From owner-chemistry@ccl.net Tue Oct 11 05:40:01 2011 From: "Sergio Manzetti sergio.manzetti!^!gmail.com" To: CCL Subject: CCL:G: Unstable Epoxide group Message-Id: <-45613-111011045902-17260-69BEVze5EKUR7yLzc3OOgg##server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=20cf307d012aff9f9a04af021d91 Date: Tue, 11 Oct 2011 10:58:54 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti]-[gmail.com] --20cf307d012aff9f9a04af021d91 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi Anders. Thanks for the file. I don't know if it was too far from the minima, but I read in a paper from 2010 that this is classical pi-stacking because of incorrect treatment by DFT methods, the use of another method wa= s the appropriate solution to these guys. I have now batched through 4 other methods and will see today. I will batch through your structure as well wit= h the B3LYP again and see if that can be a better starting structure. On Tue, Oct 11, 2011 at 9:56 AM, Anders Sundin wrote: > Hi Sergio, > > I did such rearrangements 20 years ago, both with Lewis acid catalyst, an= d > oxidative with Iodine, so I was curious about his one, and did a fast DFT > B3LYP/6-31G+* optimization. Here are the xyz coordinates of benzo[a]pyren= e > 7,8-diol-9,10-epoxide (not naming the proper stereochemistry=85). > > H -6.171389 0.239965 0.424199 > C -5.085981 0.184164 0.423301 > H -4.947054 0.072135 -1.725964 > C -4.398193 0.088997 -0.787076 > C -2.986219 0.142490 1.656417 > C -2.995222 0.015359 -0.811078 > C -4.389913 0.212161 1.632234 > C -2.274138 0.039159 0.421378 > C -2.250031 -0.073337 -2.035924 > H -4.933093 0.291136 2.571232 > C -0.888653 -0.145173 -2.040326 > H -2.797743 -0.075315 -2.975625 > H -0.362479 -0.190322 -2.988261 > C -0.130400 -0.140773 -0.815010 > C 1.280230 -0.227767 -0.788729 > C -0.847669 -0.036505 0.419216 > C 1.972047 -0.177612 0.436505 > C 1.267344 -0.056907 1.633403 > H 1.815070 -0.003398 2.573074 > C -0.135485 0.005269 1.656108 > C -2.238041 0.177552 2.883582 > H -2.784116 0.259842 3.820708 > C -0.876335 0.114495 2.883172 > H -0.323531 0.147369 3.819257 > C 2.067962 -0.354996 -2.047804 > C 3.482813 -0.312349 0.459422 > C 4.164862 0.380696 -0.730938 > C 3.508452 -0.069603 -2.043245 > H 3.875296 0.130945 1.384269 > H 5.216408 0.076514 -0.729035 > H 4.145947 -0.563558 -2.774243 > H 1.684251 -1.033133 -2.807725 > O 2.593439 0.885164 -2.616431 > O 4.130180 1.790882 -0.584009 > H 3.392939 2.117747 -1.132497 > O 3.884586 -1.693122 0.367364 > H 3.333858 -2.218172 0.969077 > > The reason you got a rearrangement to ketone is perhaps because your > starting coordinates were too far from the minima? > > -Anders Sundin > > > On Oct 10, 2011, at 14:23 , Sergio Manzetti sergio.manzetti a gmail.comwr= ote: > > > Dear CCL, I have tried to calculate in Gaussian the properties of the > benzo[a]pyrene epoxide diol form. The calculation, with the 6-311*+G basi= s > set show a spontaneous conversion into a carbonyl form after 19 steps. Th= e > oxygen of the epoxide group draws the electrons so strongly from the benz= ene > that at a few steps, the penta-coordinated carbons are found. This drawin= g > of electrons stabilizies itself to a carbonyl. > > > > Is it possible that the 6-311+*G basis set is inappropriate to calculat= e > the effects of an epoxide on a diol benzene-group ? > > > > Best wishes > > > > Sergio > > --20cf307d012aff9f9a04af021d91 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi Anders. Thanks for the file. I don't know if it was too far from the= =20 minima, but I read in a paper from 2010 that this is classical=20 pi-stacking because of incorrect treatment by DFT methods, the use of=20 another method was the appropriate solution to these guys. I have now=20 batched through 4 other methods and will see today. I will batch through your structure as well with the B3LYP again and see=A0 if that can be a=20 better starting structure.

On Tue, Oct 1= 1, 2011 at 9:56 AM, Anders Sundin <aps_ccl[-]yahoo.com> wrote:
Hi Sergio,

I did such rearrangements 20 years ago, both with Lewis acid catalyst, and = oxidative with Iodine, so I was curious about his one, and did a fast DFT B= 3LYP/6-31G+* optimization. Here are the xyz coordinates of benzo[a]pyrene 7= ,8-diol-9,10-epoxide (not naming the proper stereochemistry=85).

H =A0 =A0 =A0 -6.171389 =A0 =A0 =A00.239965 =A0 =A0 =A00.424199
C =A0 =A0 =A0 -5.085981 =A0 =A0 =A00.184164 =A0 =A0 =A00.423301
H =A0 =A0 =A0 -4.947054 =A0 =A0 =A00.072135 =A0 =A0 -1.725964
C =A0 =A0 =A0 -4.398193 =A0 =A0 =A00.088997 =A0 =A0 -0.787076
C =A0 =A0 =A0 -2.986219 =A0 =A0 =A00.142490 =A0 =A0 =A01.656417
C =A0 =A0 =A0 -2.995222 =A0 =A0 =A00.015359 =A0 =A0 -0.811078
C =A0 =A0 =A0 -4.389913 =A0 =A0 =A00.212161 =A0 =A0 =A01.632234
C =A0 =A0 =A0 -2.274138 =A0 =A0 =A00.039159 =A0 =A0 =A00.421378
C =A0 =A0 =A0 -2.250031 =A0 =A0 -0.073337 =A0 =A0 -2.035924
H =A0 =A0 =A0 -4.933093 =A0 =A0 =A00.291136 =A0 =A0 =A02.571232
C =A0 =A0 =A0 -0.888653 =A0 =A0 -0.145173 =A0 =A0 -2.040326
H =A0 =A0 =A0 -2.797743 =A0 =A0 -0.075315 =A0 =A0 -2.975625
H =A0 =A0 =A0 -0.362479 =A0 =A0 -0.190322 =A0 =A0 -2.988261
C =A0 =A0 =A0 -0.130400 =A0 =A0 -0.140773 =A0 =A0 -0.815010
C =A0 =A0 =A0 =A01.280230 =A0 =A0 -0.227767 =A0 =A0 -0.788729
C =A0 =A0 =A0 -0.847669 =A0 =A0 -0.036505 =A0 =A0 =A00.419216
C =A0 =A0 =A0 =A01.972047 =A0 =A0 -0.177612 =A0 =A0 =A00.436505
C =A0 =A0 =A0 =A01.267344 =A0 =A0 -0.056907 =A0 =A0 =A01.633403
H =A0 =A0 =A0 =A01.815070 =A0 =A0 -0.003398 =A0 =A0 =A02.573074
C =A0 =A0 =A0 -0.135485 =A0 =A0 =A00.005269 =A0 =A0 =A01.656108
C =A0 =A0 =A0 -2.238041 =A0 =A0 =A00.177552 =A0 =A0 =A02.883582
H =A0 =A0 =A0 -2.784116 =A0 =A0 =A00.259842 =A0 =A0 =A03.820708
C =A0 =A0 =A0 -0.876335 =A0 =A0 =A00.114495 =A0 =A0 =A02.883172
H =A0 =A0 =A0 -0.323531 =A0 =A0 =A00.147369 =A0 =A0 =A03.819257
C =A0 =A0 =A0 =A02.067962 =A0 =A0 -0.354996 =A0 =A0 -2.047804
C =A0 =A0 =A0 =A03.482813 =A0 =A0 -0.312349 =A0 =A0 =A00.459422
C =A0 =A0 =A0 =A04.164862 =A0 =A0 =A00.380696 =A0 =A0 -0.730938
C =A0 =A0 =A0 =A03.508452 =A0 =A0 -0.069603 =A0 =A0 -2.043245
H =A0 =A0 =A0 =A03.875296 =A0 =A0 =A00.130945 =A0 =A0 =A01.384269
H =A0 =A0 =A0 =A05.216408 =A0 =A0 =A00.076514 =A0 =A0 -0.729035
H =A0 =A0 =A0 =A04.145947 =A0 =A0 -0.563558 =A0 =A0 -2.774243
H =A0 =A0 =A0 =A01.684251 =A0 =A0 -1.033133 =A0 =A0 -2.807725
O =A0 =A0 =A0 =A02.593439 =A0 =A0 =A00.885164 =A0 =A0 -2.616431
O =A0 =A0 =A0 =A04.130180 =A0 =A0 =A01.790882 =A0 =A0 -0.584009
H =A0 =A0 =A0 =A03.392939 =A0 =A0 =A02.117747 =A0 =A0 -1.132497
O =A0 =A0 =A0 =A03.884586 =A0 =A0 -1.693122 =A0 =A0 =A00.367364
H =A0 =A0 =A0 =A03.333858 =A0 =A0 -2.218172 =A0 =A0 =A00.969077

The reason you got a rearrangement to ketone is perhaps because your starti= ng coordinates were too far from the minima?

-Anders Sundin


On Oct 10, 2011, at 14:23 , Sergio Manzetti sergio.manzetti a gmail.com wrote:

> Dear CCL, I have tried to calculate in Gaussian the properties of the = benzo[a]pyrene epoxide diol form. The calculation, with the 6-311*+G basis = set show a spontaneous conversion into a carbonyl form after 19 steps. The = oxygen of the epoxide group draws the electrons so strongly from the benzen= e that at a few steps, the penta-coordinated carbons are found. This drawin= g of electrons stabilizies itself to a carbonyl.
>
> Is it possible that the 6-311+*G basis set is inappropriate to calcula= te the effects of an epoxide on a diol benzene-group ?
>
> Best wishes
>
> Sergio



--20cf307d012aff9f9a04af021d91-- From owner-chemistry@ccl.net Tue Oct 11 09:04:00 2011 From: "Patrick Bultinck Patrick.Bultinck^^^UGent.be" To: CCL Subject: CCL:G: ROHF or given initial guess for CISD Message-Id: <-45614-111011042338-18196-yrntrnPzbGvwmBwj34pxVA[]server.ccl.net> X-Original-From: "Patrick Bultinck" Date: Tue, 11 Oct 2011 04:23:36 -0400 Sent to CCL by: "Patrick Bultinck" [Patrick.Bultinck~~UGent.be] Everybody, I would like to know if anybody knows how to "trick" Gaussian and GAMESS(US) into starting a CISD immediately from a set of orbitals that I supply. So without doing any SCF step. In other words: I supply the reference determinant. Alternatively: how could I get Gaussian to use a ROHF reference wave function for CISD/CCSD etc. It automatically uses UHF but that is pretty horrible if you have molecules where that fails miserably. Thanks, Patrick From owner-chemistry@ccl.net Tue Oct 11 16:30:00 2011 From: "Laura Albrecht lauraalbrecht/./dal.ca" To: CCL Subject: CCL: AIMall energy of water dimer gives huge error with CP/ BSSE correction Message-Id: <-45615-111011161317-25734-HP0CKoUl4rmg+QAWQiPD1g_+_server.ccl.net> X-Original-From: "Laura Albrecht" Date: Tue, 11 Oct 2011 16:13:15 -0400 Sent to CCL by: "Laura Albrecht" [lauraalbrecht..dal.ca] Hello CCL subscribers. I am attempting calculation of water dimers at MP2/aug-cc-pVTZ level theory corrected for BSSE with the Boys and Bernardi counterpoise approach (implemented with the counterpoise=2 option in G09 vs A.02). After a single point calculation the formatted checkpoint file is analyzed using the AIMall programs. I use AimQB to write the .wfn file. The resulting total energies as given by AIMall are ~318 kcal/mol greater than the G09 EUPM2 final energies. If I neglect the CP correction in G09 calculation, the AIM calculated total energies are only ~0.01 kcal/mol greater than the (more accurate) G09 energies. AIM energies are taken from the .sumviz file, no modifications. Optimizing the geometry to include CP correction does not solve the issue, and neither does improving the basis set. The virial ratio is 2.00173 for single point and 2.000978 for optimized (no CP) and 2.001699 (with CP) Is there a known issue with AIMall calculations on G09/Counterpoise output? Is it possible that G09 writes the (formatted)checkpoint file in a different way when it applies CP correction, and thus the aimQB program is misprinting the .wfn file? Finally, is it even necessary to use the BSSE corrected .fchk file for the AIM calculation since the final wavefunction should be essentially the same, since CP correction on a SP calculation just yields an energy correction factor and does not change the dimer electron density topology (?). Any hints or literature direction would be immensely appreciated. Sincerely, Laura Albrecht Dalhousie University, Halifax, NS, Canada From owner-chemistry@ccl.net Tue Oct 11 18:11:01 2011 From: "Sujit Kumar Mondal sujitharvard:+:gmail.com" To: CCL Subject: CCL: AIMall energy of water dimer gives huge error with CP/ BSSE correction Message-Id: <-45616-111011180922-23757-qA9v7MuNM4xnCzcTXoRekQ[A]server.ccl.net> X-Original-From: Sujit Kumar Mondal Content-Type: multipart/alternative; boundary=bcaec520e5af5483d304af0d2867 Date: Tue, 11 Oct 2011 17:09:12 -0500 MIME-Version: 1.0 Sent to CCL by: Sujit Kumar Mondal [sujitharvard[#]gmail.com] --bcaec520e5af5483d304af0d2867 Content-Type: text/plain; charset=ISO-8859-1 Hi Laura I am also using the AIMALL programme, i never try to use the file path .wfn but I always try to use .fchk for AIMALL calculation. You can change file path using G09 file.chk(check point file) to file .fchk and can try AIMALL for calculation. Sujit On Tue, Oct 11, 2011 at 3:13 PM, Laura Albrecht lauraalbrecht/./dal.ca < owner-chemistry*ccl.net> wrote: > > Sent to CCL by: "Laura Albrecht" [lauraalbrecht..dal.ca] > Hello CCL subscribers. > > > I am attempting calculation of water dimers at MP2/aug-cc-pVTZ level theory > corrected for BSSE with the Boys and Bernardi counterpoise approach > (implemented with the counterpoise=2 option in G09 vs A.02). After a single > point calculation the formatted checkpoint file is analyzed using the AIMall > programs. I use AimQB to write the .wfn file. > > The resulting total energies as given by AIMall are ~318 kcal/mol greater > than the G09 EUPM2 final energies. If I neglect the CP correction in G09 > calculation, the AIM calculated total energies are only ~0.01 kcal/mol > greater than the (more accurate) G09 energies. AIM energies are taken from > the .sumviz file, no modifications. > > Optimizing the geometry to include CP correction does not solve the issue, > and neither does improving the basis set. The virial ratio is 2.00173 for > single point and 2.000978 for optimized (no CP) and 2.001699 (with CP) > > Is there a known issue with AIMall calculations on G09/Counterpoise output? > Is it possible that G09 writes the (formatted)checkpoint file in a different > way when it applies CP correction, and thus the aimQB program is misprinting > the .wfn file? Finally, is it even necessary to use the BSSE corrected .fchk > file for the AIM calculation since the final wavefunction should be > essentially the same, since CP correction on a SP calculation just yields an > energy correction factor and does not change the dimer electron density > topology (?). > > Any hints or literature direction would be immensely appreciated. > > > Sincerely, > > > Laura Albrecht > Dalhousie University, > Halifax, NS, Canada> > > --bcaec520e5af5483d304af0d2867 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Laura
=A0=A0I am also using the AIMALL programme,=A0i never try to use the f= ile=A0path .wfn=A0but=A0I always try to use .fchk for AIMALL calculation. Y= ou can change=A0file path using G09 file.chk(check point file)=A0to file .f= chk=A0and=A0can=A0try AIMALL for calculation.
=A0
Sujit
=A0
=A0
=A0
On Tue, Oct 11, 2011 at 3:13 PM, Laura Albrecht = lauraalbrecht/./dal.ca <= owner-chemistry*ccl.net><= /span> wrote:

Sent to CCL by: "Laura = =A0Albrecht" [lauraalbrecht..dal.ca]
Hello CCL subscribers.


I am attempting calculation of water dime= rs at MP2/aug-cc-pVTZ level theory corrected for BSSE with the Boys and Ber= nardi counterpoise approach (implemented with the counterpoise=3D2 option i= n G09 vs A.02). After a single point calculation the formatted checkpoint f= ile is analyzed using the AIMall programs. I use AimQB to write the .wfn fi= le.

The resulting total energies as given by AIMall are ~318 kcal/mol great= er than the G09 EUPM2 final energies. If I neglect the CP correction in G09= calculation, the AIM calculated total energies are only ~0.01 kcal/mol gre= ater than the (more accurate) G09 energies. AIM energies are taken from the= .sumviz file, no modifications.

Optimizing the geometry to include CP correction does not solve the iss= ue, and neither does improving the basis set. The virial ratio is 2.00173 f= or single point and 2.000978 for optimized (no CP) and 2.001699 (with CP)
Is there a known issue with AIMall calculations on G09/Counterpoise out= put? Is it possible that G09 writes the (formatted)checkpoint file in a dif= ferent way when it applies CP correction, and thus the aimQB program is mis= printing the .wfn file? Finally, is it even necessary to use the BSSE corre= cted .fchk file for the AIM calculation since the final wavefunction should= be essentially the same, since CP correction on a SP calculation just yiel= ds an energy correction factor and does not change the dimer electron densi= ty topology (?).

Any hints or literature direction would be immensely appreciated.

Sincerely,


Laura Albrecht
Dalhousie University,
Hali= fax, NS, Canada



-=3D This is automatically added to each mes= sage by the mailing script =3D-look= up the X-Original-From: line in the mail header.

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--bcaec520e5af5483d304af0d2867-- From owner-chemistry@ccl.net Tue Oct 11 18:46:01 2011 From: "Sujit Kumar Mondal sujitharvard()gmail.com" To: CCL Subject: CCL: AIMall energy of water dimer gives huge error with CP/ BSSE correction Message-Id: <-45617-111011182546-11605-3UE551MwkRUeIjB+TLQleQ[]server.ccl.net> X-Original-From: Sujit Kumar Mondal Content-Type: multipart/alternative; boundary=bcaec51f9061f534c104af0d62c7 Date: Tue, 11 Oct 2011 17:25:36 -0500 MIME-Version: 1.0 Sent to CCL by: Sujit Kumar Mondal [sujitharvard a gmail.com] --bcaec51f9061f534c104af0d62c7 Content-Type: text/plain; charset=ISO-8859-1 Also you need to change the file.fchk to AIM wave function file .wfx during AIMALL calculation and then start the calculation. Please look at the "help" in AIMALL. Sujit On Tue, Oct 11, 2011 at 5:09 PM, Sujit Kumar Mondal wrote: > Hi Laura > I am also using the AIMALL programme, i never try to use the file path > .wfn but I always try to use .fchk for AIMALL calculation. You can > change file path using G09 file.chk(check point file) to file > .fchk and can try AIMALL for calculation. > > Sujit > > > > On Tue, Oct 11, 2011 at 3:13 PM, Laura Albrecht lauraalbrecht/./dal.ca < > owner-chemistry:ccl.net> wrote: > >> >> Sent to CCL by: "Laura Albrecht" [lauraalbrecht..dal.ca] >> Hello CCL subscribers. >> >> >> I am attempting calculation of water dimers at MP2/aug-cc-pVTZ level >> theory corrected for BSSE with the Boys and Bernardi counterpoise approach >> (implemented with the counterpoise=2 option in G09 vs A.02). After a single >> point calculation the formatted checkpoint file is analyzed using the AIMall >> programs. I use AimQB to write the .wfn file. >> >> The resulting total energies as given by AIMall are ~318 kcal/mol greater >> than the G09 EUPM2 final energies. If I neglect the CP correction in G09 >> calculation, the AIM calculated total energies are only ~0.01 kcal/mol >> greater than the (more accurate) G09 energies. AIM energies are taken from >> the .sumviz file, no modifications. >> >> Optimizing the geometry to include CP correction does not solve the issue, >> and neither does improving the basis set. The virial ratio is 2.00173 for >> single point and 2.000978 for optimized (no CP) and 2.001699 (with CP) >> >> Is there a known issue with AIMall calculations on G09/Counterpoise >> output? Is it possible that G09 writes the (formatted)checkpoint file in a >> different way when it applies CP correction, and thus the aimQB program is >> misprinting the .wfn file? Finally, is it even necessary to use the BSSE >> corrected .fchk file for the AIM calculation since the final wavefunction >> should be essentially the same, since CP correction on a SP calculation just >> yields an energy correction factor and does not change the dimer electron >> density topology (?). >> >> Any hints or literature direction would be immensely appreciated. >> >> >> Sincerely, >> >> >> Laura Albrecht >> Dalhousie University, >> Halifax, NS, Canada>> >> >> > --bcaec51f9061f534c104af0d62c7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Also you need to change the file.fchk to AIM wave function file .wfx d= uring AIMALL calculation and then start the calculation. Please look at the= "help" in AIMALL.
=A0
Sujit

On Tue, Oct 11, 2011 at 5:09 PM, Sujit Kumar Mon= dal <sujitha= rvard:gmail.com> wrote:
Hi Laura
=A0=A0I am also using the AIMALL programme,=A0i never try to use the f= ile=A0path .wfn=A0but=A0I always try to use .fchk for AIMALL calculation. Y= ou can change=A0file path using G09 file.chk(check point file)=A0to file .f= chk=A0and=A0can=A0try AIMALL for calculation.
=A0
Sujit
=A0
=A0
=A0
On Tue, Oct 11, 2011 at 3:13 PM, Laura Albrecht = lauraalbrecht/./dal.ca <owner-chemistry:ccl.net> wrote:

Sent to CCL by: "Laura = =A0Albrecht" [lauraalbrecht..dal.ca]
Hello CCL subscribers.


I am attempting calculation of water dime= rs at MP2/aug-cc-pVTZ level theory corrected for BSSE with the Boys and Ber= nardi counterpoise approach (implemented with the counterpoise=3D2 option i= n G09 vs A.02). After a single point calculation the formatted checkpoint f= ile is analyzed using the AIMall programs. I use AimQB to write the .wfn fi= le.

The resulting total energies as given by AIMall are ~318 kcal/mol great= er than the G09 EUPM2 final energies. If I neglect the CP correction in G09= calculation, the AIM calculated total energies are only ~0.01 kcal/mol gre= ater than the (more accurate) G09 energies. AIM energies are taken from the= .sumviz file, no modifications.

Optimizing the geometry to include CP correction does not solve the iss= ue, and neither does improving the basis set. The virial ratio is 2.00173 f= or single point and 2.000978 for optimized (no CP) and 2.001699 (with CP)
Is there a known issue with AIMall calculations on G09/Counterpoise out= put? Is it possible that G09 writes the (formatted)checkpoint file in a dif= ferent way when it applies CP correction, and thus the aimQB program is mis= printing the .wfn file? Finally, is it even necessary to use the BSSE corre= cted .fchk file for the AIM calculation since the final wavefunction should= be essentially the same, since CP correction on a SP calculation just yiel= ds an energy correction factor and does not change the dimer electron densi= ty topology (?).

Any hints or literature direction would be immensely appreciated.

Sincerely,


Laura Albrecht
Dalhousie University,
Hali= fax, NS, Canada



-=3D This is automatically added to each mes= sage by the mailing script =3D-look= up the X-Original-From: line in the mail header.

E-mail to subscrib= ers: CHEMISTRY:ccl.n= et or use:
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=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.s= html

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/<= br>
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--bcaec51f9061f534c104af0d62c7--