From owner-chemistry@ccl.net Wed May 19 08:23:00 2010 From: "Soren Eustis soreneustis===gmail.com" To: CCL Subject: CCL: Natural Transition Orbitals (NTO) Message-Id: <-41892-100519082212-24285-cyn5crIZaOSk0BpA6k/20w() server.ccl.net> X-Original-From: Soren Eustis Content-type: multipart/alternative; boundary="B_3357123718_11751201" Date: Wed, 19 May 2010 14:21:51 +0200 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis|gmail.com] > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3357123718_11751201 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Greetings. I am using G09 to calculate the NTOs for a bridged ring compound. I have managed to get everything to work nicely (including saveNTO), but I need some help interpreting the output. When I visualize the .fch file, I am unsure what part I am looking at. Is the HOMO the =8Cparticle=B9 as described in Martin, JCP 118 4775 (2003)? If that is true, perhaps the HOMO-1 is the =8Chole=B9. Thus, the HOMO represents the orbital to which the excited electron =8Clanded=B9 and the LUMO is the vacant orbital? I could imagine the same scenario, but with the HOMO the =8Chole=B9 and the LUMO the =8Cparticle=B9. Does anyone have experience with this method? Thanks in advance! Kind regards, Soren --=20 Dr. Soren N. Eustis ETH =AD Zurich Institute for Biogeochemistry and Pollutant Dynamics Universitatstrasse 16 8092 Zurich +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren^^env.ethz.ch --B_3357123718_11751201 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Natural Transition Orbitals (NTO) Greetings.  I am using G09 to calculate the NTOs for a bridged ring c= ompound.  I have managed to get everything to work nicely (including sa= veNTO), but I need some help interpreting the output.

When I visualize the .fch file, I am unsure what part I am looking at. &nbs= p;Is the HOMO the ‘particle’ as described in Martin, JCP 118 477= 5 (2003)?  If that is true, perhaps the HOMO-1 is the ‘hole’= ;.  Thus, the HOMO represents the orbital to which the excited electron= ‘landed’ and the LUMO is the vacant orbital?  I could imag= ine the same scenario, but with the HOMO the ‘hole’ and the LUMO= the ‘particle’.

Does anyone have experience with this method?  Thanks in advance!

Kind regards,

Soren
--
Dr. Soren N. Eustis
ETH – Zurich
Institute for Biogeochemistry and Pollutant Dynamics
Universitatstrasse 16
8092 Zurich

+41 44 632 93 48 (office)
+41 44 632 14 38 (fax)

soren^^env.ethz.ch
 --B_3357123718_11751201-- From owner-chemistry@ccl.net Wed May 19 09:14:00 2010 From: "Soren Eustis soreneustis],[gmail.com" To: CCL Subject: CCL:G: ONIOM with PCM Message-Id: <-41893-100519081953-12916-s6+p1fC1wbMPMvr+t8SAow . server.ccl.net> X-Original-From: Soren Eustis Content-type: multipart/alternative; boundary="B_3357123581_11735322" Date: Wed, 19 May 2010 14:19:35 +0200 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis**gmail.com] > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3357123581_11735322 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable I have been studying the different behaviors of explicit and implicit solvent models on a given system. One of my final calculations was to be a QM:MM calculation (1 molecule:200 waters) with IEFPCM (solvent=3Dwater). The previous run (ONIOM without PCM) ran fine and converged after a reasonable time. However with PCM and after 168 processor hours, the calculation has not left the first MM stage. See below: INPUT: %chk=3Doutput.chk %mem=3D8GB %nprocshared=3D8 # opt oniom(mpw1pw91/cc-pvdz:amber) scrf=3D(iefpcm,solvent=3Dwater,oniompcm=3Dx) geom=3Dconnectivity 22DCDPA in water box with IEFPCM 0 1 0 1 0 1 .... OUTPUT: .... ONIOM: generating point 3 -- low level on real system. ONIOM-PCM-X: Computing reaction field of low level on real system. Standard basis: Dummy (5D, 7F) There are 2130 symmetry adapted basis functions of A symmetry. Integral buffers will be 131072 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned on. 2130 basis functions, 2130 primitive gaussians, 2130 cartesian basis functions 1424 alpha electrons 1424 beta electrons nuclear repulsion energy 158651.1978886932 Hartrees. NAtoms=3D 2130 NActive=3D 2130 NUniq=3D 2130 SFac=3D 7.50D-01 NAtFMM=3D 80 NAOKFM=3D= T Big=3DT --------------------------------------------------------------------------= - --- Polarizable Continuum Model (PCM) =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Model : PCM. Atomic radii : UFF (Universal Force Field). Polarization charges : Total charges. Charge compensation : None. Solution method : Iterative solution. Cavity type : Scaled VdW (van der Waals Surface) (Alpha=3D1.100). Cavity algorithm : GePol (No added spheres) Default sphere list used, NSphG=3D 2130. Lebedev-Laikov grids with approx. 5.0 points / Ang**2. Smoothing algorithm: Karplus/York (Gamma=3D1.0000). Polarization charges: spherical gaussians, with point-specific exponents (IZeta=3D 3). Self-potential: point-specific (ISelfS=3D 7). Self-field : sphere-specific E.n sum rule (ISelfD=3D 2). 1st derivatives : Analytical E(r).r(x)/FMM algorithm (CHGder, D1EAlg=3D3). Cavity 1st derivative terms included. Solvent : Water, Eps=3D 78.355300 Eps(inf)=3D 1.777849 --------------------------------------------------------------------------= - --- AMBER calculation of energy and first derivatives. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 2 ShMem 1 Linda. CoulSu: requested number of processors reduced to: 1 ShMem 1 Linda. ***at which point I abandoned the job Does anyone have any thoughts on this. Is this specific to Amber? Is this only an initial long step, followed by more reasonable iterations later on? Is this calculation doomed?! --=20 Dr. Soren N. Eustis ETH =AD Zurich Institute for Biogeochemistry and Pollutant Dynamics Universitatstrasse 16 8092 Zurich +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren++env.ethz.ch --B_3357123581_11735322 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable ONIOM with PCM I have been studying the different behaviors of explicit and implicit solv= ent models on a given system.  One of my final calculations was to be a= QM:MM calculation (1 molecule:200 waters) with IEFPCM (solvent=3Dwater). &nbs= p;The previous run (ONIOM without PCM) ran fine and converged after a reason= able time.  However with PCM and after 168 processor hours, the calcula= tion has not left the first MM stage.  See below:

INPUT:
%chk=3Doutput.chk
%mem=3D8GB
%nprocshared=3D8
# opt oniom(mpw1pw91/cc-pvdz:amber) scrf=3D(iefpcm,solvent=3Dwater,oniompcm=3Dx)<= BR> geom=3Dconnectivity

22DCDPA in water box with IEFPCM

0 1 0 1 0 1
....

OUTPUT:
....

 ONIOM: generating point  3 -- low level on real system.
 ONIOM-PCM-X: Computing reaction field of low level on real system.  Standard basis: Dummy (5D, 7F)
 There are  2130 symmetry adapted basis functions of A  &nbs= p;symmetry.
 Integral buffers will be    131072 words long.
 Raffenetti 1 integral format.
 Two-electron integral symmetry is turned on.
  2130 basis functions,  2130 primitive gaussians,  213= 0 cartesian basis functions
  1424 alpha electrons     1424 beta electron= s
       nuclear repulsion energy  &n= bsp; 158651.1978886932 Hartrees.
 NAtoms=3D 2130 NActive=3D 2130 NUniq=3D 2130 SFac=3D 7.50D-01 NAtFMM=3D  &= nbsp;80 NAOKFM=3DT Big=3DT
 ---------------------------------------------------------------------= ---------
 Polarizable Continuum Model (PCM)
 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 Model           &nb= sp;    : PCM.
 Atomic radii         : UFF (U= niversal Force Field).
 Polarization charges : Total charges.
 Charge compensation  : None.
 Solution method      : Iterative solution.  Cavity type          : S= caled VdW (van der Waals Surface) (Alpha=3D1.100).
 Cavity algorithm     : GePol (No added spheres)             &nb= sp;           Default= sphere list used, NSphG=3D 2130.
            &nb= sp;           Lebedev= -Laikov grids with approx.  5.0 points / Ang**2.
            &nb= sp;           Smoothi= ng algorithm: Karplus/York (Gamma=3D1.0000).
            &nb= sp;           Polariz= ation charges: spherical gaussians, with
            &nb= sp;            &= nbsp;            = ;        point-specific exponents (I= Zeta=3D 3).
            &nb= sp;           Self-po= tential: point-specific (ISelfS=3D 7).
            &nb= sp;           Self-fi= eld    : sphere-specific E.n sum rule (ISelfD=3D 2).
 1st derivatives      : Analytical E(r).r(x)/= FMM algorithm (CHGder, D1EAlg=3D3).
            &nb= sp;           Cavity = 1st derivative terms included.
 Solvent           &= nbsp;  : Water, Eps=3D  78.355300 Eps(inf)=3D   1.77784= 9
 ---------------------------------------------------------------------= ---------
 AMBER calculation of energy and first derivatives.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 2 ShMem   1 Linda.
 CoulSu:  requested number of processors reduced to:   = 1 ShMem   1 Linda.
***at which point I abandoned the job

Does anyone have any thoughts on this.  Is this specific to Amber? &nb= sp;Is this only an initial long step, followed by more reasonable iterations= later on?  Is this calculation doomed?!




--
Dr. Soren N. Eustis
ETH – Zurich
Institute for Biogeochemistry and Pollutant Dynamics
Universitatstrasse 16
8092 Zurich

+41 44 632 93 48 (office)
+41 44 632 14 38 (fax)

soren++env.ethz.ch
 --B_3357123581_11735322-- From owner-chemistry@ccl.net Wed May 19 09:49:00 2010 From: "may abdelghani may01dz^yahoo.fr" To: CCL Subject: CCL: lack natural orbitals in a bond X-Y Message-Id: <-41894-100519072648-13560-+6dIZnIywd82lAI0YKX35A ~ server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-1496647685-1274264795=:86980" Date: Wed, 19 May 2010 10:26:35 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz(!)yahoo.fr] --0-1496647685-1274264795=:86980 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0A=0A=0A=0ANBO analysis for my complexes showed that they=0Alack natural o= rbitals in the bond X-Y, it mean that:=0A=0Athis bond is very weak one,ther= e no bond=A0 at all,Or, as defined By AIM method, it is a result of a close= d-shell interaction=0A or an intermediate closed-shell one.=0A=0AAny he= lp is appreciate=0A=0A=0A=0A=0A --0-1496647685-1274264795=:86980 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
= =0A=0A

NBO analysis for my compl= exes showed that they=0Alack natural orbitals in the bond X-Y, it mean that= :

=0A=0A
    this bond is very weak= one,
  1. th= ere no bond  at all,
  2. Or, as defined By AIM method, it = is a result of a closed-shell interaction=0A or an intermediate closed-= shell one.
=0A=0A

Any help is appreciate

=0A=0A

=0A=0A=0A=0A= =0A --0-1496647685-1274264795=:86980-- From owner-chemistry@ccl.net Wed May 19 10:24:00 2010 From: "Chris Swain swain..mac.com" To: CCL Subject: CCL: Mobile Molecular DataSheet v1.0.0 released Message-Id: <-41895-100519030241-3007-n27gLqdisGfbGe+aPpAM5Q|,|server.ccl.net> X-Original-From: Chris Swain Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Wed, 19 May 2010 07:02:25 +0100 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain**mac.com] Looks interesting, any plans for an iPhone version? Certainly seems to be a popular arena to work in, I keep a list of iPhone apps for chemists here http://homepage.mac.com/swain/Sites/Macinchem/iPhone/mobile_apps.html Cheers Chris On 19 May 2010, at 00:00, Alex M Clark aclark.xyz(_)gmail.com wrote: > > Sent to CCL by: "Alex M Clark" [aclark.xyz_-_gmail.com] > Dear CCL, > > For anybody who is interested in chemistry software for mobile > devices, there is a new app available for BlackBerry smartphones > called the Mobile Molecular DataSheet. Its most striking feature is > a molecular diagram sketcher which is optimised for the small screen/ > trackball/keypad interface. > > It also allows groups of molecules to be organised along with text > and numeric data, which can be edited using a spreadsheet-like > interface. Standard data formats (MDL MOL & SD) can be imported, > exported and exchanged by email. > > For more information, see the webside for Molecular Materials > Informatics, at: > > http://www.molmatinf.com > > There are also a number of demo videos which are available via > youtube, such as: > > http://www.youtube.com/watch?v=lqYXUNk6Gmw > > All comments and inquiries are welcome. > > > Best regards, > > Alex. > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > From owner-chemistry@ccl.net Wed May 19 13:32:00 2010 From: "andras.borosy{:}givaudan.com" To: CCL Subject: CCL: QSPR Software Message-Id: <-41896-100519090457-19469-6n6wftz2z9QioLgBgjAIWw(a)server.ccl.net> X-Original-From: andras.borosy[a]givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 0044A874C1257728_=" Date: Wed, 19 May 2010 14:29:57 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy_-_givaudan.com This is a multipart message in MIME format. --=_alternative 0044A874C1257728_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Mr. Naithani, The following companies must offer something you like: http://www.scienomics.com/ http://accelrys.com/products/materials-studio/ http://www.chemcomp.com/ Best wishes, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Neeraj Naithani neerajnaithani^^^gmail.com" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com/./ccl.net 19.05.2010 03:57 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: QSPR Software Sent to CCL by: "Neeraj Naithani" [neerajnaithani=3D-=3Dgmail.com] can anybody suggest QSPR software for polymeric system.=20 Thank You -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 0044A874C1257728_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Mr. Naithani,

The following companies must offer s= omething you like:

http://www.scienomics.com/

http://accelrys.com/products/materia= ls-studio/

http://www.chemcomp.com/

Best wishes,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert

Fragrance Research
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"Neeraj Naithani= neerajnaithani^^^gmail.com" <owner-chemistry/./ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com/./ccl.net

19.05.2010 03:57
Please respond to
"CCL Subscribers" <chemistry/./ccl.net>
To
"Borosy, Andras " <andras.borosy/./givaudan.com>
cc
Subject
CCL: QSPR Software






Sent to CCL by: "Neeraj  Naithani" [neerajnaithani=3D-=3Dgma= il.com]
can anybody suggest QSPR software for polymeric system.
Thank You



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--=_alternative 0044A874C1257728_=-- From owner-chemistry@ccl.net Wed May 19 14:07:00 2010 From: "Sergio Emanuel Galembeck segalemb:_:usp.br" To: CCL Subject: CCL: lack natural orbitals in a bond X-Y Message-Id: <-41897-100519125125-862-GRN37/Jwo0g/DohHpkCG5g]*[server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 19 May 2010 13:51:11 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb---usp.br] Dear May, Do you need to take care, because frequently the resonance structure obtained by NBO calculations doesn't correspond to that with the largest weight. Hope this help you, Sergio Citando "may abdelghani may01dz^yahoo.fr" : > > > > > NBO analysis for my complexes showed that they > lack natural orbitals in the bond X-Y, it mean that: > > this bond is very weak one,there no bond=A0 at all,Or, as defined By =20 > AIM method, it is a result of a closed-shell interaction > or an intermediate closed-shell one. > > Any help is appreciate > > > > > From owner-chemistry@ccl.net Wed May 19 21:31:01 2010 From: "David Zhang zhang.d.q||gmail.com" To: CCL Subject: CCL: Library enumeration software Message-Id: <-41898-100519173323-3470-HEchTXI1ow5fq8yfLINZtQ-,-server.ccl.net> X-Original-From: David Zhang Content-Type: multipart/alternative; boundary=00c09f971cb3891dee0486f874ec Date: Wed, 19 May 2010 13:39:31 -0700 MIME-Version: 1.0 Sent to CCL by: David Zhang [zhang.d.q~!~gmail.com] --00c09f971cb3891dee0486f874ec Content-Type: text/plain; charset=ISO-8859-1 Pipeline Pilot from Accelrys clearly satisfies all your requirements. See if you can get a student edition license: http://accelrys.com/solutions/industry/academic/student-edition.html Regards, David On Tue, May 18, 2010 at 1:47 PM, Richard Harper drrwharper!^!gmail.com < owner-chemistry|,|ccl.net> wrote: > > Sent to CCL by: Richard Harper [drrwharper^^^gmail.com] > What software are you using to enumerate (virtual or real) libraries > of chemicals from a scaffold and sets of reagents? Among the > requirements are the ability to enumerate large libraries (10^6 or > more compounds); some flexibility in naming (ability to record the > identifiers of the reactants); and Open Source or free academic > license (or very inexpensive). > Any suggestions are appreciated. > > Dick Harper > Indiana University-Purdue University Indianapolis (IUPUI)> > > --00c09f971cb3891dee0486f874ec Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Pipeline Pilot from Accelrys clearly satisfies all your requirements.= =A0 See if you can get a student edition license:
=A0
=A0
Regards,
=A0
David

On Tue, May 18, 2010 at 1:47 PM, Richard Harper = drrwharper!^!gmail.com &= lt;owner-chemistry|,|ccl.net&g= t; wrote:

Sent to CCL by: Richard Harp= er [drrwharper^^^gmail.com<= /a>]
What software are you using to enumerate (virtual or real) libraries
of = chemicals from a scaffold and sets of reagents? =A0Among the
requirement= s are the ability to enumerate large libraries (10^6 or
more compounds);= some flexibility in naming (ability to record the
identifiers of the reactants); and Open Source or free academic
license = (or very inexpensive).
Any suggestions are appreciated.

Dick Harp= er
Indiana University-Purdue University Indianapolis (IUPUI)



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