From owner-chemistry@ccl.net Fri Jan 13 04:29:00 2012 From: "SOLO RV rvsolo[*]gmail.com" To: CCL Subject: CCL: any base pair database? Message-Id: <-46149-120113042610-26189-Aiu6IRbELAkuJ+RLU1Gbfw-.-server.ccl.net> X-Original-From: "SOLO RV" Date: Fri, 13 Jan 2012 04:26:09 -0500 Sent to CCL by: "SOLO RV" [rvsolo#,#gmail.com] hi cclrs, is there any basepair database available where one can get the coordinates of the desire base pair by just giving the three letter code? thanks in advance rv solo From owner-chemistry@ccl.net Fri Jan 13 07:44:00 2012 From: "Ermias Leggesse ermiaslegg^_^gmail.com" To: CCL Subject: CCL:G: vibrational partition function for transition state Message-Id: <-46150-120113074242-17750-7b8yjITgBp86y41Sn+EZEw/./server.ccl.net> X-Original-From: "Ermias Leggesse" Date: Fri, 13 Jan 2012 07:42:41 -0500 Sent to CCL by: "Ermias Leggesse" [ermiaslegg__gmail.com] Dear All; I was trying to calculate the rate constant for a certain decomposition reaction using Transition state theory and Gaussian 09 optimization output. However, I am having a difficulty in finding the value for vibrational partition function for transition state from the output file. I know that the the molecular partition function is written as the product of electronic, vibrational, rotational and partition functions. For the reactant finding each value from the output file is easy but for the transiton state I couldn't decide which value should I take especially for the vibrational partition function. Any advice or reference is appreciated. Thank you! From owner-chemistry@ccl.net Fri Jan 13 11:17:00 2012 From: "Jean Jules FIFEN julesfifen*_*gmail.com" To: CCL Subject: CCL:G: vibrational partition function for transition state Message-Id: <-46151-120113103612-3675-t9c+wMkFtzPS/dQisBe5vw],[server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=20cf305b0ab67bf91204b66a9ff4 Date: Fri, 13 Jan 2012 16:36:05 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen^gmail.com] --20cf305b0ab67bf91204b66a9ff4 Content-Type: text/plain; charset=ISO-8859-1 I don't understand why. A transition state is also an equilibrium state. Therefore, you also have printed out such information. After the frequencies data, you have an output file like this: ---------------------------------------------------------------------------------------------------------------- Zero-point correction= 0.168409 (Hartree/Particle) Thermal correction to Energy= 0.183020 Thermal correction to Enthalpy= 0.183964 Thermal correction to Gibbs Free Energy= 0.125649 Sum of electronic and zero-point Energies= -799.502670 Sum of electronic and thermal Energies= -799.488058 Sum of electronic and thermal Enthalpies= -799.487114 Sum of electronic and thermal Free Energies= -799.545430 E (Thermal) CV S KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin Total 114.847 54.445 122.736 Electronic 0.000 0.000 1.377 Translational 0.889 2.981 41.972 Rotational 0.889 2.981 32.883 Vibrational 113.069 48.483 46.503 Vibration 1 0.595 1.980 5.056 Vibration 2 0.596 1.974 4.524 Vibration 3 0.601 1.958 3.707 Vibration 4 0.604 1.948 3.435 Vibration 5 0.609 1.934 3.120 Vibration 6 0.612 1.924 2.953 Vibration 7 0.623 1.889 2.521 Vibration 8 0.630 1.864 2.306 Vibration 9 0.638 1.838 2.119 Vibration 10 0.657 1.779 1.804 Vibration 11 0.659 1.775 1.785 Vibration 12 0.688 1.687 1.458 Vibration 13 0.727 1.575 1.165 Vibration 14 0.730 1.567 1.148 Vibration 15 0.756 1.496 1.008 Vibration 16 0.823 1.327 0.750 Vibration 17 0.831 1.307 0.726 Vibration 18 0.848 1.268 0.679 Vibration 19 0.850 1.263 0.673 Vibration 20 0.929 1.090 0.499 Vibration 21 0.948 1.051 0.466 Vibration 22 0.953 1.041 0.458 Vibration 23 0.963 1.021 0.441 Vibration 24 0.975 1.000 0.424 Q Log10(Q) Ln(Q) Total Bot *0.160621D-57 * -57.794197 -133.076056 Total V=0 *0.465871D+20* 19.668265 45.287855 Vib (Bot) 0.191734D-72 -72.717301 -167.437774 Vib (Bot) 1 0.466573D+01 0.668919 1.540243 Vib (Bot) 2 0.356014D+01 0.551467 1.269799 Vib (Bot) 3 0.234068D+01 0.369343 0.850443 Vib (Bot) 4 0.203140D+01 0.307795 0.708724 Vib (Bot) 5 0.172125D+01 0.235845 0.543053 Vib (Bot) 6 0.157411D+01 0.197034 0.453687 Vib (Bot) 7 0.124366D+01 0.094703 0.218062 Vib (Bot) 8 0.110187D+01 0.042132 0.097013 Vib (Bot) 9 0.988831D+00 -0.004878 -0.011231 Vib (Bot) 10 0.817520D+00 -0.087502 -0.201480 Vib (Bot) 11 0.807733D+00 -0.092732 -0.213523 Vib (Bot) 12 0.652246D+00 -0.185589 -0.427334 Vib (Bot) 13 0.526513D+00 -0.278591 -0.641478 Vib (Bot) 14 0.519648D+00 -0.284291 -0.654604 Vib (Bot) 15 0.463422D+00 -0.334023 -0.769116 Vib (Bot) 16 0.363682D+00 -0.439278 -1.011475 Vib (Bot) 17 0.354370D+00 -0.450543 -1.037414 Vib (Bot) 18 0.336605D+00 -0.472880 -1.088845 Vib (Bot) 19 0.334290D+00 -0.475877 -1.095748 Vib (Bot) 20 0.267959D+00 -0.571931 -1.316920 Vib (Bot) 21 0.255146D+00 -0.593211 -1.365918 Vib (Bot) 22 0.251942D+00 -0.598700 -1.378557 Vib (Bot) 23 0.245599D+00 -0.609773 -1.404055 Vib (Bot) 24 0.238867D+00 -0.621843 -1.431847 Vib (V=0) 0.556111D+05 4.745161 10.926137 Vib (V=0) 1 0.519244D+01 0.715371 1.647204 Vib (V=0) 2 0.409508D+01 0.612262 1.409786 Vib (V=0) 3 0.289349D+01 0.461422 1.062464 Vib (V=0) 4 0.259203D+01 0.413639 0.952440 Vib (V=0) 5 0.229240D+01 0.360291 0.829601 Vib (V=0) 6 0.215161D+01 0.332763 0.766215 Vib (V=0) 7 0.184041D+01 0.264915 0.609989 Vib (V=0) 8 0.171001D+01 0.232999 0.536500 Vib (V=0) 9 0.160806D+01 0.206301 0.475026 Vib (V=0) 10 0.145830D+01 0.163847 0.377271 Vib (V=0) 11 0.144996D+01 0.161357 0.371539 Vib (V=0) 12 0.132184D+01 0.121180 0.279026 Vib (V=0) 13 0.122610D+01 0.088525 0.203836 Vib (V=0) 14 0.122113D+01 0.086763 0.199780 Vib (V=0) 15 0.118173D+01 0.072520 0.166982 Vib (V=0) 16 0.111828D+01 0.048549 0.111788 Vib (V=0) 17 0.111284D+01 0.046434 0.106919 Vib (V=0) 18 0.110275D+01 0.042476 0.097804 Vib (V=0) 19 0.110146D+01 0.041967 0.096633 Vib (V=0) 20 0.106728D+01 0.028277 0.065110 Vib (V=0) 21 0.106134D+01 0.025853 0.059530 Vib (V=0) 22 0.105989D+01 0.025260 0.058163 Vib (V=0) 23 0.105706D+01 0.024101 0.055494 Vib (V=0) 24 0.105413D+01 0.022893 0.052714 Electronic 0.200000D+01 0.301030 0.693147 Translational 0.122221D+09 8.087147 18.621343 Rotational 0.342711D+07 6.534928 15.047227 ---------------------------------------------------------------------------------------------------------------------------------------- In this case, the vibrational partition function is: *Q* *Total Bot = 0.160621D-57* (when the reference state is assumed to be at the bottom of the well.) *Total V = 00.465871D+20* (when the reference state is assumed to be at the ZPE level). I hope this would help. Best regards, On 13 January 2012 13:42, Ermias Leggesse ermiaslegg^_^gmail.com < owner-chemistry=ccl.net> wrote: > > Sent to CCL by: "Ermias Leggesse" [ermiaslegg__gmail.com] > Dear All; > I was trying to calculate the rate constant for a certain decomposition > reaction using Transition state theory and Gaussian 09 optimization output. > However, I am having a difficulty in finding the value for vibrational > partition function for transition state from the output file. I know that > the > the molecular partition function is written as the product of electronic, > vibrational, rotational and partition functions. For the reactant finding > each > value from the output file is easy but for the transiton state I couldn't > decide which value should I take especially for the vibrational partition > function. Any advice or reference is appreciated. > Thank you!> > > Jean Jules FIFEN, University of Douala, Cameroon, Department of Physics. -- Jules. --20cf305b0ab67bf91204b66a9ff4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: base64 PGRpdiBkaXI9Imx0ciI+SSBkb24mIzM5O3QgdW5kZXJzdGFuZCB3aHkuIEEgdHJhbnNpdGlvbiBz dGF0ZSBpcyBhbHNvIGFuIGVxdWlsaWJyaXVtIHN0YXRlLiBUaGVyZWZvcmUsIHlvdSBhbHNvIGhh dmUgcHJpbnRlZCBvdXQgc3VjaCBpbmZvcm1hdGlvbi4gPGJyPkFmdGVyIHRoZSBmcmVxdWVuY2ll cyBkYXRhLCB5b3UgaGF2ZSBhbiBvdXRwdXQgZmlsZSBsaWtlIHRoaXM6PGJyPjxicj48YnI+Ci0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS08YnI+ WmVyby1wb2ludCBjb3JyZWN0aW9uPaCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgIDAuMTY4NDA5 IChIYXJ0cmVlL1BhcnRpY2xlKTxicj6gVGhlcm1hbCBjb3JyZWN0aW9uIHRvIEVuZXJneT2goKCg oKCgoKCgoKCgoKCgoKCgIDAuMTgzMDIwPGJyPgqgVGhlcm1hbCBjb3JyZWN0aW9uIHRvIEVudGhh 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OnJnYig1MSwxMDIsMjU1KSI+SnVsZXMuPC9zcGFuPjwvZm9udD48L2Rpdj4KPGJyPgo8L2Rpdj4K --20cf305b0ab67bf91204b66a9ff4-- From owner-chemistry@ccl.net Fri Jan 13 14:37:00 2012 From: "Ronald Cook cookrl!A!tda.com" To: CCL Subject: CCL:G: How to calculate ionization potential, electron affinity Message-Id: <-46152-120112204333-3065-uwqq7xbDgs2ZggR3BsrFyQ(~)server.ccl.net> X-Original-From: Ronald Cook Content-Type: multipart/alternative; boundary=bcaec51b9db186c49b04b65efd4c Date: Thu, 12 Jan 2012 18:43:23 -0700 MIME-Version: 1.0 Sent to CCL by: Ronald Cook [cookrl[]tda.com] --bcaec51b9db186c49b04b65efd4c Content-Type: text/plain; charset=ISO-8859-1 As I have posted previously.. Before you get too far in your calculations, you should probably read the references I have provided below. Most moderate to high level QM calculations will give you a pretty good value for the ionization potential (I) (or the HOMO energy if you are using the Koopman's theorem approach). However, the electron affinity (A) is another matter. The "natural" way to calculate I and A (e.g. for use in Absolute Electronegativity calculations) is from total electronic energy calculations on the N-1, N and N+1 electron systems using the geometry of the neutral molecule. I is then I=E(N-1)-E(N) and A is E(N)-E(N-1). The Koopman's approach assigns I as -HOMO energy and A as -LUMO energy. The problem arises when negative electon affinities are encountered as a result of the DFT calculations. The values you get for A are *often dicated by the size of the diffuse orbitals used in the calculation* The cautions about using electron affinities calculated using standand DFT methods and some work arounds are described in Proft et al. Faraday Discussions 135, 151 (2007), Tozer and Proft, J Phys Chem A109, 8923 (2005), Puiatu et al., Physical Chemistry Chemical Physics 10, 1394 (2008), Puiatu et al., Physical Chemistry Chemical Physics 11, 9013 (2009) On Thu, Jan 12, 2012 at 8:05 AM, Flick Coleman wcoleman_._wellesley.edu < owner-chemistry.:.ccl.net> wrote: > Remember that electronegativity is a defined rather than intrinsic > property of an atom or molecule, and that there are a number of > electronegativity scales. The most convenient form of electronegativity > to use based on calculations of IE and EA is that from Mulliken, where the > electronegativity is given by: > > EN = 0.5(IE + EA) > > > 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 Thu, Jan 12, 2012 at 5:15 AM, Flavio Ramos ffrsousa a yahoo.com < > owner-chemistry-.-ccl.net> wrote: > >> Dear Colleague, >> by definition the electron affinity is >> E(neutral)-E(anion) >> and Potential de ionization is >> E(cation)-E(neutral). >> So, you need to evaluate the energy of the neutral, >> cation and anion molecule. >> Giving an example for thymine you can give the input file >> >> #p B3LYP/6-31+G(d,p) opt freq >> >> opt >> >> 0 1 >> geometry >> >> ------------------------------------- >> for the anion >> >> #p B3LYP/6-31+G(d,p) opt freq >> >> opt >> >> -1 2 >> geometry >> >> ----------------------------------- >> anf for the cation >> #p B3LYP/6-31+G(d,p) opt freq >> >> opt >> >> +1 2 >> geometry >> >> ------------------------------------- >> >> It should give the value of 8.73 eV for Potential de ionization >> and 0.152 for the electron affinity. >> >> I dont know how to calculate trhe electronegative. >> >> >> >> Flavio >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------ >> *From:* mohamed med m.maatallah_+_ucam.ac.ma >> *To:* "Sousa, Flavio Fortes Ramos " >> *Sent:* Wednesday, January 11, 2012 12:10 PM >> *Subject:* CCL:G: How to calculate ionization potential, electron >> affinity >> >> >> Sent to CCL by: "mohamed med" [m.maatallah(~)ucam.ac.ma] >> dear collegues I am wondering How to calculate ionization potential, >> electron affinity and electro negativity values from Gaussian output files >> and suggest me the desired key word in order to calculate these values from >> output file. >> >> Thanks in advance>> the strange characters on the top line to the .:. sign. You can also** >> E-mail to subscribers: CHEMISTRY.:.ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST.:.ccl.net or use>> **>> **>> **>> >> >> >> >> > --bcaec51b9db186c49b04b65efd4c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable As I have posted previously..

Before you get too far in your calcula= tions, you should probably read the references I have provided below. Most moderate to high level QM calculations will give you a pretty good value for the ioniz= ation potential (I) (or the HOMO energy if you are using the Koopman's theor= em approach).=A0

However, the electron affinity (A) is another matter.=A0 The "natural" way to calculate I and A (e.g.=A0 for use in Absolute = Electronegativity calculations) is from total electronic energy calculations on the N-1, N and N+1 electron s= ystems using the geometry of the neutral molecule. I is then I=3DE(N-1)-E(N) and = A is E(N)-E(N-1). The Koopman's approach assigns I as -HOMO energy=A0 and A= as -LUMO energy.=A0 The problem arises when negative electon affinities are encountered as a result of the DFT calculations.=A0 The values you get for= A are often dicated by the size of the diffuse orbitals used in the calculation

The cautions about using electron affinities calculated using standand= DFT methods and some work arounds are described in Proft et al. Faraday Discus= sions 135, 151 (2007), Tozer and Proft,=A0 J Phys Chem A109, 8923 (2005), Puiatu= et al., Physical Chemistry Chemical Physics 10, 1394 (2008),=A0 =A0 Puiatu et al., Physical Chemistry Chemical Physics 11, 9013 (2009)

On Thu, Jan 12, 2012 at 8:05 AM, Flick Coleman wcoleman_._= wellesley.edu <owner-chemistry.:.ccl.net> wrote:
Remember that electronegativity is a defined rather than intr= insic property of an atom or molecule, and that there are a number of elect= ronegativity scales.=A0 The most convenient=A0 form of electronegativity to= use based on calculations of IE and EA is that from Mulliken, where the el= ectronegativity is given by:

EN =3D 0.5(IE + EA)


Cheers,
Flick

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

www.wellesle= y.edu/Chemistry/colemanw.html
www.= flicksstuff.com/photos/pictures.html new galleries coming soon




On Thu, Jan 12, 2012 at 5:15 AM, Flavio = Ramos ffrsousa a yahoo.com <owner-chemistry-.-ccl.net> wrote:
Dear Colleague,
by definition the electron affinity is
E(neutral)-E(anion)
and Potential de ionization i= s
E(cation)-E(neutral).
So, y= ou need to evaluate the energy of the neutral,
cation and anion molecule.
Giving an exam= ple for thymine you can give the input file

#p B3LYP/6-31+G(d,p) opt freq

opt

0 1
geometry
-------------------------------------
for=A0 the anion

#p B3L= YP/6-31+G(d,p) opt freq

opt

-1 2
geometry

---------= --------------------------
anf for the cation
#p B3LYP/6-31+G(d,p) o= pt freq

opt

+1 2
geometry

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

It should give= the value of 8.73 eV for Potential de ionization
and 0.152 for th= e electron affinity.

I dont know how to calculat= e trhe electronegative.



Flavio







<= /span>




From: mohamed med m.maatallah_+_ucam.ac.ma <owner-chemistry= .:.ccl.net>
To: "Sousa, Flavio For= tes Ramos " <ffrsousa.:.yahoo.com>
Sent:= Wednesday, January 11, 2012 12:10 PM
Subject: CCL:G: How to calc= ulate ionization potential, electron affinity


Sent to CCL by: "mohamed=A0 med" [m.maatallah(~)ucam.ac.ma]
dear collegues I am w= ondering How to calculate ionization potential, electron affinity and elect= ro negativity values from Gaussian output files and suggest me the desired = key word in order to calculate these values from output file.

Thanks in advance



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