From owner-chemistry@ccl.net Mon Jun 29 00:32:01 2015 From: "Abbey Meprathu Philip abbeyphilip88(_)gmail.com" To: CCL Subject: CCL:G: Transition density Message-Id: <-51476-150629002815-24861-ZDfCGHKfKMaFXEGddkFELQ..server.ccl.net> X-Original-From: "Abbey Meprathu Philip" Date: Mon, 29 Jun 2015 00:28:14 -0400 Sent to CCL by: "Abbey Meprathu Philip" [abbeyphilip88(0)gmail.com] Dear all, I am trying to generate the transition densities for a cluster of molecules (8-12 molecules) in a crystal using Gaussian software. I'm planning to take the co-ordinates of the molecules in the crystal packing and input them in Gaussian and use the following commands. ___________________________________________________________________________ # td=(singlets,nstates=12) b3lyp/6-311++g(2d,2p) geom=connectivity scf=(convergence=6,maxcycle=512) ___________________________________________________________________________ Is this a correct method to calculate the transition density for more than one molecule. And will this lead to the transition density of entire ensemble as whole or on the individual molecules of the crystal packing? Regards, Abbey From owner-chemistry@ccl.net Mon Jun 29 08:41:01 2015 From: "Frank Oellien frank.oellien]-[gmail.com" To: CCL Subject: CCL: EuCO-CC 2015 - Scientific Program / Early Bird Registration Message-Id: <-51477-150629083934-26979-9/BO6zVaZTSJV6IXPsFC1g\a/server.ccl.net> X-Original-From: Frank Oellien Content-Type: multipart/alternative; boundary=001a11427bc880b91d0519a7615c Date: Mon, 29 Jun 2015 14:39:29 +0200 MIME-Version: 1.0 Sent to CCL by: Frank Oellien [frank.oellien(a)gmail.com] --001a11427bc880b91d0519a7615c Content-Type: text/plain; charset=UTF-8 Dear Colleagues, We are pleased to present the final program of the *10th European Conference on Computational Chemistry* (www.euco-cc-2015.org) to be hold in Fulda, Germany August 31 - September 3, 2015. The whole program is available online: http://www.euco-cc-2015.org/programme.html Please consider that the deadline for the *Early Bird registration ends on June 30th*! After this date you can still register with the regular conference fee. We would be happy to see you in the baroque town Fulda on August 31, 2015 at our international event. Best regards, Frank Oellien (Chairman) --001a11427bc880b91d0519a7615c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear Colleagues,

=C2=A0

We are pleased to present the final program of the <= b>10th European Conference on Computational Chemistry (www.euco-cc-2015.org) to be hold in Fulda, Germany August 31 - September 3, 2015.

The whole program is available online: http://www.euco-cc-2015.org/progr= amme.html

=C2=A0

Please consider that the deadline for the Early B= ird registration ends on June 30th! After this date you can stil= l register with the regular conference fee.

=C2=A0

We would be happy to see you in the baroque town Ful= da on August 31, 2015 at our international event.

=C2=A0

Best regards,

Frank Oellien (Chairman)

--001a11427bc880b91d0519a7615c-- From owner-chemistry@ccl.net Mon Jun 29 09:38:01 2015 From: "Ashika Torikora ashika.torikora++gmail.com" To: CCL Subject: CCL: How to add explicit solvent molecules? Message-Id: <-51478-150629093639-3128-zJXFRS4IaTxAz+hzyjs+Kw[*]server.ccl.net> X-Original-From: "Ashika Torikora" Date: Mon, 29 Jun 2015 09:36:38 -0400 Sent to CCL by: "Ashika Torikora" [ashika.torikora-x-gmail.com] Hello everyone, I am trying to study the solvation of some organic compounds in water (let's say for example glycerol). What I have in mind is using a mixed implicit/explicit solvation approach. I have several questions regarding adding explicit water molecules to my system: -How do I pick the starting positions (distances and angles of water molecules to the organic molecule)? -How do I know how many water molecules I have to add? -What are the best functionals for taking into account hyrogen bonding? Thanks everyone () From owner-chemistry@ccl.net Mon Jun 29 11:28:01 2015 From: "Debasish Mandal debu1500[#]gmail.com" To: CCL Subject: CCL: About the calculation of Electrostatic interaction between two fragment in the TS Message-Id: <-51479-150629051504-11246-4Shk7Q8qRIRPCBB04rvV9A ~~ server.ccl.net> X-Original-From: Debasish Mandal Content-Type: multipart/alternative; boundary=089e013d100c01f3bb0519a486e2 Date: Mon, 29 Jun 2015 12:14:57 +0300 MIME-Version: 1.0 Sent to CCL by: Debasish Mandal [debu1500---gmail.com] --089e013d100c01f3bb0519a486e2 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi, Thank you very much for your reply. I have read few papers about Energy decomposition analysis and all of them are performed on closed shell system. could you please let me know EDA is reliable for open system also? Is there any way to calculate only the Coulomb interactions between the two fragments? Please let me know if there is any program for this calculations? I look forward to your kind reply. Thanks & Regards Debasish =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 Debasish Mandal Post Doctoral Research Fellow C/o- Prof. Sason Shaik Institute of Chemistry The Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem, Israel E-mail: debu1500**gmail.com Mob.No-09674211360 =E2=80=9CI=E2=80=99m thankful to all those who said =E2=80=98NO=E2=80=99 to= me it's because of them, I did it myself=E2=80=9D Einstein On Sun, Jun 28, 2015 at 10:14 PM, Fedor Goumans goumans[#]scm.com < owner-chemistry**ccl.net> wrote: > Dear Debasish, > > What you are looking for is simply applying the energy decomposition > analysis to the transition state, the so-called activation strain model b= y > Bickelhaupt: http://dx.doi.org/10.1039/B926828F (and numerous other > papers by him and co-workers where this principle is applied). > > Hope this helps, > Best wishes, > Fedor > > On 6/27/2015 10:43 PM, Debasish Mandal debu1500=3Dgmail.com wrote: > > Dear CCL users, > Could anybody please let me know if there i= s > a way to calculate the Electrostatic interaction energy between the two > fragment in the TS? > > If I split the TS into two fragments as frag1 and frag 2 and calculated > single point energies and then 'Energy of TS (opt) - (SP of frag1 + SP of > frag2) ' probably gives the interaction energy which are the sum of DEpau= li > (Pauli repulsion), DEes (electrostatic), DEpol (polarization) etc. But I > need those interactions separately. > > > I look forward for your kind response. > > Thanks & Regards > > Debasish > > =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 > Debasish Mandal > Post Doctoral Research Fellow > C/o- Prof. Sason Shaik > Institute of Chemistry > The Hebrew University of Jerusalem, > Givat Ram Campus, > Jerusalem, Israel > E-mail: debu1500 : gmail.com > Mob.No-09674211360 > > =E2=80=9CI=E2=80=99m thankful to all those who said =E2=80=98NO=E2=80= =99 to me it's because of them, I did it > > myself=E2=80=9D Einstein > > > > -- > Dr. T. P. M. (Fedor) Goumans > Business Developer > Scientific Computing & Modelling NV (SCM) > Vrije Universiteit, FEW, Theoretical Chemistry > De Boelelaan 1083 > 1081 HV Amsterdam, The Netherlands > T +31 20 598 7625https://www.scm.comhttps://twitter.com/SCM_Amsterdam > > --089e013d100c01f3bb0519a486e2 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 Thank you= very much for your reply.=C2=A0 I have read few papers about Energy decomp= osition analysis and all of them are performed on closed shell system. coul= d you please let me know EDA is reliable for open system also?
<= br>
Is there any way to calculate only the Coulomb interactions = between the two fragments? Please let me know if there is any program for t= his calculations?=C2=A0

I look forward to your k= ind reply.

Thanks & Regards

=
Debasish =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=3D=3D=3D=3D=3D=3D=3D=3D=3D
Debasish Mandal<= br>Post Doctoral Research Fellow
C/o- Prof. Sason ShaikInstitute of Chemistry
The Hebrew University of Jerusalem,
Givat Ram= Campus,
Jerusalem, Israel
E-mail: debu1500**gmail.com
Mob.No-09674211360

<=
font face=3D"verdana, sans-serif">
=E2=80=9CI=E2=80=99m thankful to all those who said =E2=80=98NO=E2=80=
=99 to me it's because of them, I did it=C2=A0
myself=E2=80=9D Ei=
nstein


On Sun, Jun 28, 2015 at 10:14 PM, Fedor Goum= ans goumans[#]scm.com <= owner-chemistr= y**ccl.net> wrote:
=20 =20 =20
Dear Debasish,

What you are looking for is simply applying the energy decomposition analysis to the transition state, the so-called activation strain model by Bickelhaupt: http://dx.doi.org/10.1039/B926828F (and numerous other papers by him and co-workers where this principle is applied).

Hope this helps,
Best wishes,
Fedor

On 6/27/2015 10:43 PM, Debasish Mandal debu1500=3Dgmail.com wrote:
Dear CCL users,
=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 Could anybody please let me know if there is a way to calculate the Electrostatic interaction energy between the two fragment in the TS?
=C2=A0
If I=C2=A0split the TS into two fragments as frag1 and frag 2 and calcu= lated single point energies and then=C2=A0'Energy of TS (opt) - (SP of frag1 + SP of frag2) ' probably give= s the interaction energy which are the sum of=C2=A0DEpaul= i (Pauli repulsion), DEes (electrostatic), DEpol (polarization) etc. But I need those interactions separately.


I look forward for your kind response.

Thanks & Regards

Debasish

 

--=20
Dr. T. P. M. (Fedor) Goumans
Business Developer
Scientific Computing & Modelling NV (SCM)
Vrije Universiteit, FEW, Theoretical Chemistry
De Boelelaan 1083
1081 HV Amsterdam, The Netherlands
T +31 20 598 7625
https://www.scm.com
https://twi=
tter.com/SCM_Amsterdam

--089e013d100c01f3bb0519a486e2-- From owner-chemistry@ccl.net Mon Jun 29 13:02:01 2015 From: "Andreas Klamt klamt:+:cosmologic.de" To: CCL Subject: CCL: How to add explicit solvent molecules? Message-Id: <-51480-150629125222-4538-nMPqtFA40k3PfamKRK+x+w,server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-15; format=flowed Date: Mon, 29 Jun 2015 18:52:13 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt===cosmologic.de] We have got some experience with adding explicit solvent molecules: The recipe is to do a COSMO calculation, put the most polar surface segments (the segments with the maximum COSMO polarization charge density) of solute and solvent on top of each other, generate a few rotamers (we do 8) around the aligned normal directions of the segments, and then optimize them. This can be done automatically within our COSMOtherm software, but surely can be done with a bit of programming yourself. This was done in the paper Towards rst principles prediction of pKa: COSMO-RS and the cluster-continuum approach https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=9&ved=0CGEQFjAI&url=https%3A%2F%2Fhal.archives-ouvertes.fr%2Fhal-00580701%2Fdocument&ei=qHaRVbbsB8TnygO41IGYDw&usg=AFQjCNEZyH_V-V7LPVfAUWfwDcHpVsB7_A&sig2=K6oR0U32MalbL_Tr7fv0Zg&bvm=bv.96783405,d.bGQ&cad=rja The question about how many you need is hard to answer. It is also a bit reflected in that paper. By the way, the use of direct-COSMO-RS may avoid the need for explicit solvent molecules. (http://www.turbomole-gmbh.com/manuals/version_6_5/Documentation_html/node322.html) Andreas Am 29.06.2015 um 15:36 schrieb Ashika Torikora ashika.torikora++gmail.com: > Sent to CCL by: "Ashika Torikora" [ashika.torikora-x-gmail.com] > Hello everyone, > > I am trying to study the solvation of some organic compounds in water > (let's say for example glycerol). What I have in mind is using a mixed > implicit/explicit solvation approach. I have several questions regarding > adding explicit water molecules to my system: > > -How do I pick the starting positions (distances and angles of water > molecules to the organic molecule)? > > -How do I know how many water molecules I have to add? > > -What are the best functionals for taking into account hyrogen bonding? > > Thanks everyone ()> > > -- -------------------------------------------------- Prof. Dr. Andreas Klamt CEO / Gesch�ftsf�hrer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt]|[cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt From owner-chemistry@ccl.net Mon Jun 29 16:30:00 2015 From: "Joseph Maxwell jaymax36_+_gmail.com" To: CCL Subject: CCL: Entropy & Water Message-Id: <-51481-150629162242-12917-jAiet2lyfzGXj4h0LyTvpQ(0)server.ccl.net> X-Original-From: "Joseph Maxwell" Date: Mon, 29 Jun 2015 16:22:41 -0400 Sent to CCL by: "Joseph Maxwell" [jaymax36~!~gmail.com] Hello; Could anyone suggest a decent reliable way to estimate or determine the theoretical entropy of the water component in an aqueous system. Especially in light of the inherent multiple structures, icosahedral [(H2O)280]and others. These factors seem to exponentially complicate standard statistical mechanic approaches. Thanks! From owner-chemistry@ccl.net Mon Jun 29 23:08:00 2015 From: "Cina Foroutan-Nejad canyslopus|a|yahoo.co.uk" To: CCL Subject: CCL: About the calculation of Electrostatic interaction between two fragment in the TS Message-Id: <-51482-150629150622-9359-njH0pmGbMe1Dg9Fnm0v9ww _ server.ccl.net> X-Original-From: Cina Foroutan-Nejad Content-Type: multipart/alternative; boundary="----=_Part_3115604_1361046588.1435604768242" Date: Mon, 29 Jun 2015 19:06:08 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Cina Foroutan-Nejad [canyslopus{:}yahoo.co.uk] ------=_Part_3115604_1361046588.1435604768242 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Debasish, About the EDA analysis I say yes; open-shell systems are also OK, unless yo= ur system dissociates to a single atom, which can be a little problematic. = Besides, please note that in an ordinary EDA analysis you have Pauli, elect= rostatic, orbital interaction energies. These energy contributions are defi= ned on the basis of an arbitrary (read chemical) scheme. These energies are= like a "process function", i.e. their magnitude depends on how you bring f= ragments together.=C2=A0However, the real=C2=A0binding energy is a let's sa= y "state function", i.e. just depends on the starting and the ending states= . So, you may look at the alternative way of energy decomposition, provided= at the end of an EDA analysis, where energy is divided into kinetics, elec= trostatics, Coulomb, and exchange-correlation parts. This part=C2=A0is not = usually used by chemists but if you insist to have pure electrostatics it i= s helpful to look at it. Sum of the electrostatics and the Coulomb parts gi= ves exact contribution of the electrostatics. For an example of using this = alternative decomposition see PCCP, 2015, 17, 6440.Alternatively, you may u= se IQA (interacting quantum atoms)=C2=A0analysis of Pendas et al. This sche= me provides three energy components namely, electrostatics, exchange-correl= ation and so called deformation energy. The deformation energy is a result = of the kinetic energy change of the atoms. The latter method is unfortunate= ly much more computationally expensive but it is on the basis of a non-over= lapping atomic scheme and includes no arbitrary intermediate state. Good luck,Cina -----------------------------------------------Cina Foroutan-Nejad, PhDCEIT= EC-Central European Institute of Technology.Masaryk University, Brno, Czech= Republichttps://muni.academia.edu/CinaForoutanNejad =20 On Monday, 29 June 2015, 19:39, Debasish Mandal debu1500[#]gmail.com <= owner-chemistry|,|ccl.net> wrote: =20 Hi,=C2=A0 =C2=A0 =C2=A0 =C2=A0 Thank you very much for your reply.=C2=A0 I= have read few papers about Energy decomposition analysis and all of them a= re performed on closed shell system. could you please let me know EDA is re= liable for open system also? Is there any way to calculate only the Coulomb interactions between the two= fragments? Please let me know if there is any program for this calculation= s?=C2=A0 I look forward to your kind reply. Thanks & Regards Debasish =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=3D=3D=3D=3D=3D=3D=3D=3D=3D Debasish Mandal Post Doctoral Research FellowC/o- Prof. Sason Shaik Institute of Chemistry The Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem, Israel E-mail: debu1500:_:gmail.com Mob.No-09674211360 =E2=80=9CI=E2=80=99m thankful to all those who said =E2=80=98NO=E2=80=99 to= me it's because of them, I did it=C2=A0myself=E2=80=9D Einstein On Sun, Jun 28, 2015 at 10:14 PM, Fedor Goumans goumans[#]scm.com wrote: Dear Debasish, =20 What you are looking for is simply applying the energy decomposition analy= sis to the transition state, the so-called activation strain model by Bicke= lhaupt: http://dx.doi.org/10.1039/B926828F (and numerous other papers by hi= m and co-workers where this principle is applied).=20 =20 Hope this helps, Best wishes, Fedor =20 On 6/27/2015 10:43 PM, Debasish Mandal debu1500=3Dgmail.com wrote: =20 Dear CCL users, =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 Could anybody please let m= e know if there is a way to calculate the Electrostatic interaction energy = between the two fragment in the TS? =C2=A0 If I=C2=A0split the TS into two = fragments as frag1 and frag 2 and calculated single point energies and then= =C2=A0'Energy of TS (opt) - (SP of frag1 + SP of frag2) ' probably gives th= e interaction energy which are the sum of=C2=A0DEpauli (Pauli repulsion), D= Ees (electrostatic), DEpol (polarization) etc. But I need those interaction= s separately.=20 =20 I look forward for your kind response.=20 Thanks & Regards=20 Debasish=20 =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 Debasish Mandal Post Doctoral Research Fellow C/o- Prof. Sason Shaik Institute of Chemistry The Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem, Israel E-mail: debu1500 : gmail.com Mob.No-09674211360 =20 =20 =E2=80=9CI=E2=80=99m thankful to all those who said =E2=80=98NO=E2=80=99 t= o me it's because of them, I did it=C2=A0myself=E2=80=9D Einstein=20 =20 =20 --=20 Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 https://www.scm.com https://twitter.com/SCM_Amsterdam =20 ------=_Part_3115604_1361046588.1435604768242 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Debasish,

Ab= out the EDA analysis I say yes; open-shell systems are also OK, unless your= system dissociates to a single atom, which can be a little problematic.
Besides, pleas= e note that in an ordinary EDA analysis you have Pauli, electrostatic, orbi= tal interaction energies. These energy contributions are defined on the bas= is of an arbitrary (read chemical) scheme. These energies are like a "proce= ss function", i.e. their magnitude depends on how you bring fragments toget= her. However, the real binding energy is a let's say "state funct= ion", i.e. just depends on the starting and the ending states. So, you may = look at the alternative way of energy decomposition, provided at the end of= an EDA analysis, where energy is divided into kinetics, electrostatics, Co= ulomb, and exchange-correlation parts. This part is not usually used b= y chemists but if you insist to have pure electrostatics it is helpful to l= ook at it. Sum of the electrostatics and the Coulomb parts gives exact cont= ribution of the electrostatics. For an example of using this alternative de= composition see PCCP, 2015, 17, 6440.
Alternatively, you may use IQA (interacting quantu= m atoms) analysis of Pendas et al. This scheme provides three energy c= omponents namely, electrostatics, exchange-correlation and so called deform= ation energy. The deformation energy is a result of the kinetic energy chan= ge of the atoms. The latter method is unfortunately much more computational= ly expensive but it is on the basis of a non-overlapping atomic scheme and = includes no arbitrary intermediate state.

Good luck,
Cina

-------------------------------------= ----------
Cina Foroutan-Nejad, PhD
CEITEC-Central European Instit= ute of Technology.
Masaryk University, Brno, Czech Republic


On Monday, 29 June 2015, 19:39, Debasish Mandal debu1500[#]g= mail.com <owner-chemistry|,|ccl.net> wrote:

Hi,
    &nb= sp;   Thank you very much for your reply.  I have read few papers= about Energy decomposition analysis and all of them are performed on close= d shell system. could you please let me know EDA is reliable for open syste= m also?

Is t= here any way to calculate only the Coulomb interactions between the two fra= gments? Please let me know if there is any program for this calculations?&n= bsp;

I look = forward to your kind reply.

Thanks & Regards

Debasish  

=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
Debasish Mandal
Post Doctoral Research Fellow
<= span style=3D"font-family: garamond, serif;">C/o- Prof. Sason Shaik<= font face=3D"garamond, serif">
Institute of Chemistry
The Hebrew Univ= ersity of Jerusalem,
Givat Ram Campus,
Jerusalem, Israel
E-mail: <= a href=3D"mailto:debu1500:_:gmail.com" target=3D"_blank" rel=3D"nofollow" y= mailto=3D"mailto:debu1500:_:gmail.com">debu1500:_:gmail.com
Mob.No-0= 9674211360

=

<= pre>
=E2=80=9CI=E2=80=99m thankful to all those who= said =E2=80=98NO=E2=80=99 to me it's because of them, I did it 
=
myself=E2=80=9D Einstein


On Sun, Jun 28, 2015 at 10:14 P= M, Fedor Goumans goumans[#]scm.com <owner-chemistry:_:ccl.net> wrote:
=
=20 =20 =20
Dear Debasish,

What you are looking for is simply applying the energy decomposition analysis to the transition state, the so-called activation strain model by Bickelhaupt: http://dx.doi.org/10.1039/B926828F (an= d numerous other papers by him and co-workers where this principle is applied).

Hope this helps,
Best wishes,
Fedor

On 6/27/2015 10:43 PM, Debasish Mandal debu1500=3Dgmail.com wrote:
Dear CCL users,
      &n= bsp;                     =   Could anybody please let me know if there is a way to calculate the Electrostatic interaction energy between the two fragment in the TS?
 
If I split the TS into two fragments as frag1 and frag 2 and calculated single point energies and then 'Energy of TS (opt) - (SP of frag1 + SP of frag2) ' probably gives the interaction energy which are the sum of DEpauli (Pauli repulsion), DEes (electrostatic), DEpol (polarization) etc. But I need those interactions separately.


I look forward for your kind response.

Thanks & Regards

Debasish

=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
Debasis= h Mandal
Post Doctoral Research Fellow
C/= o- Prof. Sason Shaik
Institute of Chemistry
The Hebrew University of Jerusalem,
Givat Ram Campus,
Jerusalem, Israel
E-mail: debu1500 : gmail.com
Mob.No-09674211360
 




=E2=80=9CI=E2=80=99m =
thankful to all those who said =E2=80=98NO=E2=80=99 to me it's because of t=
hem, I did it 
myself=E2=80=9D Einstein

<= font color=3D"#888888"> 

--=20
Dr. T. P. M. (Fedor) Goumans
Business Developer
Scientific Computing & Modelling NV (SCM)
Vrije Universiteit, FEW, Theoretical Chemistry
De Boelelaan 1083
1081 HV Amsterdam, The Netherlands
T +31 20 598 7625
https:/=
/www.scm.com
https://twitter.com/SCM_Amsterdam



------=_Part_3115604_1361046588.1435604768242-- From owner-chemistry@ccl.net Mon Jun 29 23:43:01 2015 From: "Fedor Goumans goumans-,-scm.com" To: CCL Subject: CCL: About the calculation of Electrostatic interaction between two fragment in the TS Message-Id: <-51483-150629151350-9753-I4C9u9aIYJMTTMfvIPc4QA=server.ccl.net> X-Original-From: Fedor Goumans Content-Type: multipart/alternative; boundary="------------000303060507090608080701" Date: Mon, 29 Jun 2015 21:13:40 +0200 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans()scm.com] This is a multi-part message in MIME format. --------------000303060507090608080701 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Dear Debasish, I can only tell about the little bit I know about the Ziegler-Rauk ETS implementation of EDA in in ADF. Within ADF, one can do EDA just fine with open-shell systems, however, for technical reasons in the current implementation one would have to prepare the fragments using restricted orbitals, as e.g. described in this example: http://www.scm.com/Doc/Doc2014/ADF/Examples/page148.html Best wishes, Fedor On 6/29/2015 11:14 AM, Debasish Mandal debu1500[#]gmail.com wrote: > Hi, > Thank you very much for your reply. I have read few papers about > Energy decomposition analysis and all of them are performed on closed > shell system. could you please let me know EDA is reliable for open > system also? > > Is there any way to calculate only the Coulomb interactions between > the two fragments? Please let me know if there is any program for this > calculations? > > I look forward to your kind reply. > > Thanks & Regards > > Debasish > > ====================================== > Debasish Mandal > Post Doctoral Research Fellow > C/o- Prof. Sason Shaik > Institute of Chemistry > The Hebrew University of Jerusalem, > Givat Ram Campus, > Jerusalem, Israel > E-mail: debu1500:_:gmail.com > Mob.No-09674211360 > * > * > * > * > > “I’m thankful to all those who said ‘NO’ to me it's because of them, I > did it > > myself” Einstein > > > > On Sun, Jun 28, 2015 at 10:14 PM, Fedor Goumans goumans[#]scm.com > > wrote: > > Dear Debasish, > > What you are looking for is simply applying the energy > decomposition analysis to the transition state, the so-called > activation strain model by Bickelhaupt: > http://dx.doi.org/10.1039/B926828F (and numerous other papers by > him and co-workers where this principle is applied). > > Hope this helps, > Best wishes, > Fedor > > On 6/27/2015 10:43 PM, Debasish Mandal debu1500=gmail.com > wrote: >> Dear CCL users, >> Could anybody please let me know if there is a way to >> calculate the Electrostatic interaction energy between the two >> fragment in the TS? >> If I split the TS into two fragments as frag1 and frag 2 and >> calculated single point energies and then 'Energy of TS (opt) - >> (SP of frag1 + SP of frag2) ' probably gives the interaction >> energy which are the sum of DEpauli (Pauli repulsion), DEes >> (electrostatic), DEpol (polarization) etc. But I need those >> interactions separately. >> >> >> I look forward for your kind response. >> >> Thanks & Regards >> >> Debasish >> >> ====================================== >> Debasish Mandal >> Post Doctoral Research Fellow >> C/o- Prof. Sason Shaik >> Institute of Chemistry >> The Hebrew University of Jerusalem, >> Givat Ram Campus, >> Jerusalem, Israel >> E-mail: debu1500 : gmail.com >> Mob.No-09674211360 >> * >> * >> * >> * >> >> “I’m thankful to all those who said ‘NO’ to me it's because of >> them, I did it >> >> myself” Einstein >> >> > > -- > Dr. T. P. M. (Fedor) Goumans > Business Developer > Scientific Computing & Modelling NV (SCM) > Vrije Universiteit, FEW, Theoretical Chemistry > De Boelelaan 1083 > 1081 HV Amsterdam, The Netherlands > T+31 20 598 7625 > https://www.scm.com > https://twitter.com/SCM_Amsterdam > > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 https://www.scm.com https://twitter.com/SCM_Amsterdam --------------000303060507090608080701 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Dear Debasish,

I can only tell about the little bit I know about the Ziegler-Rauk ETS implementation of EDA in in ADF.

Within ADF, one can do EDA just fine with open-shell systems, however, for technical reasons in the current implementation one would have to prepare the fragments using restricted orbitals, as e.g. described in this example:
http://www.scm.com/Doc/Doc2014/ADF/Examples/page148.html

Best wishes,
Fedor

On 6/29/2015 11:14 AM, Debasish Mandal debu1500[#]gmail.com wrote:
Hi,
        Thank you very much for your reply.  I have read few papers about Energy decomposition analysis and all of them are performed on closed shell system. could you please let me know EDA is reliable for open system also?

Is there any way to calculate only the Coulomb interactions between the two fragments? Please let me know if there is any program for this calculations? 

I look forward to your kind reply.

Thanks & Regards

Debasish  

======================================
Debasish Mandal
Post Doctoral Research Fellow
C/o- Prof. Sason Shaik
Institute of Chemistry
The Hebrew University of Jerusalem,
Givat Ram Campus,
Jerusalem, Israel
E-mail: debu1500:_:gmail.com
Mob.No-09674211360
 




“I’m thankful to all those who said ‘NO’ to me it's because of them, I did it 
myself” Einstein


On Sun, Jun 28, 2015 at 10:14 PM, Fedor Goumans goumans[#]scm.com <owner-chemistry:_:ccl.net> wrote:
Dear Debasish,

What you are looking for is simply applying the energy decomposition analysis to the transition state, the so-called activation strain model by Bickelhaupt: http://dx.doi.org/10.1039/B926828F (and numerous other papers by him and co-workers where this principle is applied).

Hope this helps,
Best wishes,
Fedor

On 6/27/2015 10:43 PM, Debasish Mandal debu1500=gmail.com wrote:
Dear CCL users,
                              Could anybody please let me know if there is a way to calculate the Electrostatic interaction energy between the two fragment in the TS?
 
If I split the TS into two fragments as frag1 and frag 2 and calculated single point energies and then 'Energy of TS (opt) - (SP of frag1 + SP of frag2) ' probably gives the interaction energy which are the sum of DEpauli (Pauli repulsion), DEes (electrostatic), DEpol (polarization) etc. But I need those interactions separately.


I look forward for your kind response.

Thanks & Regards

Debasish

======================================
Debasish Mandal
Post Doctoral Research Fellow
C/o- Prof. Sason Shaik
Institute of Chemistry
The Hebrew University of Jerusalem,
Givat Ram Campus,
Jerusalem, Israel
E-mail: debu1500 : gmail.com
Mob.No-09674211360
 




“I’m thankful to all those who said ‘NO’ to me it's because of them, I did it 
myself” Einstein


-- 
Dr. T. P. M. (Fedor) Goumans
Business Developer
Scientific Computing & Modelling NV (SCM)
Vrije Universiteit, FEW, Theoretical Chemistry
De Boelelaan 1083
1081 HV Amsterdam, The Netherlands
T +31 20 598 7625
https://www.scm.com
https://twitter.com/SCM_Amsterdam 


-- 
Dr. T. P. M. (Fedor) Goumans
Business Developer
Scientific Computing & Modelling NV (SCM)
Vrije Universiteit, FEW, Theoretical Chemistry
De Boelelaan 1083
1081 HV Amsterdam, The Netherlands
T +31 20 598 7625
https://www.scm.com
https://twitter.com/SCM_Amsterdam
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