Gaussian is in units of km/mol. It is directly related to the integra= ted absorption coefficient, which is defined as an integral over the observed molar absorption coefficient epsilon. This= in turn is defined as epsilon =3D A/Cd, where A is the absorbance (A =3D lo= g(I0/I), C is the concentration (mol/L), and d is the path length (cm). For a= discussion of units, see this link:

http://akira.ruc.dk/~spanget/IR_intensity_.pdf

Yours, Jens >--<

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

JENS SPANGET-LARSEN   &n= bsp;     Office:      +45 4674 2= 710

Dept. of Science (18.1)  &nbs= p; Fax:         +45 4674 3011<= o:p>

Roskilde University   &n= bsp;     Mobile:      +45 2320 6= 246

P.O.Box 260    &nbs= p;            E-Mail:=      spanget[#]ruc.dk

DK-4000 Roskilde, Denmark   http://www.ruc.dk/~spanget<= /p>
------------------------------------------------------

From: owner-chemistry+spanget=3D=3Druc.dk[#]ccl.net [mailto:own= er-chemistry+spanget=3D=3Druc.dk[#]ccl.net] On Behalf Of Flick Coleman wcoleman#wellesley.edu
Sent: 05 September 2012 01:42
To: Jens Spanget-Larsen
Subject: CCL:G: Regarding the format of IR spectrum=

Ambrish, I be= lieve that you are confusing the term intensity from Gaussian calculations w= ith that in Beer's Law. They are not the same. The intensities in Beer's Law refer to the light intensity before and after the sample, whi= le those computed in Gaussian are based on the dipole derivatives - the chan= ge in dipole moment on a particular vibration. These intensities are f= ar more closely related to the absorptivity in Beer's Law - a quantity that relates back to the transition probability.= My original answer stands - you cannot calculate %transmittance from t= he intensities from a quantum mechanical calculation.

Cheers,

Flick

_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481

On Tue, Sep 4, 2012 at 6:18 PM, Flick Coleman <wcoleman++wellesley= .edu> wrote:

My answer still holds - the vibrational inte= nsities are proportional to changes in dipole moment on vibration. Wit= hin a given molecule peak intensities that are determined spectroscopically might mirror those that are calculated, but an absolute n= umber, such as %transmittance, cannot be calculated . Using Beer's Law= , both the spectral path length and molecule concentration are needed, toget= her with a quantity that will be proportional to the intensity, in order to compute absorbance or % transmittance.

Cheers,

Flick

_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481

On Tue, Sep 4, 2012 at 4:26 PM, AMBRISH KUMAR SRIVAST= AVA ambrishphysics*o*gmail.co= m <owne= r-chemistry++ccl.net> wrote:

Sorry sir,
According to Beer's law:
A =3D a.L.C. here C is concentration and
A =3D log10(1 / T) =3D =E2=80=93log10T =3D =E2=80=93log I/I0
So, how can we expect that only transmittance, but not intensity, is a funct= ion of concentration.
More ever, in the case of a mixture, various peaks may have different IR int= ensities because there are molecules present in different concentration.
= I just need an IR spectrum in %T vs wave number instead of Intensity vs wave= number as obtained from gaussian program. What i want to know: Is there any= specific keyword in Gaussian to get it?
and/or Is there any software program/utility/link to do the job? =

On Tue, Sep 4, 2012 at 11:16 PM, Flick Coleman wcolem= an,,wellesley.edu <= ;owner-chemis= try-x-ccl.net> wrote:

Ambrish, the %= transmittance is a function of concentration of a sample so the calculation= cannot give you that.

Cheers,

Flick

_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481

www.wellesley.edu/Chemistry/colemanw.html
www.flicksstuff.com/photos/pictures.html new galleries coming soon

On Tue, Sep 4, 2012 at 6:44 AM, AMBRISH KUMAR SRIVAST= AVA ambrishphysics---gmail.com <owner-chemistry(!)ccl.net> wrote:

Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" [ambrishphysics[#]gmail.com]
respected all,
Is there any way to get IR spectrum with %Transmittance Vs wavenumber in Gau= ssian 03 w ? In fact, I already have that with intensity Vs wavenumber but d= on't know how to convert it? is there any additional software to do this job= ? Please help and suggest me.
I am very sorry for this naive problem.
Thanking you all!
Ambrish K. Srivastava
ambrishphysics^gmail.co= m

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Ambrish K. Srivastava
CSIR Junior Research Fellow
Department of Physics
University of Lucknow
Lucknow, India-226007

= --Apple-Mail-E05BCA79-B396-4DAE-BD83-7F9F38AC0105-- From owner-chemistry@ccl.net Wed Sep 5 12:46:00 2012 From: "Robert Hinde rhinde=-=utk.edu" To: CCL Subject: CCL:G: infrared intensities ... Message-Id: <-47536-120905121148-20000-JZnyi3qFLczR9KNSDtkp5A---server.ccl.net> X-Original-From: "Robert Hinde" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 5 Sep 2012 12:11:26 -0400 MIME-Version: 1.0 Sent to CCL by: "Robert Hinde" [rhinde!A!utk.edu] Also highly recommended, although written from a physicist's perspective: Robert C. Hilborn, "Einstein coefficients, cross sections, f values, dipole moments, and all that" http://arxiv.org/abs/physics/0202029 This is a revised version of a paper by the same author that appeared in the American Journal of Physics, vol. 50, p. 982 (1982). Cheers, RJH On Wed, September 5, 2012 10:34 am, Steve Williams willsd:_:appstate.edu wrote: > Thanks, Jens. > I've struggled with units for IR intensity several times, so I really > appreciate your .pdf that puts this in such a clear light. > Steve Williams > > Sent from my iPad > > On Sep 5, 2012, at 3:38 AM, "Jens Spanget-Larsen spanget^^^ruc.dk" > wrote: > >> Hello again! >> The IR absorption intensity predicted and printed by Gaussian is in >> units of km/mol. It is directly related to the integrated absorption >> coefficient, which is defined as an integral over the observed molar >> absorption coefficient epsilon. This in turn is defined as epsilon = >> A/Cd, where A is the absorbance (A = log(I0/I), C is the concentration >> (mol/L), and d is the path length (cm). For a discussion of units, see >> this link: >> >> http://akira.ruc.dk/~spanget/IR_intensity_.pdf >> >> Yours, Jens >--< >> >> ------------------------------------------------------ >> JENS SPANGET-LARSEN Office: +45 4674 2710 >> Dept. of Science (18.1) Fax: +45 4674 3011 >> Roskilde University Mobile: +45 2320 6246 >> P.O.Box 260 E-Mail: spanget[#]ruc.dk >> DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget >> ------------------------------------------------------ >> >> From: owner-chemistry+spanget==ruc.dk[#]ccl.net >> [mailto:owner-chemistry+spanget==ruc.dk[#]ccl.net] On Behalf Of Flick >> Coleman wcoleman#wellesley.edu >> Sent: 05 September 2012 01:42 >> To: Jens Spanget-Larsen >> Subject: CCL:G: Regarding the format of IR spectrum >> >> Ambrish, I believe that you are confusing the term intensity from >> Gaussian calculations with that in Beer's Law. They are not the same. >> The intensities in Beer's Law refer to the light intensity before and >> after the sample, while those computed in Gaussian are based on the >> dipole derivatives - the change in dipole moment on a particular >> vibration. These intensities are far more closely related to the >> absorptivity in Beer's Law - a quantity that relates back to the >> transition probability. My original answer stands - you cannot >> calculate %transmittance from the intensities from a quantum mechanical >> calculation. >> >> >> Cheers, >> >> Flick >> >> _______________ >> William F. Coleman >> Professor of Chemistry >> Wellesley College >> Wellesley MA 02481 >> >> >> >> >> >> >> On Tue, Sep 4, 2012 at 6:18 PM, Flick Coleman >> wrote: >> My answer still holds - the vibrational intensities are proportional to >> changes in dipole moment on vibration. Within a given molecule peak >> intensities that are determined spectroscopically might mirror those >> that are calculated, but an absolute number, such as %transmittance, >> cannot be calculated . Using Beer's Law, both the spectral path length >> and molecule concentration are needed, together with a quantity that >> will be proportional to the intensity, in order to compute absorbance or >> % transmittance. >> >> >> Cheers, >> >> Flick >> >> _______________ >> William F. Coleman >> Professor of Chemistry >> Wellesley College >> Wellesley MA 02481 >> >> >> >> >> >> >> On Tue, Sep 4, 2012 at 4:26 PM, AMBRISH KUMAR SRIVASTAVA >> ambrishphysics*o*gmail.com wrote: >> Sorry sir, >> According to Beer's law: >> A = a.L.C. here C is concentration and >> A = log10(1 / T) = –log10T = –log I/I0 >> So, how can we expect that only transmittance, but not intensity, is a >> function of concentration. >> More ever, in the case of a mixture, various peaks may have different IR >> intensities because there are molecules present in different >> concentration. >> I just need an IR spectrum in %T vs wave number instead of Intensity vs >> wave number as obtained from gaussian program. What i want to know: Is >> there any specific keyword in Gaussian to get it? >> and/or Is there any software program/utility/link to do the job? >> >> On Tue, Sep 4, 2012 at 11:16 PM, Flick Coleman wcoleman,,wellesley.edu >> wrote: >> Ambrish, the % transmittance is a function of concentration of a sample >> so the calculation cannot give you that. >> >> Cheers, >> >> Flick >> >> _______________ >> William F. Coleman >> Professor of Chemistry >> Wellesley College >> Wellesley MA 02481 >> >> www.wellesley.edu/Chemistry/colemanw.html >> www.flicksstuff.com/photos/pictures.html new galleries coming soon >> >> >> >> >> On Tue, Sep 4, 2012 at 6:44 AM, AMBRISH KUMAR SRIVASTAVA >> ambrishphysics---gmail.com wrote: >> >> Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" [ambrishphysics[#]gmail.com] >> respected all, >> Is there any way to get IR spectrum with %Transmittance Vs wavenumber in >> Gaussian 03 w ? In fact, I already have that with intensity Vs >> wavenumber but don't know how to convert it? is there any additional >> software to do this job? Please help and suggest me. >> I am very sorry for this naive problem. >> Thanking you all! >> Ambrish K. Srivastava >> ambrishphysics^gmail.com>> E-mail to subscribers: CHEMISTRY(!)ccl.net or use:> >> E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net or use >> > > > > > >> > >> >> >> >> >> -- >> Ambrish K. Srivastava >> CSIR Junior Research Fellow >> Department of Physics >> University of Lucknow >> Lucknow, India-226007 >> >> > ----- Robert Hinde Professor of Chemistry Associate Dean for Academic Programs College of Arts and Sciences University of Tennessee About my research: http://tiny.utk.edu/hinde-group Locate my Chemistry office: http://tiny.utk.edu/hinde-lab From owner-chemistry@ccl.net Wed Sep 5 13:22:00 2012 From: "Kaliappan Muthukumar muthukumar2k3~!~gmail.com" To: CCL Subject: CCL: Final call - Extended deadline September 30th - Doped Nano Structures Message-Id: <-47537-120905123648-3120-r16h1PwCHY5Dps+6E/Y8Fg*server.ccl.net> X-Original-From: Kaliappan Muthukumar Content-Type: multipart/alternative; boundary=f46d042f9e929250bc04c8f6fa44 Date: Wed, 5 Sep 2012 18:36:37 +0200 MIME-Version: 1.0 Sent to CCL by: Kaliappan Muthukumar [muthukumar2k3_._gmail.com] --f46d042f9e929250bc04c8f6fa44 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL ers, Apologies for this cross posting!!! We have the pleasure to inform you that we are organizing a (peer-reviewed) themed issue entitled 'Doped Nano-Materials for Energy and Electronic Applications' to be published in 'Advanced Chemistry Letters'. A journal published by the American Scientific Publishers, this December. If your research field (both experimental and theoretical) matches any of the following themes 1) Doped Nanomaterials for Energy (Photovoltaic and Electrochemical Applications) and Electronic Devices, 2) Synthesis, Growth, Fabrication and Processing of Functional Materials, 3) Characterization of Doped Nanomaterials and Molecules on Surfaces, 4) Dopants, Vacancies and Defects in Surfaces and Interfaces, 5) Further Studies Advancing and Understanding the Function of Doped Materials. we welcome your submission (Article /communication /Review) to this issue. The last date for the submission of manuscript is 30th September 2012, and i suggest you the following webpage http://www.aspbs.com/acl/cfp.pdf for further information and instructions for the preparation of manuscripts. According to the journal policy, all research papers will be peer-reviewed by experts in the field and we would be grateful if you would inform us about your intention to submit well in advance. Further, If you need more information please do not hesitate to contact me (kaliappan.muthukumar#%#gmail.com) and we look forward to hearing from you. Best regards, Dr. Muthukumar and Dr. Larsson -- -- Dr. Muthukumar Kaliappan, Institute for Theoretical Physics, Goethe University, Frankfurt Am Main Germany Email : Kaliappan.Muthukumar#%#gmail.com "To get Profit without risk, Experience without danger & Reward without Hard work is as impossible as it is to live without being born" -'Anonymous' --f46d042f9e929250bc04c8f6fa44 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear CCL ers,

Apologies=A0for this cross posting!!!

We have the pleasure to inform you that we are organizing

a (pee= r-reviewed) themed issue entitled 'Doped=A0Nano-Materials for Energy an= d Electronic
Applications' to be published in 'Advanced Chemistry Letters'.<= br>A journal published by the American Scientific Publishers, this December= .

If your research field (both experimental and theoretical)

matches any of the following themes=A0

1) Dope= d=A0Nanomaterials for Energy (Photovoltaic and Electrochemical

Applicati= ons) and Electronic Devices,

2) Synthesis, Growth, Fabr= ication and Processing of Functional Materials,

3) Cha= racterization of Doped=A0Nanomaterials and Molecules on Surfaces,

4) Dopants, Vacancies an= d Defects in Surfaces and Interfaces,

5) Further Studies Advancing and Understanding= the Function of Doped

Materials.

we welcome your submission=A0(Article /communi= cation /Review)=A0to this issue.=A0

The last date = for the submission of manuscript=A0

is 30th September 2012, and=A0i suggest=A0you the following webpage

http://www.aspbs.com/acl/cfp.pdf

for further information and instructions for the preparation of = manuscripts.=A0

According to the journal policy, all research papers will be=A0

peer-reviewed by experts=A0in the field and we would be grateful= =A0

if you=A0would inform us about your intention to submit well = in advance.

Further,=A0If you need more information please do not hesita= te=A0

to contact me (kaliappan.muthukumar= #%#gmail.com)

and we look forward to hearing from you.

Best= regards,

Dr. Muthukumar and Dr. Larsson

Dr. Muthukumar Kaliappan,

Institute for Theoretical Physics,=

Goethe University,

Frankfurt Am Main

Germany

Email=A0 : Kaliappan.Muthukumar#%#gmail.com

"To = get Profit without risk, Experience without danger & Reward without Har= d work is as impossible as it is to live without being born"

-'Anonymous'

--f46d042f9e929250bc04c8f6fa44-- From owner-chemistry@ccl.net Wed Sep 5 15:11:00 2012 From: "Cris Ramirez farmramirez|-|yahoo.com.ar" To: CCL Subject: CCL: qst2 orbital isomer Message-Id: <-47538-120905151002-13435-RhFH3EqNlvZQBgR1s3OyuQ||server.ccl.net> X-Original-From: "Cris Ramirez" Date: Wed, 5 Sep 2012 15:10:00 -0400 Sent to CCL by: "Cris Ramirez" [farmramirez::yahoo.com.ar] Good morning, I was wondering if anyone has ever performed a QTS2 calculation in order to find a ts for orbital isomers. I'm submitting like this: # ucam-b3lyp/6-31+G* opt(calcfc,noeigentest,loose,nooptreactant,nooptproduct,qst2) freq(noraman) nosymm gfinput iop(6/7=3) Pop=full SCRF(Solvent=dichloromethane) after one day running, it aborts and the message is something related to "Inconsistency" .... My structures are the same as reactant and product, only some differences in distances and angles. One has the HOMO localized on a side, and the other has it all symmetrically delocalized on the structure. Thank you very much in advanced for som help. Cristina From owner-chemistry@ccl.net Wed Sep 5 17:37:01 2012 From: "Abrash, Sam sabrash*_*richmond.edu" To: CCL Subject: CCL:G: infrared intensities ... Message-Id: <-47539-120905143430-9874-m0iGVTYfSTb7Uzo2UvYANw .. server.ccl.net> X-Original-From: "Abrash, Sam" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Wed, 5 Sep 2012 18:34:19 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Sam" [sabrash**richmond.edu] While it is correct that one neither gets absolute absorbences or transmittances from a calculation, what is truly important for IR spectroscopists, (such as myself) are the relative peak heights, whether in the format of absorbances or transmittances. Since A=epsilon*l*c, and gaussian gives us epsilon, the spectrum gaussian produces has the same relative absorbances as an absorption spectrum would have. Since that is the case, and since A = - log (I/I0) and %T = (I/I0) x 100%, the relative peak heights for the transmittance spectrum can be obtained by taking the negative antilog of the gaussian intensities, ie. 10^-(elc). However, I don't really see the point of this since it is almost certainly easier to convert the infrared spectrum in transmittance units to absorbance, and then do a direct comparison. Best, Sam Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash=richmond.edu Web-page: http://www.richmond.edu/~sabrash "In 1893 Charles Hinton left Japan to become a mathematics instructor at Princeton University, where he invented a baseball-pitching machine that used gunpowder to propel the balls, like a cannon. After several accidents, the device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian Steward and Jack Cohen, The Science of Diskworld III -----Original Message----- > From: owner-chemistry+sabrash==richmond.edu=ccl.net [mailto:owner-chemistry+sabrash==richmond.edu=ccl.net] On Behalf Of Robert Hinde rhinde=-=utk.edu Sent: Wednesday, September 05, 2012 12:11 PM To: Abrash, Sam Subject: CCL:G: infrared intensities ... Sent to CCL by: "Robert Hinde" [rhinde!A!utk.edu] Also highly recommended, although written from a physicist's perspective: Robert C. Hilborn, "Einstein coefficients, cross sections, f values, dipole moments, and all that" http://arxiv.org/abs/physics/0202029 This is a revised version of a paper by the same author that appeared in the American Journal of Physics, vol. 50, p. 982 (1982). Cheers, RJH On Wed, September 5, 2012 10:34 am, Steve Williams willsd:_:appstate.edu wrote: > Thanks, Jens. > I've struggled with units for IR intensity several times, so I really > appreciate your .pdf that puts this in such a clear light. > Steve Williams > > Sent from my iPad > > On Sep 5, 2012, at 3:38 AM, "Jens Spanget-Larsen spanget^^^ruc.dk" > wrote: > >> Hello again! >> The IR absorption intensity predicted and printed by Gaussian is in >> units of km/mol. It is directly related to the integrated absorption >> coefficient, which is defined as an integral over the observed molar >> absorption coefficient epsilon. This in turn is defined as epsilon = >> A/Cd, where A is the absorbance (A = log(I0/I), C is the concentration >> (mol/L), and d is the path length (cm). For a discussion of units, see >> this link: >> >> http://akira.ruc.dk/~spanget/IR_intensity_.pdf >> >> Yours, Jens >--< >> >> ------------------------------------------------------ >> JENS SPANGET-LARSEN Office: +45 4674 2710 >> Dept. of Science (18.1) Fax: +45 4674 3011 >> Roskilde University Mobile: +45 2320 6246 >> P.O.Box 260 E-Mail: spanget[#]ruc.dk >> DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget >> ------------------------------------------------------ >> >> From: owner-chemistry+spanget==ruc.dk[#]ccl.net >> [mailto:owner-chemistry+spanget==ruc.dk[#]ccl.net] On Behalf Of Flick >> Coleman wcoleman#wellesley.edu >> Sent: 05 September 2012 01:42 >> To: Jens Spanget-Larsen >> Subject: CCL:G: Regarding the format of IR spectrum >> >> Ambrish, I believe that you are confusing the term intensity from >> Gaussian calculations with that in Beer's Law. They are not the same. >> The intensities in Beer's Law refer to the light intensity before and >> after the sample, while those computed in Gaussian are based on the >> dipole derivatives - the change in dipole moment on a particular >> vibration. These intensities are far more closely related to the >> absorptivity in Beer's Law - a quantity that relates back to the >> transition probability. My original answer stands - you cannot >> calculate %transmittance from the intensities from a quantum mechanical >> calculation. >> >> >> Cheers, >> >> Flick >> >> _______________ >> William F. Coleman >> Professor of Chemistry >> Wellesley College >> Wellesley MA 02481 >> >> >> >> >> >> >> On Tue, Sep 4, 2012 at 6:18 PM, Flick Coleman >> wrote: >> My answer still holds - the vibrational intensities are proportional to >> changes in dipole moment on vibration. Within a given molecule peak >> intensities that are determined spectroscopically might mirror those >> that are calculated, but an absolute number, such as %transmittance, >> cannot be calculated . Using Beer's Law, both the spectral path length >> and molecule concentration are needed, together with a quantity that >> will be proportional to the intensity, in order to compute absorbance or >> % transmittance. >> >> >> Cheers, >> >> Flick >> >> _______________ >> William F. Coleman >> Professor of Chemistry >> Wellesley College >> Wellesley MA 02481 >> >> >> >> >> >> >> On Tue, Sep 4, 2012 at 4:26 PM, AMBRISH KUMAR SRIVASTAVA >> ambrishphysics*o*gmail.com wrote: >> Sorry sir, >> According to Beer's law: >> A = a.L.C. here C is concentration and >> A = log10(1 / T) = â€“log10T = â€“log I/I0 >> So, how can we expect that only transmittance, but not intensity, is a >> function of concentration. >> More ever, in the case of a mixture, various peaks may have different IR >> intensities because there are molecules present in different >> concentration. >> I just need an IR spectrum in %T vs wave number instead of Intensity vs >> wave number as obtained from gaussian program. What i want to know: Is >> there any specific keyword in Gaussian to get it? >> and/or Is there any software program/utility/link to do the job? >> >> On Tue, Sep 4, 2012 at 11:16 PM, Flick Coleman wcoleman,,wellesley.edu >> wrote: >> Ambrish, the % transmittance is a function of concentration of a sample >> so the calculation cannot give you that. >> >> Cheers, >> >> Flick >> >> _______________ >> William F. Coleman >> Professor of Chemistry >> Wellesley College >> Wellesley MA 02481 >> >> www.wellesley.edu/Chemistry/colemanw.html >> www.flicksstuff.com/photos/pictures.html new galleries coming soon >> >> >> >> >> On Tue, Sep 4, 2012 at 6:44 AM, AMBRISH KUMAR SRIVASTAVA >> ambrishphysics---gmail.com wrote: >> >> Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" [ambrishphysics[#]gmail.com] >> respected all, >> Is there any way to get IR spectrum with %Transmittance Vs wavenumber in >> Gaussian 03 w ? In fact, I already have that with intensity Vs >> wavenumber but don't know how to convert it? is there any additional >> software to do this job? Please help and suggest me. >> I am very sorry for this naive problem. >> Thanking you all! >> Ambrish K. Srivastava >> ambrishphysics^gmail.com>> E-mail to subscribers: CHEMISTRY(!)ccl.net or use:> >> E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net or use >> > > > > > >> > >> >> >> >> >> -- >> Ambrish K. Srivastava >> CSIR Junior Research Fellow >> Department of Physics >> University of Lucknow >> Lucknow, India-226007 >> >> > ----- Robert Hinde Professor of Chemistry Associate Dean for Academic Programs College of Arts and Sciences University of Tennessee About my research: http://tiny.utk.edu/hinde-group Locate my Chemistry office: http://tiny.utk.edu/hinde-labhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Sep 5 22:25:01 2012 From: "Theodore S Dibble tsdibble]-[esf.edu" To: CCL Subject: CCL: qst2 orbital isomer Message-Id: <-47540-120905222342-6820-NXiF5WPR9HXwNjj9BqvbrQ : server.ccl.net> X-Original-From: "Theodore S Dibble" Date: Wed, 5 Sep 2012 22:23:40 -0400 Sent to CCL by: "Theodore S Dibble" [tsdibble^^^esf.edu] Cristina, If you have two >>orbital<< isomers, then one probably has an unstable wavefunction. The "stable" keyword can determine this. If one isomer has an unstable wavefunction, there is likely no smooth path connecting the two isomers on a single potential energy surface. This would lead to failure of the TS optimization. The "unstable" isomer may be a real excited state, or just an artifact. Good luck! Ted Theodore S. Dibble Chemistry Department SUNY-Environmental Science and Forestry 1 Forestry Drive Syracuse, NY 13210 (315) 470-6596 (315) 470-6856 (fax) http://www.esf.edu/faculty/dibble/ > "Cris Ramirez farmramirez|-|yahoo.com.ar" wrote: > > Sent to CCL by: "Cris Ramirez" [farmramirez::yahoo.com.ar] > Good morning, I was wondering if anyone has ever performed a QTS2 calculation in order to find a ts for orbital isomers. > I'm submitting like this: > # ucam-b3lyp/6-31+G* > opt(calcfc,noeigentest,loose,nooptreactant,nooptproduct,qst2) > freq(noraman) nosymm > gfinput iop(6/7=3) Pop=full > SCRF(Solvent=dichloromethane) > > after one day running, it aborts and the message is something related to "Inconsistency" .... > My structures are the same as reactant and product, only some differences in distances and angles. One has the HOMO localized on a side, and the other has it all symmetrically delocalized on the structure. > Thank you very much in advanced for som help. > Cristina > >