From owner-chemistry@ccl.net Fri Jun 11 02:54:00 2010 From: "Jamin Krinsky jamink*_*berkeley.edu" To: CCL Subject: CCL: tautomer ratios Message-Id: <-42095-100611020755-3847-wPFp0kz7Tk01Po4BTd6TEg---server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=00c09f9b0bf128188a0488ba270e Date: Thu, 10 Jun 2010 22:10:08 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink-$-berkeley.edu] --00c09f9b0bf128188a0488ba270e Content-Type: text/plain; charset=ISO-8859-1 Dear Serdar, The ratio you calculated is actually a really good result for DFT. Remember that a difference of a few kcal/mol can perturb an equilibrium to from 1:1 to 99:1, and the best accuracy you can expect from B3LYP is a few kcal/mol error, so if your ratio is correct within an order of magnitude that's the best you're going to do. If you want better accuracy you're going to have to go to something like QCISD(T) or G3 or MAYBE a double hybrid like B2PLYP (although even that is expensive for large systems). Personally I'd give myself a pat on the back if I got an answer that is "about 50/50" and favoring the correct isomer... Regards, Jamin On Thu, Jun 10, 2010 at 3:02 AM, Serdar Bado?lu sbadoglu.[a].gazi.edu.tr < owner-chemistry[a]ccl.net> wrote: > > Sent to CCL by: "Serdar Bado?lu" [sbadoglu * gazi.edu.tr] > Hi all, > > I have computed the Gibbs free energy difference between the tautomers and > then by using the Boltzmann distribution to get the ratio. I have tested > this method on some papers, and it worked well. Unfortunately, in my > situation it failed. A previous paper reported the raio as 7 : 3 from the > NMR (in heavy water) experiment, but my calculation gave a 5.1 : 4.9 > ratio. My calculation level is B3LYP / 6-311++G** and the solvent effect > is included. I suppose experimental and theoretical results are > inconsistent in this case. I'm trying to figure out what can be the cause > of this discrepancy. > > Any ideas? > > Regards > > > -- > Serdar BADOGLU > Gazi University > Department of Physics> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink[a]berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --00c09f9b0bf128188a0488ba270e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Serdar,

The ratio you calculated is actually a really good resu= lt for DFT. Remember that a difference of a few kcal/mol can perturb an equ= ilibrium to from 1:1 to 99:1, and the best accuracy you can expect from B3L= YP is a few kcal/mol error, so if your ratio is correct within an order of = magnitude that's the best you're going to do. If you want better ac= curacy you're going to have to go to something like QCISD(T) or G3 or M= AYBE a double hybrid like B2PLYP (although even that is expensive for large= systems). Personally I'd give myself a pat on the back if I got an ans= wer that is "about 50/50" and favoring the correct isomer...

Regards,
Jamin


On Thu, Jun 10,= 2010 at 3:02 AM, Serdar Bado?lu sbadoglu.[a].= gazi.edu.tr <owner-chemistry[a]ccl.net> wrote:

Sent to CCL by: "Serdar Bado?lu" [sbadoglu * gazi.edu.tr]
Hi all,

I have computed the Gibbs free energy difference between the tautomers and<= br> then by using the Boltzmann distribution to get the ratio. I have tested this method on some papers, and it worked well. Unfortunately, in my
situation it failed. A previous paper reported the raio as 7 : 3 from the NMR (in heavy water) experiment, but my calculation gave a 5.1 : 4.9
ratio. My calculation level is B3LYP / 6-311++G** and the solvent effect is included. I suppose experimental and theoretical results are
inconsistent in this case. I'm trying to figure out what can be the cau= se
of this discrepancy.

Any ideas?

Regards


--
Serdar BADOGLU
Gazi University
Department of Physics



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--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink[a]berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--00c09f9b0bf128188a0488ba270e-- From owner-chemistry@ccl.net Fri Jun 11 08:02:00 2010 From: "setare mostajabi setare_mostajabi_+_yahoo.com" To: CCL Subject: CCL: difference between nbo & nao Message-Id: <-42096-100611023820-17142-Gv0dSkACF+VUjYZbmvNKmA,,server.ccl.net> X-Original-From: "setare mostajabi" Date: Fri, 11 Jun 2010 02:38:19 -0400 Sent to CCL by: "setare mostajabi" [setare_mostajabi. * .yahoo.com] Dear CCL list members, i want know difference between nbo & nao prayers and regards From owner-chemistry@ccl.net Fri Jun 11 11:53:00 2010 From: "Deskins, N Aaron nadeskins__WPI.EDU" To: CCL Subject: CCL: Constructing nanoparticles Message-Id: <-42097-100611110914-4047-4hPUVTgXOF6FXrfBj3gHyA||server.ccl.net> X-Original-From: "Deskins, N Aaron" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_A43FA9C6AD151B4BB262595A1B438A60237BF77EB3EXCHANGEMAILa_" Date: Fri, 11 Jun 2010 10:18:10 -0400 MIME-Version: 1.0 Sent to CCL by: "Deskins, N Aaron" [nadeskins(!)WPI.EDU] --_000_A43FA9C6AD151B4BB262595A1B438A60237BF77EB3EXCHANGEMAILa_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hello all, Is there software (free or commercial) that can be used to construct atom= ic models of crystalline nanoparticles - not clusters, but real nanopartic= les (5-50 nm) for molecular dynamics simulations? I'm mostly interested in = particles with well-defined faces. Thank you, Aaron --_000_A43FA9C6AD151B4BB262595A1B438A60237BF77EB3EXCHANGEMAILa_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello all,

  Is there software (free or commercial) that can be used to construct atomic models of crystalline nanoparticles  – not clusters, but real nanoparticles (5-50 nm) for molecular dynamics simulations? I’m mostl= y interested in particles with well-defined faces.

 

Thank you,

Aaron

--_000_A43FA9C6AD151B4BB262595A1B438A60237BF77EB3EXCHANGEMAILa_-- From owner-chemistry@ccl.net Fri Jun 11 12:27:00 2010 From: "Tobias Kraemer tobias.kraemer**chem.ox.ac.uk" To: CCL Subject: CCL: Calculationg the Energy Density H(r) in AIM200 Message-Id: <-42098-100611075846-4372-guIQ21pWCzveboQljYID1A() server.ccl.net> X-Original-From: Tobias Kraemer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 11 Jun 2010 12:26:50 +0100 MIME-Version: 1.0 Sent to CCL by: Tobias Kraemer [tobias.kraemer++chem.ox.ac.uk] Dear collegues, I would like to raise a question regarding AIM theory (the same question has been asked before and can be found in the list archive, however I could not find any answers). Using AIM2000, I want to calculate the energy density H(r) = G(r) + V(r), at the bond critical points, where G(r) is the kinetic energy density and V(r) the potential energy density. In particular, I am aiming to reproduce the numbers from a paper by Cremer and Kraka (Angew. Chem. Int. Ed. 1984, 23, 627), before applying this to my own system. The AIM2000 "data report" at the critical points lists Lagragian and Hamiltonian kinetic energies, among other things. I am unsure, if any of these is actually the kinetic energy density G(r). Further, how would I get V(r)? I've used the equation 2G(r) + V(r) = 1/2 nabla^2 RHO, but as I said, I am not certain that I can simply use the value reported for G(r) from the record. My numbers so far are orders of magnitude smaller than in the above paper, which makes me think I am missing a crucial thing. Any comments or advice from more experienced people on this would be very much appreciated Tobi -- _________________________________________ dipl.-chem. tobias kraemer department of chemistry inorganic chemistry laboratory university of oxford south parks road oxford OX1 3QR united kingdom |phone| +44 (0)1865 272 135 |email| tobias.kraemer..chem.ox.ac.uk |email| tobias.kraemer..linacre.ox.ac.uk _________________________________________ From owner-chemistry@ccl.net Fri Jun 11 16:57:00 2010 From: "Radoslaw Kaminski rkaminski.rk---gmail.com" To: CCL Subject: CCL: Calculationg the Energy Density H(r) in AIM200 Message-Id: <-42099-100611152439-20313-PSdynCfptnDCkWeF/srY3A(!)server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=0015174c11c2adc6910488c5ab52 Date: Fri, 11 Jun 2010 14:54:37 -0400 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk%x%gmail.com] --0015174c11c2adc6910488c5ab52 Content-Type: text/plain; charset=ISO-8859-1 Hi Tobi, Maybe you should check does your unit coincide with those from the Cramer's paper? AIM2000 gives everything in atomic units and I'm almost sure (I didn't use the program for a while) that it prints both the G and V explicitly in the output (despite very uncomfortable GUI). The equation at the bottom you gave is in atomic units. Hope this helps. Cheers, Radek 2010/6/11 Tobias Kraemer tobias.kraemer**chem.ox.ac.uk < owner-chemistry[-]ccl.net> > > Sent to CCL by: Tobias Kraemer [tobias.kraemer++chem.ox.ac.uk] > Dear collegues, > > > I would like to raise a question regarding AIM theory (the same question > has been asked before and can be found in the list archive, however I could > not find any answers). > Using AIM2000, I want to calculate the energy density H(r) = G(r) + V(r), > at the bond critical points, where G(r) is the kinetic energy density and > V(r) the potential energy density. > In particular, I am aiming to reproduce the numbers from a paper by Cremer > and Kraka (Angew. Chem. Int. Ed. 1984, 23, 627), before applying this to my > own system. > > The AIM2000 "data report" at the critical points lists Lagragian and > Hamiltonian kinetic energies, among other things. I am unsure, if any of > these is actually the kinetic energy density G(r). > Further, how would I get V(r)? I've used the equation 2G(r) + V(r) = 1/2 > nabla^2 RHO, but as I said, I am not certain that I can simply use the value > reported for G(r) from the record. > My numbers so far are orders of magnitude smaller than in the above paper, > which makes me think I am missing a crucial thing. > > Any comments or advice from more experienced people on this would be very > much appreciated > > > Tobi > > > > > > > > > > > > -- > _________________________________________ > > dipl.-chem. tobias kraemer > department of chemistry > inorganic chemistry laboratory university of oxford > south parks road > oxford OX1 3QR > united kingdom > > |phone| +44 (0)1865 272 135 > |email| tobias.kraemer-$-chem.ox.ac.uk > |email| tobias.kraemer-$-linacre.ox.ac.uk > _________________________________________http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --0015174c11c2adc6910488c5ab52 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Tobi,

Maybe you should check does your unit coincide with those f= rom the Cramer's paper? AIM2000 gives everything in atomic units and I&= #39;m almost sure (I didn't use the program for a while) that it prints= both the G and V explicitly in the output (despite very uncomfortable GUI)= . The equation at the bottom you gave is in atomic units. Hope this helps.<= br>
Cheers,

Radek


2010/6/11 To= bias Kraemer tobias.kraemer**chem.ox.ac.uk= <owner= -chemistry[-]ccl.net>

Sent to CCL by: Tobias Kraemer [tobias.kraemer++chem.ox.ac.uk]
Dear collegues,


I would like to raise a question regarding AIM theory (the same question ha= s been asked before and can be found in the list archive, however I could n= ot find any answers).
Using AIM2000, I want to calculate the energy density H(r) =3D G(r) + V(r),= at the bond critical points, where G(r) is the kinetic energy density and = V(r) the potential energy density.
In particular, I am aiming to reproduce the numbers from a paper by Cremer = and Kraka (Angew. Chem. Int. Ed. 1984, 23, 627), before applying this to my= own system.

The AIM2000 "data report" at the critical points lists Lagragian = and Hamiltonian kinetic energies, among other things. I am unsure, if any o= f these is actually the kinetic energy density G(r).
Further, how would I get V(r)? I've used the equation 2G(r) + V(r) =3D = 1/2 nabla^2 RHO, but as I said, I am not certain that I can simply use the = value reported for G(r) from the record.
My numbers so far are orders of magnitude smaller than in the above paper, = which makes me think I am missing a crucial thing.

Any comments or advice from more experienced people on this would be very m= uch appreciated


Tobi











--
_________________________________________

=A0dipl.-chem. tobias kraemer
=A0department of chemistry
=A0inorganic chemistry laboratory =A0university of oxford
=A0south parks road
=A0oxford OX1 3QR
=A0united kingdom
=A0 =A0 =A0 =A0
=A0|phone| +44 (0)1865 272 135
=A0|email| tobias.kraemer-$-chem.ox.ac.uk
=A0|email| tobias.kraemer-$-linacre.ox.ac.uk
_________________________________________



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--0015174c11c2adc6910488c5ab52-- From owner-chemistry@ccl.net Fri Jun 11 19:44:00 2010 From: "zouzou adnani zinebeladnani],[hotmail.com" To: CCL Subject: CCL: optimisation problem Message-Id: <-42100-100611194209-5473-4X4PxMtV4LHfK0NH/45eaA[*]server.ccl.net> X-Original-From: "zouzou adnani" Date: Fri, 11 Jun 2010 19:42:06 -0400 Sent to CCL by: "zouzou adnani" [zinebeladnani]^[hotmail.com] hi, I'm trying to study the interaction between one iron atom and some quinoxaline derivatives, each time I end up with some very odd geometries even though I changed the iron position several times and I tried some of the propositions I found in the CCL archive (Maxcycle, Vshift, QC...). here is one of my input files, please help me: %chk=mol2fer-dft-cep121g.chk %nproc=1 #p opt freq b3lyp nosymm guess=save cep-121g 0 1 C C 1 B1 H 1 B2 2 A1 C 1 B3 2 A2 3 D1 C 2 B4 1 A3 4 D2 H 2 B5 1 A4 4 D3 C 5 B6 2 A5 1 D4 C 4 B7 1 A6 2 D5 H 5 B8 2 A7 1 D6 H 7 B9 5 A8 2 D7 H 8 B10 4 A9 1 D8 N 2 B11 1 A10 4 D9 C 12 B12 2 A11 1 D10 O 13 B13 12 A12 2 D11 C 13 B14 12 A13 2 D12 O 15 B15 13 A14 12 D13 N 15 B16 13 A15 12 D14 H 17 B17 15 A16 13 D15 Fe 15 B18 13 A17 12 D16 B1 1.40644101 B2 2.14928644 B3 1.39759508 B4 1.39765674 B5 2.08511317 B6 1.39253612 B7 1.39257680 B8 1.08638027 B9 1.08486967 B10 1.08486443 B11 1.39557266 B12 1.38144585 B13 1.21473476 B14 1.53434602 B15 1.21479365 B16 1.38128209 B17 1.01319508 B18 2.48818517 A1 145.95140520 A2 119.79706010 A3 119.77892540 A4 143.20945469 A5 120.09436720 A6 120.08836427 A7 119.29734053 A8 119.58833605 A9 119.59281559 A10 118.07480691 A11 126.52180143 A12 122.62536055 A13 115.40288341 A14 121.97364409 A15 115.41203166 A16 114.40037764 A17 74.26757538 D1 -0.00336246 D2 0.00283977 D3 -179.98326314 D4 0.00000000 D5 -0.00385223 D6 -180.00000000 D7 179.99662248 D8 -179.99638223 D9 -180.00000000 D10 -0.02573946 D11 -179.98395853 D12 0.01264207 D13 -179.98079972 D14 0.03738560 D15 -179.99076401 D16 -83.15595137 From owner-chemistry@ccl.net Fri Jun 11 21:53:01 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim-#-compchem.net" To: CCL Subject: CCL: optimisation problem Message-Id: <-42101-100611215139-12358-FRy10eX8okL0JrfiTU3gAw[*]server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e64c1c987f35430488cb7e43 Date: Sat, 12 Jun 2010 02:51:28 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim(-)compchem.net] --0016e64c1c987f35430488cb7e43 Content-Type: text/plain; charset=ISO-8859-1 Dear Adnani I have visualized your molecule, you should check the charge and multiplicity of your molecule. In addition, I would recommend to use larger basis set to get bonding between Fe and aromatic ring. Sincerely; M. Ibrahim On Sat, Jun 12, 2010 at 12:42 AM, zouzou adnani zinebeladnani],[hotmail.com wrote: > > Sent to CCL by: "zouzou adnani" [zinebeladnani]^[hotmail.com] > hi, > I'm trying to study the interaction between one iron atom and some > quinoxaline derivatives, each time I end up with some very odd geometries > even though I changed the iron position several times and I tried some of > the propositions I found in the CCL archive (Maxcycle, Vshift, QC...). > here is one of my input files, please help me: > > %chk=mol2fer-dft-cep121g.chk > %nproc=1 > > #p opt freq b3lyp nosymm guess=save cep-121g > > 0 1 > > C > C 1 B1 > H 1 B2 2 A1 > C 1 B3 2 A2 3 > D1 > C 2 B4 1 A3 4 > D2 > H 2 B5 1 A4 4 > D3 > C 5 B6 2 A5 1 > D4 > C 4 B7 1 A6 2 > D5 > H 5 B8 2 A7 1 > D6 > H 7 B9 5 A8 2 > D7 > H 8 B10 4 A9 1 > D8 > N 2 B11 1 A10 4 > D9 > C 12 B12 2 A11 1 > D10 > O 13 B13 12 A12 2 > D11 > C 13 B14 12 A13 2 > D12 > O 15 B15 13 A14 12 > D13 > N 15 B16 13 A15 12 > D14 > H 17 B17 15 A16 13 > D15 > Fe 15 B18 13 A17 12 > D16 > > B1 1.40644101 > B2 2.14928644 > B3 1.39759508 > B4 1.39765674 > B5 2.08511317 > B6 1.39253612 > B7 1.39257680 > B8 1.08638027 > B9 1.08486967 > B10 1.08486443 > B11 1.39557266 > B12 1.38144585 > B13 1.21473476 > B14 1.53434602 > B15 1.21479365 > B16 1.38128209 > B17 1.01319508 > B18 2.48818517 > A1 145.95140520 > A2 119.79706010 > A3 119.77892540 > A4 143.20945469 > A5 120.09436720 > A6 120.08836427 > A7 119.29734053 > A8 119.58833605 > A9 119.59281559 > A10 118.07480691 > A11 126.52180143 > A12 122.62536055 > A13 115.40288341 > A14 121.97364409 > A15 115.41203166 > A16 114.40037764 > A17 74.26757538 > D1 -0.00336246 > D2 0.00283977 > D3 -179.98326314 > D4 0.00000000 > D5 -0.00385223 > D6 -180.00000000 > D7 179.99662248 > D8 -179.99638223 > D9 -180.00000000 > D10 -0.02573946 > D11 -179.98395853 > D12 0.01264207 > D13 -179.98079972 > D14 0.03738560 > D15 -179.99076401 > D16 -83.15595137> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim _ compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016e64c1c987f35430488cb7e43 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Adnani
I have visualized your molecule, you should check the charg= e and multiplicity of your molecule. In addition,=A0I would recommend to us= e larger basis set to get bonding between Fe and aromatic ring.
Sincerely;
M. Ibrahim

On Sat, J= un 12, 2010 at 12:42 AM, zouzou adnani zinebeladnani],[hotmail.com <owner-chemistry _ ccl.net> wrote:

Sent to CCL by: "zouzou =A0adnani" [zinebeladnani]^[hotmail.com]
hi,
I'm trying to study the interaction between one iron atom and some quin= oxaline =A0derivatives, each time I end up with some very odd geometries ev= en though =A0I changed the iron position several times and I tried some of = the propositions I found in the CCL archive (Maxcycle, Vshift, QC...).
here is one of my input files, please help me:

%chk=3Dmol2fer-dft-cep121g.chk
%nproc=3D1

#p opt freq b3lyp nosymm guess=3Dsave cep-121g

0 1

=A0C
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B1
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B2 =A0= =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A1
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B3 =A0= =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A2 =A0 =A03 =A0 =A0 =A0 =A0 =A0 =A0 =A0D1<= br> =A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0B4 =A0= =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A3 =A0 =A04 =A0 =A0 =A0 =A0 =A0 =A0 =A0D2<= br> =A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0B5 =A0= =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A4 =A0 =A04 =A0 =A0 =A0 =A0 =A0 =A0 =A0D3<= br> =A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A05 =A0 =A0 =A0 =A0 =A0 =A0 =A0B6 =A0= =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A5 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0D4<= br> =A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A04 =A0 =A0 =A0 =A0 =A0 =A0 =A0B7 =A0= =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A6 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0D5<= br> =A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A05 =A0 =A0 =A0 =A0 =A0 =A0 =A0B8 =A0= =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A7 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0D6<= br> =A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A07 =A0 =A0 =A0 =A0 =A0 =A0 =A0B9 =A0= =A05 =A0 =A0 =A0 =A0 =A0 =A0 =A0A8 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0D7<= br> =A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A08 =A0 =A0 =A0 =A0 =A0 =A0 B10 =A0 = =A04 =A0 =A0 =A0 =A0 =A0 =A0 =A0A9 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0D8 =A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 B11 =A0 = =A01 =A0 =A0 =A0 =A0 =A0 =A0 A10 =A0 =A04 =A0 =A0 =A0 =A0 =A0 =A0 =A0D9
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 12 =A0 =A0 =A0 =A0 =A0 =A0 B12 =A0 =A0= 2 =A0 =A0 =A0 =A0 =A0 =A0 A11 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 D10
=A0O =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 13 =A0 =A0 =A0 =A0 =A0 =A0 B13 =A0 12 = =A0 =A0 =A0 =A0 =A0 =A0 A12 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 D11
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 13 =A0 =A0 =A0 =A0 =A0 =A0 B14 =A0 12 = =A0 =A0 =A0 =A0 =A0 =A0 A13 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 D12
=A0O =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 15 =A0 =A0 =A0 =A0 =A0 =A0 B15 =A0 13 = =A0 =A0 =A0 =A0 =A0 =A0 A14 =A0 12 =A0 =A0 =A0 =A0 =A0 =A0 D13
=A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 15 =A0 =A0 =A0 =A0 =A0 =A0 B16 =A0 13 = =A0 =A0 =A0 =A0 =A0 =A0 A15 =A0 12 =A0 =A0 =A0 =A0 =A0 =A0 D14
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 17 =A0 =A0 =A0 =A0 =A0 =A0 B17 =A0 15 = =A0 =A0 =A0 =A0 =A0 =A0 A16 =A0 13 =A0 =A0 =A0 =A0 =A0 =A0 D15
=A0Fe =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A015 =A0 =A0 =A0 =A0 =A0 =A0 B18 =A0 13 = =A0 =A0 =A0 =A0 =A0 =A0 A17 =A0 12 =A0 =A0 =A0 =A0 =A0 =A0 D16

=A0 B1 =A0 =A0 =A0 =A0 =A0 =A0 1.40644101
=A0 B2 =A0 =A0 =A0 =A0 =A0 =A0 2.14928644
=A0 B3 =A0 =A0 =A0 =A0 =A0 =A0 1.39759508
=A0 B4 =A0 =A0 =A0 =A0 =A0 =A0 1.39765674
=A0 B5 =A0 =A0 =A0 =A0 =A0 =A0 2.08511317
=A0 B6 =A0 =A0 =A0 =A0 =A0 =A0 1.39253612
=A0 B7 =A0 =A0 =A0 =A0 =A0 =A0 1.39257680
=A0 B8 =A0 =A0 =A0 =A0 =A0 =A0 1.08638027
=A0 B9 =A0 =A0 =A0 =A0 =A0 =A0 1.08486967
=A0 B10 =A0 =A0 =A0 =A0 =A0 =A01.08486443
=A0 B11 =A0 =A0 =A0 =A0 =A0 =A01.39557266
=A0 B12 =A0 =A0 =A0 =A0 =A0 =A01.38144585
=A0 B13 =A0 =A0 =A0 =A0 =A0 =A01.21473476
=A0 B14 =A0 =A0 =A0 =A0 =A0 =A01.53434602
=A0 B15 =A0 =A0 =A0 =A0 =A0 =A01.21479365
=A0 B16 =A0 =A0 =A0 =A0 =A0 =A01.38128209
=A0 B17 =A0 =A0 =A0 =A0 =A0 =A01.01319508
=A0 B18 =A0 =A0 =A0 =A0 =A0 =A02.48818517
=A0 A1 =A0 =A0 =A0 =A0 =A0 145.95140520
=A0 A2 =A0 =A0 =A0 =A0 =A0 119.79706010
=A0 A3 =A0 =A0 =A0 =A0 =A0 119.77892540
=A0 A4 =A0 =A0 =A0 =A0 =A0 143.20945469
=A0 A5 =A0 =A0 =A0 =A0 =A0 120.09436720
=A0 A6 =A0 =A0 =A0 =A0 =A0 120.08836427
=A0 A7 =A0 =A0 =A0 =A0 =A0 119.29734053
=A0 A8 =A0 =A0 =A0 =A0 =A0 119.58833605
=A0 A9 =A0 =A0 =A0 =A0 =A0 119.59281559
=A0 A10 =A0 =A0 =A0 =A0 =A0118.07480691
=A0 A11 =A0 =A0 =A0 =A0 =A0126.52180143
=A0 A12 =A0 =A0 =A0 =A0 =A0122.62536055
=A0 A13 =A0 =A0 =A0 =A0 =A0115.40288341
=A0 A14 =A0 =A0 =A0 =A0 =A0121.97364409
=A0 A15 =A0 =A0 =A0 =A0 =A0115.41203166
=A0 A16 =A0 =A0 =A0 =A0 =A0114.40037764
=A0 A17 =A0 =A0 =A0 =A0 =A0 74.26757538
=A0 D1 =A0 =A0 =A0 =A0 =A0 =A0-0.00336246
=A0 D2 =A0 =A0 =A0 =A0 =A0 =A0 0.00283977
=A0 D3 =A0 =A0 =A0 =A0 =A0-179.98326314
=A0 D4 =A0 =A0 =A0 =A0 =A0 =A0 0.00000000
=A0 D5 =A0 =A0 =A0 =A0 =A0 =A0-0.00385223
=A0 D6 =A0 =A0 =A0 =A0 =A0-180.00000000
=A0 D7 =A0 =A0 =A0 =A0 =A0 179.99662248
=A0 D8 =A0 =A0 =A0 =A0 =A0-179.99638223
=A0 D9 =A0 =A0 =A0 =A0 =A0-180.00000000
=A0 D10 =A0 =A0 =A0 =A0 =A0 -0.02573946
=A0 D11 =A0 =A0 =A0 =A0 -179.98395853
=A0 D12 =A0 =A0 =A0 =A0 =A0 =A00.01264207
=A0 D13 =A0 =A0 =A0 =A0 -179.98079972
=A0 D14 =A0 =A0 =A0 =A0 =A0 =A00.03738560
=A0 D15 =A0 =A0 =A0 =A0 -179.99076401
=A0 D16 =A0 =A0 =A0 =A0 =A0-83.15595137



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--0016e64c1c987f35430488cb7e43-- From owner-chemistry@ccl.net Fri Jun 11 23:41:01 2010 From: "Jan Labanowski janl*o*speakeasy.net" To: CCL Subject: CCL: Funding Opportunity and Invitation to DARPA PROPHECY Teaming Dayng Opportunity and Invitation to DARPA PROPHECY Teaming Day Message-Id: <-42102-100611233907-17206-VuxkDEQQpfR/RU88oDVRWQ^-^server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Date: Fri, 11 Jun 2010 23:38:58 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl(_)speakeasy.net] Funding Opportunity and Invitation to DARPA PROPHECY Teaming Dayng Opportun= ity and Invitation to DARPA PROPHECY Teaming Day Forwarded to CCL by its manager The PDF attachment with details is available at: http://www.ccl.net/DARPA-SN-10-48_Prophecy_Workshop.pdf Sent on behalf of Michael Callahan, M.D., DTM&H, Program Manager for Prophe= cy: Predicting Pathogen Evolution. Dear Dr. Labanowski, I am contacting you in regard to a novel funding opportunity which may be of interest to participants in the Computational Chemistry List serve. DARPA's viral pathogen surveillance program known as "Prophecy" is based on= a multi-year investment in the preemptive prediction of emerging viruses using in-silica models validated by high-throughput biological validation systems= , all of which are corrected by the real-time reporting of mutations in animal reservoirs or humans. A Broad Agency Announcement (BAA) will soon be releas= ed for Prophecy which will seek integrated multi-disciplinary solutions to predict= ing viral pathogens before emergence in natural ecologies. Talented scientists will be critical to the success of this program. It is = our belief that the members of the CCL community may offer novel approaches, methodologies and trans-discipline solutions which would greatly assist DAR= PA in this challenging program. As you are likely aware, this belief is supported= by the successes of DARPA's Protein Design Process program which brought compu= ter scientists and molecular biologists together to challenge paradigms in conventional protein design and evolution. Due to the interdisciplinary nature of the program Prophecy and its goal of predicting pathogen evolution, collaborations will be necessary and we envi= sion that it may take time to formulate productive teams. To this end DARPA will= be holding teaming meetings to introduce potential responders to the Prophecy = BAA and encourage their collaboration in the pursuit of multidisciplinary appro= aches to the program. There will be 2 meetings which are described in the attached Special Notice (DARPA-SN-10-48). We hope that you will forward this Special Notice to the CCL listserv and t= hat the expertise of your community will help DARPA in achieving these challeng= ing objectives. Please note that there are two meetings over the next four week= s that will precede the publication of the BAA. Regards, Michael Callahan MD Program Manager, Prophecy