From owner-chemistry@ccl.net Fri Mar 9 06:17:01 2007 From: "nihcho[*]barc.gov.in" To: CCL Subject: CCL: free energy of hydration from free energy of solvation Message-Id: <-33770-070308010658-10069-pUo12+yGB+SLoLlbQ9rXFA^server.ccl.net> X-Original-From: nihcho()barc.gov.in Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 08 Mar 2007 10:27:14 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: nihcho-*-barc.gov.in Free energy of hydration is nothing but a special case of free energy of solvation, where solvent is water. Free energy of solvation (hydration) generally defined as the change in free energy when a particular species is transfered from vacuum to the splvent (water). This has nothing to do with a reaction. If however you want to calculate change in solvation (or hydration) free energy between the reactant and product, then simply subtract. In case of a reaction, a more important quantity is the potential of mean force (PMF), which is nothing but free energy change as a function of a suitable reaction coordinate or order parameter (which describe the reaction). Hope this will help. Niharendu Choudhury ----------------------------------------- Dr. N. Choudhury Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre Mumbai 400 085 INDIA email: niharc2002]-[yahoo.com, niharc2007]-[gmail.com, nihcho]-[barc.gov.in Quoting "CCL CCL computationalchemist .. gmail.com" : > Dear Friends, > > this may be a naive question, but i'm very new to the field. so, forgive me > if i'm wrong. > > I was struggling with a problem, since morning. Could be fine if any one > helps me to come out. > > I, have a system say,, A+B ---> TS ---> C > > I computed the free energy of solvation [ delG(solv) ] for all these species > ( chemsol - online programe) and they are ( solvent being water), > > A = -19.9 > B = -9.6 > TS = -36.3 > C = -50.9 > My question is how to calculate free energy of hydration, [ delG(hyd) ] > from these value. > > Any pointers or suggestions will be greatly apprciated. > > > > > > -- > Regards, > Dr. Sanjay > ------------------------------------------------- From owner-chemistry@ccl.net Fri Mar 9 11:47:00 2007 From: "Aggelos Avramopoulos aggavramop{=}yahoo.gr" To: CCL Subject: CCL:G: NBO and GAUSSIAN Message-Id: <-33771-070309114604-31995-Udbot1UbJ9GJBN9h/1Aj1g-,-server.ccl.net> X-Original-From: Aggelos Avramopoulos Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-704130593-1173458737=:3177" Date: Fri, 9 Mar 2007 16:45:37 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Aggelos Avramopoulos [aggavramop ~~ yahoo.gr] --0-704130593-1173458737=:3177 Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 8bit Dear CCLs I made a calculation of the natural population analysis of a system by using the NBO program employed in GAUSSIAN 98. However, in the output file, just before the printing of the Summary of the Pop. analysis the following warning was appeared: WARNING: Population inversion found on atom Xe 1 Population inversion found on atom H 2 Population inversion found on atom C 3 Population inversion found on atom C 4 Population inversion found on atom Xe 5 Population inversion found on atom C 6 Population inversion found on atom C 7 Population inversion found on atom Xe 8 Population inversion found on atom H 9 Natural Population Natural ----------------------------------------------- Atom No Charge Core Valence Rydberg Total ----------------------------------------------------------------------- Xe 1 0.78167 45.99924 7.15753 0.06157 53.21833 H 2 -0.09591 0.00000 1.08564 0.01027 1.09591 C 3 -0.58778 1.99822 4.53350 0.05606 6.58778 C 4 -0.59076 1.99809 4.54330 0.04937 6.59076 Xe 5 0.98590 45.99876 6.93525 0.08009 53.01410 C 6 -0.59075 1.99809 4.54327 0.04938 6.59075 C 7 -0.58794 1.99822 4.53365 0.05606 6.58794 Xe 8 0.78167 45.99924 7.15749 0.06160 53.21833 H 9 -0.09610 0.00000 1.08583 0.01027 1.09610 ======================================================================= * Total * 0.00000 145.98988 41.57546 0.43466 188.00000 Is there anyone who knows how to interpret this warning? Thanks in advance for every comment Aggelos Avramopoulos --------------------------------- Χρησιμοποιείτε Yahoo! Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail διαθέτει την καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων http://login.yahoo.com/config/mail?.intl=gr --0-704130593-1173458737=:3177 Content-Type: text/html; charset=iso-8859-7 Content-Transfer-Encoding: 8bit
Dear CCLs
 
I made a calculation of the natural population analysis of a system
by using the NBO program employed in GAUSSIAN 98. However,
in the output file, just before the printing of the Summary of the Pop.
analysis the following warning was appeared:
 
WARNING: Population inversion found on atom Xe 1
           Population inversion found on atom  H 2
           Population inversion found on atom  C 3
           Population inversion found on atom  C 4
           Population inversion found on atom Xe 5
           Population inversion found on atom  C 6
           Population inversion found on atom  C 7
           Population inversion found on atom Xe 8
           Population inversion found on atom  H 9
                                     Natural Population
               Natural   -----------------------------------------------
    Atom No    Charge        Core      Valence    Rydberg      Total
 -----------------------------------------------------------------------
     Xe  1    0.78167     45.99924     7.15753    0.06157    53.21833
      H  2   -0.09591      0.00000     1.08564    0.01027     1.09591
      C  3   -0.58778      1.99822     4.53350    0.05606     6.58778
      C  4   -0.59076      1.99809     4.54330    0.04937     6.59076
     Xe  5    0.98590     45.99876     6.93525    0.08009    53.01410
      C  6   -0.59075      1.99809     4.54327    0.04938     6.59075
      C  7   -0.58794      1.99822     4.53365    0.05606     6.58794
     Xe  8    0.78167     45.99924     7.15749    0.06160    53.21833
      H  9   -0.09610      0.00000     1.08583    0.01027     1.09610
 =======================================================================
   * Total *  0.00000    145.98988    41.57546    0.43466   188.00000
Is there anyone who knows how to interpret this warning?
 
Thanks in advance for every comment
 
Aggelos Avramopoulos

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http://login.yahoo.com/config/mail?.intl=gr --0-704130593-1173458737=:3177-- From owner-chemistry@ccl.net Fri Mar 9 12:42:00 2007 From: "Adrian Villegas adriano::eps.mcgill.ca" To: CCL Subject: CCL: Bond Type (character of atom-atom interaction) from Hartree-Fock calc. Message-Id: <-33772-070309124036-27079-NHcid933ixUI3bG/c5mWig.:.server.ccl.net> X-Original-From: "Adrian Villegas" Date: Fri, 9 Mar 2007 12:40:32 -0500 Sent to CCL by: "Adrian Villegas" [adriano : eps.mcgill.ca] Hi, I am a bit confused as to how to obtain information on the character of the interaction (bond type) between a specific atom-atom pair from the energies and MO coefficients obtained from a converged geometry optimization (Hartree-Fock 6-31G**). In other words, what I want is to obtain an additional criterion to determine whether a particular atom-atom interaction has a covalent, ionic or hydrogen-bond character. Any piece of information would be greatly appreciated AV From owner-chemistry@ccl.net Fri Mar 9 22:47:00 2007 From: "Joaquin Barroso Flores joaco_barroso^yahoo.com" To: CCL Subject: CCL:G: NBO and GAUSSIAN Message-Id: <-33773-070309224551-28903-EWczmJ5prg3hlF3oD9C7tg(-)server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-2041902454-1173498330=:31103" Date: Fri, 9 Mar 2007 21:45:30 -0600 (CST) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso:+:yahoo.com] --0-2041902454-1173498330=:31103 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi Aggelos In the NBO analysis the principal quantum numbers for the NAO's are assigned on the basis of the energy order in the HF matrix, or according to their occupancy. When this order doesnt coincide then the warning message warning "population inversion" appears. In other words there are some NBOs with higher occupancies than others that are lower in energy, as would be expected by regular theory. According to tutorials by Weinhold himself (available at http://www.chem.wisc.edu/~nbo5/ ) this isnt that much a problem. I hope I was helpful "Aggelos Avramopoulos aggavramop{=}yahoo.gr" escribiσ: Dear CCLs I made a calculation of the natural population analysis of a system by using the NBO program employed in GAUSSIAN 98. However, in the output file, just before the printing of the Summary of the Pop. analysis the following warning was appeared: WARNING: Population inversion found on atom Xe 1 Population inversion found on atom H 2 Population inversion found on atom C 3 Population inversion found on atom C 4 Population inversion found on atom Xe 5 Population inversion found on atom C 6 Population inversion found on atom C 7 Population inversion found on atom Xe 8 Population inversion found on atom H 9 Natural Population Natural ----------------------------------------------- Atom No Charge Core Valence Rydberg Total ----------------------------------------------------------------------- Xe 1 0.78167 45.99924 7.15753 0.06157 53.21833 H 2 -0.09591 0.00000 1.08564 0.01027 1.09591 C 3 -0.58778 1.99822 4.53350 0.05606 6.58778 C 4 -0.59076 1.99809 4.54330 0.04937 6.59076 Xe 5 0.98590 45.99876 6.93525 0.08009 53.01410 C 6 -0.59075 1.99809 4.54327 0.04938 6.59075 C 7 -0.58794 1.99822 4.53365 0.05606 6.58794 Xe 8 0.78167 45.99924 7.15749 0.06160 53.21833 H 9 -0.09610 0.00000 1.08583 0.01027 1.09610 ======================================================================= * Total * 0.00000 145.98988 41.57546 0.43466 188.00000 Is there anyone who knows how to interpret this warning? Thanks in advance for every comment Aggelos Avramopoulos --------------------------------- Χρησιμοποιείτε Yahoo! Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail διαθέτει την καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων http://login.yahoo.com/config/mail?.intl=gr ********************************************************** Dr. Joaquin Barroso-Flores Centro de Investigaciσn en Polνmeros COMEX Marcos Achar Lobatσn 2 Tepexpan, Mpo. de Acolman Mexico Correos alternos: joaquin.barroso()gmail.com jbarroso()cip.org jbarrosof()comex.com.mx ********************************************************** --------------------------------- Do You Yahoo!? La mejor conexiσn a Internet y 2GB extra a tu correo por $100 al mes. http://net.yahoo.com.mx --0-2041902454-1173498330=:31103 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi Aggelos
 
In the NBO analysis the principal quantum numbers for the NAO's are assigned on the basis of the energy order in the HF matrix, or according to their occupancy. When this order doesnt coincide then the warning message warning "population inversion" appears. In other words there are some NBOs with higher occupancies than others that are lower in energy, as would be expected by regular theory. According to tutorials by Weinhold himself (available at http://www.chem.wisc.edu/~nbo5/ ) this isnt that much a problem.
 
I hope I was helpful

"Aggelos Avramopoulos aggavramop{=}yahoo.gr" <owner-chemistry()ccl.net> escribiσ:
Dear CCLs
 
I made a calculation of the natural population analysis of a system
by using the NBO program employed in GAUSSIAN 98. However,
in the output file, just before the printing of the Summary of the Pop.
analysis the following warning was appeared:
 
WARNING: Population inversion found on atom Xe 1
           Population inversion found on atom  H 2
           Population inversion found on atom  C 3
           Population inversion found on atom  C 4
           Population inversion found on atom Xe 5
           Population inversion found on atom  C 6
           Population inversion found on atom  C 7
           Population inversion found on atom Xe 8
           Population inversion found on atom  H 9
                                     Natural Population
               Natural   -----------------------------------------------
    Atom No    Charge        Core      Valence    Rydberg      Total
 -----------------------------------------------------------------------
     Xe  1    0.78167     45.99924     7.15753    0.06157    53.21833
      H  2   -0.09591      0.00000     1.08564    0.01027     1.09591
      C  3   -0.58778      1.99822     4.53350    0.05606     6.58778
      C  4   -0.59076      1.99809     4.54330    0.04937     6.59076
     Xe  5    0.98590     45.99876     6.93525    0.08009    53.01410
      C  6   -0.59075      1.99809     4.54327    0.04938     6.59075
      C  7   -0.58794      1.99822     4.53365    0.05606     6.58794
     Xe  8    0.78167     45.99924     7.15749    0.06160    53.21833
      H  9   -0.09610      0.00000     1.08583    0.01027     1.09610
 =======================================================================
   * Total *  0.00000    145.98988    41.57546    0.43466   188.00000
Is there anyone who knows how to interpret this warning?
 
Thanks in advance for every comment
 
Aggelos Avramopoulos
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**********************************************************
Dr. Joaquin Barroso-Flores

Centro de Investigaciσn en Polνmeros
COMEX
Marcos Achar Lobatσn 2
Tepexpan, Mpo. de Acolman
Mexico

Correos alternos: joaquin.barroso()gmail.com
jbarroso()cip.org
jbarrosof()comex.com.mx

**********************************************************

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