Re: Visualization of Natural Transition Orbitals (NTO)

> --0016e6d99efada892b04868a5276 Content-Type: text/html; charset=windows-1256 Content-Transfer-Encoding: quoted-printable

Dear Professor Ahmed El-Nahas and all
Thanks for reply. According to= IUPAC, the defination of solvation energy is "The change=20 in Gibbs energy when an ion or molecule is transferred from a=20 vacuum=20 (or the gas phase) to a solvent. The main contributions to=20 the solvation=20 energy come from: (a) the cavitation energy of formation of=20 the=20 hole which preserves the dissolved species in the solvent; (b) the=20 orientation energy of partial orientation of the dipoles; (c)=20 the isotropic=20 interaction energy of electrostatic and dispersion origin;=20 and (d)=20 the anisotropic energy of specific interactions, e.g. hydrogen =20 bonds, donor-acceptor interactions etc."
However, I c= alculated Ni2+ cation in water, please see this part of output:

Vari= ational PCM results
=A0=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D
=A0<psi(f)|=A0=A0 H=A0=A0=A0 |psi(f)>=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (a.u.) =3D=A0=A0 -15= 07.146446
=A0<psi(f)|H+V(f)/2|psi(f)>=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0 (a.u.) =3D=A0=A0 -1507.887943
=A0Total free energy in= solution:
=A0 with all non electrostatic terms=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 (a.u.) =3D=A0=A0 -1507.882504
=A0-----------------------------= ---------------------------------------
=A0(Polarized solute)-S= olvent=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (kcal/mol) =3D=A0=A0=A0 -4= 65.30
=A0--------------------------------------------------------= ------------
=A0Cavitation energy=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (kcal/mol) =3D=A0=A0=A0=A0=A0=A0 3.41
=A0Dispersion energy=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 (kcal/mol) =3D=A0=A0=A0=A0=A0=A0 0.00
=A0Repulsion energ= y=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (= kcal/mol) =3D=A0=A0=A0=A0=A0=A0 0.00
=A0Total non electrostatic=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (kcal/mol) =3D=A0=A0=A0=A0=A0=A0= 3.41
------------------------------------------------------------------= --

Did you mean by solvation energy the highlight one?
Thanks,
CCG1=

=C8=CA=C7=D1=ED=CE 13 = =E3=C7=ED=E6, 2010 05:08 =D5=A1 =CC=C7=C1 =E3=E4 Ahmed El-Nahas amelnahas!= =3D!hotmail.com <owner-chemistry(~)ccl.net>:

=A0
People add solvent (in term of PCM) to the reactants and products; the = solvation of=A0bar metal ions=A0releases=A0a lot of kcal/mols at the expens= e of=A0the=A0total reaction enthalpy. If you look at the energy of solvatio= n of the ligand, metal ion and complex, separately, you will realize this f= act. I have a similar situation with a difference of about 150-300 kcal/mol= between gas phase and solution, depending of your metal ion, ligand and th= e resulting complex.
=A0

=A0
=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
Professor Ahmed El-Nahas
Physical Chemistry (Quantum Chemistry)=
Computational Chemistry= Unit (CCU)
= Chemistry Department
Faculty of Science
El-Menoufia University<= /b>
Shebin El= -Kom
Egyp= t
Email: amelnahas:_:hotmail.com
= Tel: +2-016-4607974; +81-09062124377
=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

=A0
> From: owner-chemistry:_:ccl.net
> To: amelnahas:_:hotmail.com
> Subject: CCL: Bi= nding Enthalpy in vacuum and solvent
> Date: Wed, 12 May 2010 09:29:15 -0400
>
>
> Sent t= o CCL by: "Comp Chem Group " [compchemgroup1 a gmail.com]
> Dear All,
> By su= rveying on "Interaction Enthalpy" of transition metal complex in = vacuum and solvent (PCM or other model), I found in all cases that the enth= alpy change in vacuum is larger than that solvent. For example, if delta H = in vacuum=3D -1000 kcal/mol, in solvent=3D -200 kcal/mol. Could anyone expl= ain why?
> Regards,
> CCG1
>
>
>
>
>
&g= t;
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&g= t;
>
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&gt! ;
>
>
>
>

Hotmail: Trust= ed email with powerful SPAM protection. Sign up now.

--0016e6d99efada892b04868a5276-- From owner-chemistry@ccl.net Fri May 14 10:48:01 2010 From: "qing shao shaoqingfly1981++gmail.com" To: CCL Subject: CCL: simulation Message-Id: <-41851-100512214303-27143-KiRb8PxADjxAu2tfYFhrxw.:.server.ccl.net> X-Original-From: qing shao Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 12 May 2010 17:40:19 -0700 MIME-Version: 1.0 Sent to CCL by: qing shao [shaoqingfly1981^-^gmail.com] Ramya I think you can try "editconf" to put your solute in the center of your box and "genbox" to generate your solvents. Please read the manual for more information. Regards Qing On Wed, May 12, 2010 at 2:57 AM, rinu iyer rinuiyer{:}gmail.com wrote: > dear subscribers, > =A0=A0=A0=A0=A0=A0=A0=A0 i am using gromacs . i want to run a calculation= in which i want to > place a molecule in the centre during the generation of the box to do > molecular dynamics simulation. the molecule is surrounded by solvents. > can u tell me please how to run this calculation. > > Thanks in advance > K.R.Ramya > research fellow > Indian Institute of science,Pune > Tower, Sai Trinity Building, Sutarwadi Road, Pashan, > Pune 411021, INDIA > From owner-chemistry@ccl.net Fri May 14 11:23:01 2010 From: "morteza moghimi M.MOGHIMI.W-#-gmail.com" To: CCL Subject: CCL: difference between oniom & extrabasis Message-Id: <-41852-100513052624-20425-6l8OPyqulokhrBtE7fwGfg#server.ccl.net> X-Original-From: "morteza moghimi" Date: Thu, 13 May 2010 05:26:23 -0400 Sent to CCL by: "morteza moghimi" [M.MOGHIMI.W!A!gmail.com] i want to know the difference between the application of oniom and extrabasis. From owner-chemistry@ccl.net Fri May 14 11:57:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim() compchem.net" To: CCL Subject: CCL: Effect of sulphate ions on the preparation of the enzyme Message-Id: <-41853-100514111536-29017-K8wgSODFPx0usDUPH/zwoQ .. server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=001485f7244cdb489104868f56fa Date: Fri, 14 May 2010 16:15:02 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim ~ compchem.net] --001485f7244cdb489104868f56fa Content-Type: text/plain; charset=ISO-8859-1 Dear Basma I don't see why you are doing that, replacing sulfate ion with water molecules!!! Removing an ion close to the active site affects the binding efficiency, because of electrostatic interactions. I remember once I was working on a biosystem, during files preparation step using xleap (inside AMEBR), One Na+ ion has been added mistakely by xleap at 7 Ang. far apart from the active site, leaded to changing the binding mode. So, I believe removing sulfate ion (-2 charge) will dis-stabilize your system without any doubt. You may like to post why you want to do that, and there should be other tricks to solve your problem rather than removing the sulfate ion. Sincerely; M. Ibrahim On Wed, May 12, 2010 at 10:50 AM, Basma Ghazal basmaghazal**ymail.com < owner-chemistry##ccl.net> wrote: > > Hello, > Because I am still beginner in the field I need the advices in the > following items: > > The PDB structure that I use for docking have two sulphate ions, one of > them is very close to the active site and make interaction with it is > residue. The other is far from it. > 1- If I removed the sulfate ions from the pocket containing the active > site am I need to do partial optimization of this part? Because removing > them give more compact pocket by partial optimization. > 2- Instead, I think to add two water molecules in the same places of two > sulfate ions, do you think this way will compensate the removing of sulfate > ions to avoid the conformational change during the docking? > 3- But the sulfate ions are *charged* and replacement them by explicit > water molecules may not be equivalent, right? > > I look forward to any response. > Thanks, > Basma > > > > -- 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 --001485f7244cdb489104868f56fa Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Basma
I don't see why you are doing that, replacing sulfate io= n with water molecules!!!
Removing an ion close to the active sit= e affects the binding efficiency, because of electrostatic =A0 interactions= . I remember once I was working on a biosystem, during files preparation st= ep using xleap (inside AMEBR), One Na+ ion has been added mistakely by xlea= p at 7 Ang. far apart from the active site, leaded to changing the binding = mode. So, I believe removing sulfate ion (-2 charge) will=A0dis-stabilize= =A0your system without any doubt.

You may like to post why you want to do that, and there should be othe= r tricks to solve your problem rather than removing the sulfate ion.
<= div>Sincerely;
M. Ibrahim

On Wed, May 12, 2010 at 10:50 AM, Basma Ghazal basmaghazal**ymail.com <owner-chemistry##ccl.net> wrote:

Hello,
Because I am still=A0beginner in the field I need the advices in the following items:

The PDB structure= that I use for docking have two sulphate ions, one of them is very close to the active site and make interaction with it is residue. The other is far from it.
1- If I removed the sulfate ions from the pocket containing the active site am I ne= ed to do partial optimization of this part? Because removing them give more compact pocket by partial optimization.
2- Instead, I think to add two water molecules in the same places of two sulfate ions, do you think th= is way will compensate the removing of sulfate ions to avoid the conformationa= l change during the docking?
3- But the sulfate ions are charged and replacement them by explicit water molecules may not be equivalent, ri= ght?

= I look forward to any response.
Thanks,
Basma

--
=A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0= The University of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim##compche= m.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623= 42601

--001485f7244cdb489104868f56fa-- From owner-chemistry@ccl.net Fri May 14 12:32:00 2010 From: "Soren Eustis soreneustis!A!gmail.com" To: CCL Subject: CCL: simulation Message-Id: <-41854-100514114755-26520-Sf5etctm5DtqfDYHOQItUQ a server.ccl.net> X-Original-From: Soren Eustis Content-transfer-encoding: quoted-printable Content-type: text/plain; charset="ISO-8859-1" Date: Fri, 14 May 2010 17:47:38 +0200 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis]*[gmail.com] Ramya, In addition, Packmol works very well for this. It can be downloaded at: http://www.ime.unicamp.br/~martinez/packmol/. 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 On 5/13/10 2:40 AM, "qing shao shaoqingfly1981++gmail.com" wrote: >=20 > Sent to CCL by: qing shao [shaoqingfly1981^-^gmail.com] >=20 > Ramya > I think you can try "editconf" to put your solute in the center of > your box and "genbox" to generate your solvents. Please read the > manual for more information. > Regards > Qing >=20 > On Wed, May 12, 2010 at 2:57 AM, rinu iyer rinuiyer{:}gmail.com > wrote: >> dear subscribers, >> =A0=A0=A0=A0=A0=A0=A0=A0 i am using gromacs . i want to run a calculation in which i wan= t to >> place a molecule in the centre during the generation of the box to do >> molecular dynamics simulation. the molecule is surrounded by solvents. >> can u tell me please how to run this calculation. >>=20 >> Thanks in advance >> K.R.Ramya >> research fellow >> Indian Institute of science,Pune >> Tower, Sai Trinity Building, Sutarwadi Road, Pashan, >> Pune 411021, INDIA >>=20 >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script =3D->=20>=20>=20>=20>=20>=20>=20>=20>=20 >=20 From owner-chemistry@ccl.net Fri May 14 14:28:00 2010 From: "Anthony F kwyjib09]^[gmail.com" To: CCL Subject: CCL: Freq and Stability Message-Id: <-41855-100514133403-24319-2k3YdQJGeRjduStzc+k4gQ:-:server.ccl.net> X-Original-From: "Anthony F" Date: Fri, 14 May 2010 13:34:01 -0400 Sent to CCL by: "Anthony F" [kwyjib09*_*gmail.com] Dear CCL, I've been running geometry optimizations and found stationary points. I have also been using SCF = QC (also UB3LYP/6-311+G(d,p) NOSYMM). How can I be sure that my final answer is a local minimum? When I perform a frequency job after the optimization, I sometimes obtain imaginary frequencies, suggesting an nth-order saddle point (n is the number of imaginary frequencies). Does this also have to do with the stability of my wavefunction? I have used the keyword Stable=Opt for verification. But I find that I can have both a stable wavefunction and imaginary frequencies. How do I then find true local minima? Also, is it possible to run both a STABLE and geometry OPT job with the same route? Or do I have to use the Link1 keyword? If so, is it possible to copy my checkpoint file through the route section? Thanks Anthony From owner-chemistry@ccl.net Fri May 14 16:36:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim]|[compchem.net" To: CCL Subject: CCL:G: Binding Enthalpy in vacuum and solvent Message-Id: <-41856-100514112346-3145-g1+awv9xGYHVSQVScouMSA(~)server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e6db2ad42418d304868f7548 Date: Fri, 14 May 2010 16:23:30 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim*compchem.net] --0016e6db2ad42418d304868f7548 Content-Type: text/plain; charset=windows-1256 Content-Transfer-Encoding: quoted-printable Dear CCG1 You can use SCFVAC (in G03) or DOVACUMM (in G09) options in SCRF to calculate delta G solvation energy directly in one calculation. This option performs one calculation in gas phase. Note: these options are defined by "read" card in SCRF. Sincerely; M. Ibrahim 2010/5/14 CompChem Group compchemgroup1 _ gmail.com > Dear *Professor Ahmed El-Nahas and all* > Thanks for reply. According to IUPAC, the defination of solvation energy = is > "The change in Gibbs energy when an ion or molecule is transferred from a > vacuum (or the gas phase) to a solvent. The main contributions to the > solvation energy come from: (a) the cavitation energy of formation of the > hole which preserves the dissolved species in the solvent; (b) the > orientation energy of partial orientation of the dipoles; (c) the isotrop= ic > interaction energy of electrostatic and dispersion origin; and (d) the > anisotropic energy of specific interactions, e.g. hydrogen bonds, > donor-acceptor interactions etc." > However, I calculated Ni2+ cation in water, please see this part of outpu= t: > > Variational PCM results > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > (a.u.) =3D -1507.146446 > (a.u.) =3D -1507.887943 > Total free energy in solution: > with all non electrostatic terms (a.u.) =3D -1507.882504 > -------------------------------------------------------------------- > (Polarized solute)-Solvent (kcal/mol) =3D -465.30 > -------------------------------------------------------------------- > Cavitation energy (kcal/mol) =3D 3.41 > Dispersion energy (kcal/mol) =3D 0.00 > Repulsion energy (kcal/mol) =3D 0.00 > Total non electrostatic (kcal/mol) =3D 3.41 > -------------------------------------------------------------------- > > Did you mean by solvation energy the highlight one? > Thanks, > CCG1 > > =C8=CA=C7=D1=ED=CE 13 =E3=C7=ED=E6, 2010 05:08 =D5=A1 =CC=C7=C1 =E3=E4 Ah= med El-Nahas amelnahas!=3D! > hotmail.com >: > >> >> People add solvent (in term of PCM) to the reactants and products; the >> solvation of bar metal ions releases a lot of kcal/mols at the expense >> of the total reaction enthalpy. If you look at the energy of solvation o= f >> the ligand, metal ion and complex, separately, you will realize this fac= t. I >> have a similar situation with a difference of about 150-300 kcal/mol bet= ween >> gas phase and solution, depending of your metal ion, ligand and the >> resulting complex. >> >> >> >> =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 >> *Professor Ahmed El-Nahas* >> *Physical Chemistry (Quantum Chemistry)* >> *Computational Chemistry Unit (CCU)* >> *Chemistry Department* >> *Faculty of Science* >> *El-Menoufia University* >> *Shebin El-Kom* >> *Egypt* >> *Email: amelnahas:_:hotmail.com* >> *Tel: +2-016-4607974; +81-09062124377* >> =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 >> >> >> >> >> > From: owner-chemistry:_:ccl.net >> > To: amelnahas:_:hotmail.com >> > Subject: CCL: Binding Enthalpy in vacuum and solvent >> > Date: Wed, 12 May 2010 09:29:15 -0400 >> > >> > >> > Sent to CCL by: "Comp Chem Group " [compchemgroup1 a gmail.com] >> > Dear All, >> > By surveying on "Interaction Enthalpy" of transition metal complex in >> vacuum and solvent (PCM or other model), I found in all cases that the >> enthalpy change in vacuum is larger than that solvent. For example, if d= elta >> H in vacuum=3D -1000 kcal/mol, in solvent=3D -200 kcal/mol. Could anyone= explain >> why? >> > Regards, >> > CCG1 >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> >! ; >> > >> > >> > >> > >> >> ------------------------------ >> Hotmail: Trusted email with powerful SPAM protection. Sign up now. >> > --=20 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 --0016e6db2ad42418d304868f7548 Content-Type: text/html; charset=windows-1256 Content-Transfer-Encoding: quoted-printable Dear=A0CCG1
You can use SCFVAC (in G03) or DOVACUMM (in G09) options in= SCRF =A0to calculate delta G solvation energy directly in one calculation.= This option performs one calculation in gas phase.
Note: these o= ptions are defined by "read" card in SCRF.

Sincerely;
M. Ibrahim

2010/5/14 CompChem Group compchemgroup1 _ gmail.com <owner-chemistry ~~ ccl.net>

Dear Professor Ahmed El-Nahas and all
Thanks for reply. According to= IUPAC, the defination of solvation energy is "The change=20 in Gibbs energy when an ion or molecule is transferred from a=20 vacuum=20 (or the gas phase) to a solvent. The main contributions to=20 the solvation=20 energy come from: (a) the cavitation energy of formation of=20 the=20 hole which preserves the dissolved species in the solvent; (b) the=20 orientation energy of partial orientation of the dipoles; (c)=20 the isotropic=20 interaction energy of electrostatic and dispersion origin;=20 and (d)=20 the anisotropic energy of specific interactions, e.g. hydrogen =20 bonds, donor-acceptor interactions etc."
However, I c= alculated Ni2+ cation in water, please see this part of output:

Vari= ational PCM results
=A0=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D
=A0<psi(f)|=A0=A0 H=A0=A0=A0 |psi(f)>=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (a.u.) =3D=A0=A0 -15= 07.146446
=A0<psi(f)|H+V(f)/2|psi(f)>=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0 (a.u.) =3D=A0=A0 -1507.887943
=A0Total free energy in= solution:
=A0 with all non electrostatic terms=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 (a.u.) =3D=A0=A0 -1507.882504
=A0-----------------------------= ---------------------------------------
=A0(Polarized solute)-Sol= vent=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (kcal/mol) =3D=A0=A0=A0 -465= .30
=A0----------------------------------------------------------= ----------
=A0Cavitation energy=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (kcal/mol) =3D=A0=A0=A0=A0=A0=A0 3.41
=A0Dispersion energy=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 (kcal/mol) =3D=A0=A0=A0=A0=A0=A0 0.00
=A0Repulsion energ= y=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (= kcal/mol) =3D=A0=A0=A0=A0=A0=A0 0.00
=A0Total non electrostatic=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (kcal/mol) =3D=A0=A0=A0=A0=A0=A0= 3.41
------------------------------------------------------------------= --

Did you mean by solvation energy the highlight one?
Thanks,
CCG1=

=C8=CA=C7=D1=ED=CE 13 = =E3=C7=ED=E6, 2010 05:08 =D5=A1 =CC=C7=C1 =E3=E4 Ahmed El-Nahas amelnahas!= =3D!hotmail.com <owner-chemistry^_^ccl.net>:

=A0
= People add solvent (in term of PCM) to the reactants and products; the solv= ation of=A0bar metal ions=A0releases=A0a lot of kcal/mols at the expense of= =A0the=A0total reaction enthalpy. If you look at the energy of solvation of= the ligand, metal ion and complex, separately, you will realize this fact.= I have a similar situation with a difference of about 150-300 kcal/mol bet= ween gas phase and solution, depending of your metal ion, ligand and the re= sulting complex.
= =A0

=A0
=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
Professor Ahmed El-Nahas
Physical Chemistry (Quantum Chemistry)=
Computational Chemistry= Unit (CCU)
= Chemistry Department
Faculty of Science
El-Menoufia University<= /b>
Shebin El= -Kom
Egyp= t
Email: amelnahas:_:hotmail.com
= Tel: +2-016-4607974; +81-09062124377
=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

=A0
> From: owner-chemistry:_:ccl.net
> To: amelnahas:_:hotmail.com
> Subject: CCL: Bi= nding Enthalpy in vacuum and solvent
> Date: Wed, 12 May 2010 09:29:15 -0400
>
>
> Sent t= o CCL by: "Comp Chem Group " [compchemgroup1 a gmail.com]
> Dear All,
> By su= rveying on "Interaction Enthalpy" of transition metal complex in = vacuum and solvent (PCM or other model), I found in all cases that the enth= alpy change in vacuum is larger than that solvent. For example, if delta H = in vacuum=3D -1000 kcal/mol, in solvent=3D -200 kcal/mol. Could anyone expl= ain why?
> Regards,
> CCG1
>
>
>
>
>
&g= t;
>
>
>
>
>
>
>
>
&g= t;
>
>
>
>
>
>
>
>
>
>
&gt! ;
>
>
>
>

Hotmail: Trust= ed email with powerful SPAM protection. Sign up now.

--
=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi= ty of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim ~~ compche= m.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623= 42601

--0016e6db2ad42418d304868f7548-- From owner-chemistry@ccl.net Fri May 14 17:11:00 2010 From: "Joaquin Barroso Flores joaco_barroso .. yahoo.com" To: CCL Subject: CCL: Help with halogen bonding Message-Id: <-41857-100514130218-2681-Dh6jtSH7jJ41ge0pV7ARCw!^!server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Type: multipart/alternative; boundary="0-1757933950-1273856525=:21562" Date: Fri, 14 May 2010 10:02:05 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso()yahoo.com] --0-1757933950-1273856525=:21562 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello =0ARemember atoms are not hard spheres=A0and that Allcock's definitio= n of secondary bonding as rij=A0<=A0(rvdwi + rvdwj) is an arbitrary one=A0b= ased on=A0a very intuitive idea of having these radii as the boundaries of = atoms.=A0Such a definition was created to account for intermolecular intera= ctions in the solid state.=A0In short I think you might still call them hal= ogen bonds but at the same time you should perform some population analysis= to assess the electron density between the interacting atoms so you know w= hether or not you have a bond between them. =0ASome time ago=A0we wrote a p= aper on the topic. =0A=0ABarroso-Flores, J. et al J. Organomet. Chem. 689 (= 2004) 2096-2102 doi:10.1016/j.jorganchem.2004.03.035=0A=0AHope this helps= =0A=0AJoaqu=EDn=0A=A0=0A=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=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0AJoaquin Barroso-Flores, Ph. D.=0A= Centro Conjunto de Investigacion en Quimica Sustentable=0AInstituto de Quim= ica=0AUNAM =0A=0A-> http://joaquinbarroso.wordpress.com=0A=0Ajoaquin.barros= o''a''gmail.com =0A=0A"Blogastronom=EDa": http://joaquinbarroso.blogspot.co= m =0A=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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D =0A=0A=0A=0A=0A________________________________=0ADe:= Mariya al-Rashida maria_al_rashida(!)hotmail.com = =0APara: "Flores, Joaquin Barroso " =0AEnv= iado: viernes, 14 de mayo, 2010 2:28:21=0AAsunto: CCL: Help with halogen bo= nding=0A=0A=0ASent to CCL by: "Mariya=A0 al-Rashida" [maria_al_rashida~!~ho= tmail.com]=0AHello everyone=0A=0AIm currently investigating crystal structu= res of some organic halogen compounds. I'm pretty sure i've come across som= e "Halogen Bonds" [haolgen bonds are non covalent interactions C-X...Y wher= e X =3D halogen acting as lewis acceptor and Y =3D N or O acting lewis base= ]. What i know from literature, both exp and theoretical is that these inte= ractions are found at distances equal to or slightly shorter than sum of va= n der wall radii. Whereas i'm getting these interactions at distance which = is equal to sum of van der wall radii + 0.1. Does this still count as a hal= ogen bond ??? Or should it be rather a weak type of haolgen bonding?=0A=0AA= lso does anyone know of any relavent theoretical literature for halogen bon= ding=0A=0AYour comments will be highly apreciated=0AMariiya=0A=0A=0A=0A-=3D= This is automatically added to each message by the mailing script =3D-=0AT= o recover the email address of the author of the message, please change=0At= he strange characters on the top line to the /./ sign. You can also=0Alook up= the X-Original-From: line in the mail header.=0A=0AE-mail to subscribers: = CHEMISTRY/./ccl.net or use:=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send= _ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST/./ccl.net or us= e=0A=A0 =A0 =A0=0A=0ASubscr= ibe/Unsubscribe: =0A=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.shtm= l=0A=0A=0A=0AJob: htt= p://www.ccl.net/jobs =0AConferences: http://server.ccl.net/chemistry/announ= cements/conferences/=0A=0ASearch Messages: http://www.ccl.net/chemistry/sea= rchccl/index.shtml=0A=0AIf your mail bounces from CCL with 5.7.1 error, che= ck:=0A=A0 =A0 =A0=0A=0ARTFI: http://www.ccl= .net/chemistry/aboutccl/instructions/=0A=0A=0A --0-1757933950-1273856525=:21562 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A
Hello
=0A
Remember atoms are n= ot hard spheres and that Allcock's definition of secondary bonding as = rij < (rvdwi + rvdwj) is an arbitrary one based on a= very intuitive idea of having these radii as the boundaries of atoms. = ;Such a definition was created to account for intermolecular interactions i= n the solid state. In short I think you might still call them halogen = bonds but at the same time you should perform some population analysis to a= ssess the electron density between the interacting atoms so you know whethe= r or not you have a bond between them.
=0A
Some time ago we = wrote a paper on the topic.
=0A

=0A
Barroso-Flore= s, J. et al J. Organomet. Chem. 689 (2004) 2096-2102 doi:10.1016/j.jorganch= em.2004.03.035
=0A

=0A
Hope this helps
=0A
=0A
Joaqu=EDn
=0A

=0A
=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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
Joaquin Barroso-Flores, Ph. D.
Centro Conjunto de Investigacion en Q= uimica Sustentable
Instituto de Quimica
UNAM
=0A
-> ht= tp://joaquinbarroso.wordpress.com

=0A
joaquin.barroso''a''gmai= l.com

=0A
"Blogastronom=EDa": http://joaquinbarroso.blogspot.= com
=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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D =0A

=0A

=0A
=0A
=0A= De: Mariya al-Rashida maria_al_rashida(!)hotmail.com <owner-c= hemistry/./ccl.net>
Para: "Flores, Joaquin Barroso " <joaco_barroso/./yahoo.com>
Enviado: viernes, 14 de mayo,= 2010 2:28:21
Asunto: CC= L: Help with halogen bonding

Sent to CCL by: "Mariya = ; al-Rashida" [maria_al_rashida~!~hotmail.com]
Hello everyone

Im = currently investigating crystal structures of some organic halogen compound= s. I'm pretty sure i've come across some "Halogen Bonds" [haolgen bonds are= non covalent interactions C-X...Y where X =3D halogen acting as lewis acce= ptor and Y =3D N or O acting lewis base]. What i know from literature, both= exp and theoretical is that these interactions are found at distances equa= l to or slightly shorter than sum of van der wall radii. Whereas i'm getting these interactions at distance which i= s equal to sum of van der wall radii + 0.1. Does this still count as a halo= gen bond ??? Or should it be rather a weak type of haolgen bonding?

= Also does anyone know of any relavent theoretical literature for halogen bo= nding

Your comments will be highly apreciated
Mariiya

=
-=3D This is automatically added to each message by the mailing script = =3D-
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=0A=0A=0A=0A = --0-1757933950-1273856525=:21562-- From owner-chemistry@ccl.net Fri May 14 17:46:01 2010 From: "CompChem Group compchemgroup1---gmail.com" To: CCL Subject: CCL: Effect of sulphate ions on the preparation of the enzyme Message-Id: <-41858-100514141506-22399-dUCGwPz5JgwMk+ZhzLiDsQ- -server.ccl.net> X-Original-From: CompChem Group Content-Type: multipart/alternative; boundary=0016363ba1f42bb591048691da3c Date: Fri, 14 May 2010 19:14:55 +0100 MIME-Version: 1.0 Sent to CCL by: CompChem Group [compchemgroup1]=[gmail.com] --0016363ba1f42bb591048691da3c Content-Type: text/plain; charset=ISO-8859-1 Dear Basma, Removal of sulfate ions from BDP file is sometime * necessary* because they often come from the buffer used in crystalization. Anyhow, you have to ensure that the sulfate ions do not belong to the intrested protein stucure. My recommendation is to read the experimental paper of extraction of this protein, go to BDP website, you may found information. I think all points you asked are very logic and need to answers. Regards, CCG1 2010/5/14 Mahmoud A. A. Ibrahim m.ibrahim() compchem.net < owner-chemistry[a]ccl.net> > Dear Basma > I don't see why you are doing that, replacing sulfate ion with water > molecules!!! > Removing an ion close to the active site affects the binding efficiency, > because of electrostatic interactions. I remember once I was working on a > biosystem, during files preparation step using xleap (inside AMEBR), One Na+ > ion has been added mistakely by xleap at 7 Ang. far apart from the active > site, leaded to changing the binding mode. So, I believe removing sulfate > ion (-2 charge) will dis-stabilize your system without any doubt. > You may like to post why you want to do that, and there should be other > tricks to solve your problem rather than removing the sulfate ion. > Sincerely; > M. Ibrahim > > > On Wed, May 12, 2010 at 10:50 AM, Basma Ghazal basmaghazal**ymail.com < > owner-chemistry[*]ccl.net> wrote: > >> >> Hello, >> Because I am still beginner in the field I need the advices in the >> following items: >> >> The PDB structure that I use for docking have two sulphate ions, one of >> them is very close to the active site and make interaction with it is >> residue. The other is far from it. >> 1- If I removed the sulfate ions from the pocket containing the active >> site am I need to do partial optimization of this part? Because removing >> them give more compact pocket by partial optimization. >> 2- Instead, I think to add two water molecules in the same places of two >> sulfate ions, do you think this way will compensate the removing of sulfate >> ions to avoid the conformational change during the docking? >> 3- But the sulfate ions are *charged* and replacement them by explicit >> water molecules may not be equivalent, right? >> >> I look forward to any response. >> Thanks, >> Basma >> >> >> >> > > > -- > 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 > --0016363ba1f42bb591048691da3c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Basma,
Removal of sulfate ions from BDP file is so= metime=A0 necessary because they often come from the buffer used in = crystalization. Anyhow, you have to ensure that the sulfate ions do not bel= ong to the intrested protein stucure. My recommendation is to read the expe= rimental paper of extraction of this protein, go to BDP website, you may fo= und information. I think all points you asked are very logic and need to an= swers.=A0
Regards,
CCG1

2010/5/14 Mahmoud A. A. = Ibrahim m.ibrahim() compchem.net <owner-chemistry[a]= ccl.net>

Dear Basma
I = don't see why you are doing that, replacing sulfate ion with water mole= cules!!!

Removing an ion close to the active site affects the binding efficienc= y, because of electrostatic =A0 interactions. I remember once I was working= on a biosystem, during files preparation step using xleap (inside AMEBR), = One Na+ ion has been added mistakely by xleap at 7 Ang. far apart from the = active site, leaded to changing the binding mode. So, I believe removing su= lfate ion (-2 charge) will=A0dis-stabilize=A0your system without any doubt.=

You may like to post why you want to do that, and there should be othe= r tricks to solve your problem rather than removing the sulfate ion.
<= div>Sincerely;
M. Ibrahim

On Wed, May 12, 2010 at 10:50 AM, Basma Ghazal basmaghazal**ymail.com <owner-chemistry[*]c= cl.net> wrote:

Hello, Because I am still=A0beginner in the field I need the advices in the following items:

The PDB st= ructure that I use for docking have two sulphate ions, one of them is very close to the active site and make interaction with it is residue. The other is far from it.
1- If I removed the sulfate ions from the pocket containing the active site am I ne= ed to do partial optimization of this part? Because removing them give more compact pocket by partial optimization.
2- Instead, I think to add two water molecules in the same places of two sulfate ions, do you think th= is way will compensate the removing of sulfate ions to avoid the conformationa= l change during the docking?
3- But the sulfate ions are charged and replacement them by explicit water molecules may not be equivalent, I look forward to any response.
Thanks,
Basma

--
=A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0= The University of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim[*]compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: www.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 Fax No.: +20862342601

--0016363ba1f42bb591048691da3c-- From owner-chemistry@ccl.net Fri May 14 18:21:00 2010 From: "mohamed aish mhmdaish:-:yahoo.com" To: CCL Subject: CCL: Binding Enthalpy in vacuum and solvent Message-Id: <-41859-100514131241-10019-4IDBzyZmjgCJGedZuwhJXA() server.ccl.net> X-Original-From: mohamed aish Content-Type: multipart/alternative; boundary="0-17952624-1273853537=:85143" Date: Fri, 14 May 2010 09:12:17 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: mohamed aish [mhmdaish[*]yahoo.com] --0-17952624-1273853537=:85143 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable =0A=0AHi;=0A=0AThe highlight=0Aone is the total electrostatic. =0A=0ADGsolv= =0A=3D total electrostatic + total non-electrostatic=0A=0A=C2=A0=0A=0AGood = Lock =0A=0A=0A=0A=0A --- On Fri, 5/14/10, CompChem Group compchemgroup1 _ gmail.com wrote: > From: CompChem Group compchemgroup1 _ gmail.com Subject: CCL: Binding Enthalpy in vacuum and solvent To: "Aish, Mhmd Ahmd " Received: Friday, May 14, 2010, 12:16 PM Dear Professor=0A Ahmed El-Nahas and all Thanks for reply. According to IUPAC, the defination of solvation energy is= "The change =0A in Gibbs energy when an ion or molecule is transf= erred from a =0Avacuum =0A (or =09the gas phase) to a solvent. The= main contributions to =0Athe solvation =0A energy come from: (a) = the =09cavitation energy of formation of =0Athe =0A hole which pre= serves the dissolved species in the solvent; (b)=0A =09the =0A ori= entation energy of partial orientation of the dipoles; (c) =0Athe isotropic= =0A interaction energy of =09electrostatic and dispersion origin;= =0Aand (d) =0A the anisotropic energy of specific interactions, e= .g. =09hydrogen=0A =0A bonds, donor-acceptor interactions etc." However, I calculated Ni2+ cation in water, please see this part of output: Variational PCM results =C2=A0=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 (a.u.) =3D=C2=A0=C2=A0 -1507.146446 =0A=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 (a.u.) =3D=C2=A0=C2=A0 -1507.887943 =C2=A0Total free energy in solution: =C2=A0 with all non electrostatic terms=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (a.u.) =3D=C2=A0=C2=A0 -1507.882504 =C2=A0-------------------------------------------------------------------- =0A=C2=A0(Polarized solute)-Solvent=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (kcal/mol) =3D=C2=A0=C2=A0=C2= =A0 -465.30 =C2=A0-------------------------------------------------------------------- =C2=A0Cavitation energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 (kcal/mol) =3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 3.41 =0A=C2=A0Dispersion energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 (kcal/mol) =3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00 =C2=A0Repulsion energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 (kcal/mol) =3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00 =C2=A0Total non electrostatic=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (kcal/mol) =3D=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 3.41 -------------------------------------------------------------------- =0A Did you mean by solvation energy the highlight one? Thanks,=20 CCG1 =D8=A8=D8=AA=D8=A7=D8=B1=D9=8A=D8=AE 13 =D9=85=D8=A7=D9=8A=D9=88, 2010 05:0= 8 =D8=B5=D8=8C =D8=AC=D8=A7=D8=A1 =D9=85=D9=86 Ahmed El-Nahas amelnahas!=3D= !hotmail.com :=0A=0A=0A=0A=0A=0A=C2=A0 =0APeople add solvent (in term of PCM) to the reactants and products; the s= olvation of=C2=A0bar metal ions=C2=A0releases=C2=A0a lot of kcal/mols at th= e expense of=C2=A0the=C2=A0total reaction enthalpy. If you look at the ener= gy of solvation of the ligand, metal ion and complex, separately, you will = realize this fact. I have a similar situation with a difference of about 15= 0-300 kcal/mol between gas phase and solution, depending of your metal ion,= ligand and the resulting complex.=20 =0A=0A=C2=A0 =0A =C2=A0 =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 Professor Ahmed El-Nahas Physical Chemistry (Quantum Chemistry) =0AComputational Chemistry Unit (CCU) Chemistry Department Faculty of Science =0AEl-Menoufia University Shebin El-Kom Egypt =0AEmail: amelnahas:_:hotmail.com Tel: +2-016-4607974; +81-09062124377 =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 =0A =C2=A0 > From: owner-chemistry:_:ccl.net > To: amelnahas:_:hotmail.com > Subject: CCL: Binding Enthalpy in vacuum and solvent =0A> Date: Wed, 12 May 2010 09:29:15 -0400 >=20 >=20 > Sent to CCL by: "Comp Chem Group " [compchemgroup1 a gmail.com] > Dear All, > By surveying on "Interaction Enthalpy" of transition metal complex in vac= uum and solvent (PCM or other model), I found in all cases that the enthalp= y change in vacuum is larger than that solvent. For example, if delta H in = vacuum=3D -1000 kcal/mol, in solvent=3D -200 kcal/mol. Could anyone explain= why?=20 =0A> Regards, > CCG1 >=20 >=20 >=20 > > > > >=20 > > >=20 > > >=20 > > >=20 > >=20 > > >=20 > =0A>=20 > >!=0A ; >=20 > >=20 >=20 =09=09 =09 =09=09 =20 Hotmail: Trusted email with powerful SPAM protection. Sign up now.=0A=0A=0A= =0A --0-17952624-1273853537=:85143 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable <= /tr>
=0A=0A
Hi;
=0A=0A
The highlight=0Aone is the total electrostatic= .
=0A=0A
DG_solv= =0A=3D total electrostatic + total non-electrostatic
= =0A=0A
<= /o:p>
=0A=0A
<= span style=3D"font-size:14.0pt;=0Amso-bidi-font-size:12.0pt;font-family:Ari= al">Good Lock
=0A=0A=0A=0A=0A
--= - On Fri, 5/14/10, CompChem Group compchemgroup1 _ gmail.com <owne= r-chemistry _ ccl.net> wrote:

From= : CompChem Group compchemgroup1 _ gmail.com <owner-chemistry _ ccl.net>=
Subject: CCL: Binding Enthalpy in vacuum and solvent
To: "Aish, Mhmd= Ahmd " <mhmdaish _ yahoo.com>
Received: Friday, May 14, 201= 0, 12:16 PM

Dear Professo= r=0A Ahmed El-Nahas and all
Thanks for reply. Accordin= g to IUPAC, the defination of solvation energy is "The change =0A = in Gibbs energy when an ion or molecule is transferred from a =0Avacuum =0A= (or =09the gas phase) to a solvent. The main contributions to =0A= the solvation =0A energy come from: (a) the =09cavitation energy o= f formation of =0Athe =0A hole which preserves the dissolved speci= es in the solvent; (b)=0A =09the =0A orientation energy of partial= orientation of the dipoles; (c) =0Athe isotropic =0A interaction = energy of =09electrostatic and dispersion origin; =0Aand (d) =0A t= he anisotropic energy of specific interactions, e.g. =09hydrogen=0A =0A = bonds, donor-acceptor interactions etc."
However, I calculat= ed Ni2+ cation in water, please see this part of output:

Variational= PCM results
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D
<psi(f)|   H    |ps= i(f)>           &= nbsp;         (a.u.) =3D  = ; -1507.146446
=0A <psi(f)|H+V(f)/2|psi(f)>   =             &nb= sp;     (a.u.) =3D   -1507.887943
To= tal free energy in solution:
with all non electrostatic terms&nbs= p;           (a.u.) =3D&n= bsp; -1507.882504
------------------------------------------= --------------------------
=0A (Polarized solute)-Solvent     &nbs= p;         (kcal/mol) =3D &nbs= p; -465.30
------------------------------------------= --------------------------
Cavitation energy   &nbs= p;            &= nbsp;       (kcal/mol) =3D   &= nbsp;   3.41
=0A Dispersion energy    = ;            &n= bsp;       (kcal/mol) =3D   &n= bsp;   0.00
Repulsion energy    &nbs= p;            &= nbsp;       (kcal/mol) =3D   &= nbsp;   0.00
Total non electrostatic   &n= bsp;            = ; (kcal/mol) =3D       3.41
--------= ------------------------------------------------------------
=0A
Did = you mean by solvation energy the highlight one?
Thanks,
CCG1

=
=D8=A8=D8=AA=D8=A7=D8=B1=D9=8A= =D8=AE 13 =D9=85=D8=A7=D9=8A=D9=88, 2010 05:08 =D8=B5=D8=8C =D8=AC=D8=A7=D8= =A1 =D9=85=D9=86 Ahmed El-Nahas amelnahas!=3D!hotmail.com <= owner-chemistry= ^_^ccl.net>:
=0A
=0A=0A=0A=0A
=0A
=0APeople add solvent (in term= of PCM) to the reactants and products; the solvation of bar metal ion= s releases a lot of kcal/mols at the expense of the tot= al reaction enthalpy. If you look at the energy of solvation of the ligand,= metal ion and complex, separately, you will realize this fact. I have a si= milar situation with a difference of about 150-300 kcal/mol between gas pha= se and solution, depending of your metal ion, ligand and the resulting comp= lex.
=0A=0A
=0A

=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
<= b>Professor Ahmed El-Nahas
Physical Chemistry (Quantum Chemistry)
=0A<= font size=3D"3" face=3D"Garamond, Times, Serif">Computational Chemistry = Unit (CCU)
<= b>Chemistry Department
Faculty of Science
=0AEl-Menoufia University
Shebin El-Kom
Egypt
=0AEmail: amelnahas:_:hotmail.com
Tel: +2-016-4607974; +81-09062124377=
=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
=0A

> From: owne= r-chemistry:_:ccl.net
> To: amelnahas:_:hotmail.com
> Subject: CCL: Binding E= nthalpy in vacuum and solvent
=0A> Date: Wed, 12 May 2010 09:29:15 -0= 400
>
>
> Sent to CCL by: "Comp Chem Group " [compchemg= roup1 a gma= il.com]
> Dear All,
> By surveying on "Interaction Enthalpy= " of transition metal complex in vacuum and solvent (PCM or other model), I= found in all cases that the enthalpy change in vacuum is larger than that = solvent. For example, if delta H in vacuum=3D -1000 kcal/mol, in solvent=3D= -200 kcal/mol. Could anyone explain why?
=0A> Regards,
> CCG1=
>
>
>
>
>
>
>
>
>= ;
>
>
>
>
>
>
>
>
>= ;
>
>
>
>
>
=0A>
>
&gt!= =0A ;
>
>
>
>
=09=09 =09 =09=09
H= otmail: Trusted email with powerful SPAM protection. Sig= n up now.
=0A
=0A

--0-17952624-1273853537=:85143-- From owner-chemistry@ccl.net Fri May 14 18:56:00 2010 From: "Soren Eustis soreneustis*gmail.com" To: CCL Subject: CCL:G: Visualization of Natural Transition Orbitals (NTO) Message-Id: <-41860-100514114139-21287-5cY3l86rit5A2Rgsg74OWQ . server.ccl.net> X-Original-From: Soren Eustis Content-type: multipart/alternative; boundary="B_3356703687_16366390" Date: Fri, 14 May 2010 17:41:25 +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_3356703687_16366390 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Greetings CCl=B9ers, I have just begun to play around with the Gaussian implementation of Miller=B9s Natural Transition Orbital technique (JCP 118, 4775 (2003). Everything worked well (after a few tries) and I am able to visualize the results from my .fch file. The question/problem is that I am not 100% percent sure what the formalism is here. Is the HOMO the =8Chole=B9 and the LUMO the =8Cparticle=B9? This makes sense to me, but I could imagine other ways of representing this as well. =20 or perhaps GaussView is not recognizing the added =8CTransition=B2 orbitals tacked at the end of the .fch file: *** ETran NETS I 20 ETran NETV I 48 ETran scalars I N=3D 20 3 16 1 10 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ETran spin I N=3D 3 0 0 0 ETran sym I N=3D 3 0 0 0 ETran state values R N=3D 48 -1.66529786E+03 -1.47008050E+00 6.54162749E-02 3.48503519E-03 2.18105997E-01 -9.24974818E-03 3.82623440E-04 1.28001368E-01 6.48648777E-02 -6.69081128E-01 -1.60599753E-01 7.89170623E-02 -7.74204259E-02 -7.04496950E-02 1.54721359E-01 -1.61008131E-01 -1.66529399E+03 -8.11271006E-01 -1.85516313E-01 2.65267629E-01 1.23585532E-01 2.72696660E-02 -4.08849102E-02 1.12857587E-01 -1.55860702E-01 5.68566041E-01 3.16504680E-02 9.79011339E-02 -9.50912287E-02 2.85377462E-01 1.07275382E-01 -1.76314207E-01 -1.66528897E+03 2.80174144E-01 5.51437854E-01 3.55579492E-01 -4.52107931E-02 -8.70060853E-02 -5.50728611E-02 2.34131483E-01 -9.03618379E-01 8.38528669E-01 6.66347848E-01 -6.44756979E-02 -1.40167067E-01 3.46417072E-01 2.60159041E-01 -1.05075791E-01 I appreciate any comments or suggestions. 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_3356703687_16366390 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Re: Visualization of Natural Transition Orbitals (NTO) Greetings CCl’ers,

     I have just begun to play around with the Gau= ssian implementation of Miller’s Natural Transition Orbital technique = (JCP 118, 4775 (2003). Everything worked well (after a few tries) and = I am able to visualize the results from my .fch file.

    The question/problem is that I am not 100% percent = sure what the formalism is here. Is the HOMO the ‘hole’ an= d the LUMO the ‘particle’? This makes sense to me, but I c= ould imagine other ways of representing this as well.

   or perhaps GaussView is not recognizing the added ‘= Transition” orbitals tacked at the end of the .fch file:

***
ETran NETS           &nbs= p;            &n= bsp;        I    &nbs= p;          20
ETran NETV           &nbs= p;            &n= bsp;        I    &nbs= p;          48
ETran scalars           &= nbsp;            = ;      I   N=3D    &nbs= p;     20
           3 &= nbsp;       16     &n= bsp;     1       &nbs= p;  10           = ;1           0
           0 &= nbsp;        0    &nb= sp;      0       = ;    0         &= nbsp; 0           0            0 &= nbsp;        0    &nb= sp;      0       = ;    0         &= nbsp; 0           0            0 &= nbsp;        0
ETran spin           &nbs= p;            &n= bsp;        I   N=3D &= nbsp;        3
           0 &= nbsp;        0    &nb= sp;      0
ETran sym            = ;            &nb= sp;         I   N=3D &n= bsp;         3
           0 &= nbsp;        0    &nb= sp;      0
ETran state values          &n= bsp;            =   R   N=3D         = ; 48
-1.66529786E+03 -1.47008050E+00 6.54162749E-02 3.48503519= E-03 2.18105997E-01
-9.24974818E-03 3.82623440E-04 1.28001368E-01 6.486= 48777E-02 -6.69081128E-01
-1.60599753E-01 7.89170623E-02 -7.74204259E-02 -7.04496950E-02 = 1.54721359E-01
-1.61008131E-01 -1.66529399E+03 -8.11271006E-01 -1.85516313E-01 = ;2.65267629E-01
  1.23585532E-01 2.72696660E-02 -4.08849102E-02 1.128= 57587E-01 -1.55860702E-01
  5.68566041E-01 3.16504680E-02 9.79011339E-02 -9.509= 12287E-02 2.85377462E-01
  1.07275382E-01 -1.76314207E-01 -1.66528897E+03 2.80174144= E-01 5.51437854E-01
  3.55579492E-01 -4.52107931E-02 -8.70060853E-02 -5.50728611E-02 = 2.34131483E-01
-9.03618379E-01 8.38528669E-01 6.66347848E-01 -6.44756979= E-02 -1.40167067E-01
  3.46417072E-01 2.60159041E-01 -1.05075791E-01

I appreciate any comments or suggestions.

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_3356703687_16366390-- From owner-chemistry@ccl.net Fri May 14 19:31:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim%x%compchem.net" To: CCL Subject: CCL: Help with halogen bonding Message-Id: <-41861-100514110015-9652-mMhCc7zLGCfLZ0QczuOQMA ~~ server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016367fa7603a7f5a04868f2154 Date: Fri, 14 May 2010 16:00:01 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim . compchem.net] --0016367fa7603a7f5a04868f2154 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Mariya The distance between the two bonded atoms should equal to or less than the sum of the VDW radii of the atoms. NBO and AIM could be used as a further analysis to prove if there is a bond or not. Halogen bonds are weak bonds, you should use MP2 (better) or B3LYP (not recommended because of lacking of dispersion in DFT; but one paper shows a comparison between performance of these two methods regarding to halogen bonding, and proved that both of them are giving good results) with big basis set with diffuse functions, most of the papers done on halogen bonds used B3LYP/aug-cc-pVDZ. Your calculation shaw that the distance between the halogen atom and the Y atom is around VDW + 0.1, I think you didn't use a big basis set. If you ar= e studying Flourine or Chlorine atom (X), you should use 6-311+G** at least a= s a basis set. For Bromine or Iodine, you should use aug-cc-pVDZ basis set to include relativistic effect. There are many papers/reviews on this subject, you may like to have a look on the following: * Fourmigu=E9, M. "Halogen bonding: Recent advances." Current Opinion in So= lid State and Materials Science 13(3-4): 36-45. * Auffinger, P., F. A. Hays, et al. (2004). "Halogen bonds in biological molecules." Proceedings of the National Academy of Sciences of the United States of America 101(48): 16789-16794. Kov=E1cs, A. and Z. Varga (2006). "Halogen acceptors in hydrogen bonding." Coordination Chemistry Reviews 250(5-6): 710-727. * Politzer, P., P. Lane, et al. (2007). "An overview of halogen bonding." Journal of Molecular Modeling 13(2): 305-311. Sincerely; M. Ibrahim On Fri, May 14, 2010 at 8:28 AM, Mariya al-Rashida maria_al_rashida(!) hotmail.com wrote: > > Sent to CCL by: "Mariya al-Rashida" [maria_al_rashida~!~hotmail.com] > Hello everyone > > Im currently investigating crystal structures of some organic halogen > compounds. I'm pretty sure i've come across some "Halogen Bonds" [haolgen > bonds are non covalent interactions C-X...Y where X =3D halogen acting as > lewis acceptor and Y =3D N or O acting lewis base]. What i know from > literature, both exp and theoretical is that these interactions are found= at > distances equal to or slightly shorter than sum of van der wall radii. > Whereas i'm getting these interactions at distance which is equal to sum = of > van der wall radii + 0.1. Does this still count as a halogen bond ??? Or > should it be rather a weak type of haolgen bonding? > > Also does anyone know of any relavent theoretical literature for halogen > bonding > > Your comments will be highly apreciated > Mariiya > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 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*o*compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016367fa7603a7f5a04868f2154 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Mariya
The distance between the two bonded atoms should equal to o= r less than the sum of the VDW radii of the atoms. NBO and AIM could be use= d as a further analysis to prove if there is a bond or not.
Halog= en bonds are weak bonds, you should use MP2 (better) or B3LYP (not recommen= ded=A0because=A0of lacking=A0of dispersion in DFT; but one paper shows a co= mparison between performance of these two methods=A0regarding=A0to halogen = bonding, and proved that both of them are giving good results) with big=A0b= asis=A0set with diffuse functions, most of the papers done on halogen bonds= used B3LYP/aug-cc-pVDZ.

Your calculation shaw that the distance between the halogen atom and t= he Y atom is around VDW + 0.1, I think you didn't use a big basis set. = If you are studying Flourine or Chlorine atom (X), you should use 6-311+G**= at least as a basis set. For Bromine or Iodine, you should use aug-cc-pVDZ= basis set to include=A0relativistic=A0effect.

There are many papers/reviews on this subject, you may like to have a = look on the following:

* Fourmigu=E9, M. "Hal= ogen bonding: Recent advances." Current Opinion in Solid State and Mat= erials Science 13(3-4): 36-45.

* Auffinger, P., F. A. Hays, et al. (2004). "Halogen bonds in bio= logical molecules." Proceedings of the National Academy of Sciences of= the United States of America 101(48): 16789-16794.
Kov=E1cs, A. = and Z. Varga (2006). "Halogen acceptors in hydrogen bonding." Coo= rdination Chemistry Reviews 250(5-6): 710-727.

* Politzer, P., P. Lane, et al. (2007). "An overview of halogen b= onding." Journal of Molecular Modeling 13(2): 305-311.
=A0
Sincerely;
M. Ibrahim=A0

On Fri, May 14, 2010 at 8:28 AM, Mariya al-Rashida maria_al_rashida(!)hotmail.com <owner-c= hemistry*o*ccl.net> wrote:

Sent to CCL by: "Mariya =A0al-Rashida" [maria_al_rashida~!~hotmail.com]
Hello everyone

Im currently investigating crystal structures of some organic halogen compo= unds. I'm pretty sure i've come across some "Halogen Bonds&quo= t; [haolgen bonds are non covalent interactions C-X...Y where X =3D halogen= acting as lewis acceptor and Y =3D N or O acting lewis base]. What i know = > from literature, both exp and theoretical is that these interactions are fo= und at distances equal to or slightly shorter than sum of van der wall radi= i. Whereas i'm getting these interactions at distance which is equal to= sum of van der wall radii + 0.1. Does this still count as a halogen bond ?= ?? Or should it be rather a weak type of haolgen bonding?

Also does anyone know of any relavent theoretical literature for halogen bo= nding

Your comments will be highly apreciated
Mariiya

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=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi= ty of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
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=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

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--0016367fa7603a7f5a04868f2154-- From owner-chemistry@ccl.net Fri May 14 20:06:00 2010 From: "David Hose anthrax_brothers^hotmail.com" To: CCL Subject: CCL:G: Freq and Stability Message-Id: <-41862-100514162900-30529-l0o1/zYzWwGvVfzY6L4t+Q],[server.ccl.net> X-Original-From: "David Hose" Date: Fri, 14 May 2010 16:28:58 -0400 Sent to CCL by: "David Hose" [anthrax_brothers(_)hotmail.com] Anthony, You might want to read Chris Cramer's posting about this from 2007. http://ftp.ccl.net/chemistry/resources/messages/2007/06/14.012-dir/index.html You'll also find some other useful tips in the days prior to Chris' posting. > From personal experience, using a finer integration grid (int=ultrafine in G03) solves the problem of a number of small imaginary (<50 cm-1) frequencies. However, you'll have to rerun all of other calculations for your series of compounds with the same grid size if you want to compare energies. Also, you'll have to take a hit on computational speed. Regards, Dave. ---------------- Dear CCL, I've been running geometry optimizations and found stationary points. I have also been using SCF = QC (also UB3LYP/6-311+G(d,p) NOSYMM). How can I be sure that my final answer is a local minimum? When I perform a frequency job after the optimization, I sometimes obtain imaginary frequencies, suggesting an nth-order saddle point (n is the number of imaginary frequencies). Does this also have to do with the stability of my wavefunction? I have used the keyword Stable=Opt for verification. But I find that I can have both a stable wavefunction and imaginary frequencies. How do I then find true local minima? Also, is it possible to run both a STABLE and geometry OPT job with the same route? Or do I have to use the Link1 keyword? If so, is it possible to copy my checkpoint file through the route section? Thanks Anthony