From owner-chemistry@ccl.net Sat Jun 14 03:29:01 2014
From: "Susi Lehtola susi.lehtola.++.alumni.helsinki.fi" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: Exchange correlation
Message-Id: <-50216-140614032234-22811-1UUDijLvccfrVJX/Tu2A2Q++server.ccl.net>
X-Original-From: Susi Lehtola <susi.lehtola a alumni.helsinki.fi>
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Date: Sat, 14 Jun 2014 10:22:26 +0300
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Sent to CCL by: Susi Lehtola [susi.lehtola\a/alumni.helsinki.fi]
On Fri, 13 Jun 2014 16:16:19 +0200
"Sergio Manzetti sergio.manzetti a outlook.com"
<owner-chemistry*ccl.net> wrote:
> Dear Robert, I am not familiar with the method for applying an exchange correlation. But is this applied by using perturbation on the Hamiltonian of the multi/electron system, that is a perturbation Hamiltonian which applied the effect from the exchange?
When you talk about exchange-correlation, you're talking about
Kohn-Sham DFT. There is no exchange to worry about in wave-function
based methods, because that's handled 100% by Hartree-Fock, and what
you build on top (Møller-Plesset, configuration interaction, coupled
cluster) only tries to handle the correlation part.
DFT is fundamentally different to wave-function theory, where exchange
and correlation are parametrized in a single unknown functional, to
which there is a zoo of different approximations, starting from the
local density approximation where the exchange-correlation energy is
parametrized as a function of the local density only
E = \int n(r) e_{xc} (n(r)) d^3 r.
You should start by reading a book, or review articles on DFT. Kohn's
Nobel lecture [1] is a pretty good place to start. For more recent
articles, see e.g. Burke [2] and Becke [3].
[1] W. Kohn, Rev. Mod. Phys. 71, 1253 (1998)
[2] K. Burke, J. Chem. Phys. 136, 150901 (2012)
[3] A. D. Becke, J. Chem. Phys. 140, 18A301 (2014)
--
---------------------------------------------------------------
Mr. Susi Lehtola, PhD Research Associate
susi.lehtola*alumni.helsinki.fi Department of Applied Physics
http://www.helsinki.fi/~jzlehtol Aalto University
Finland
---------------------------------------------------------------
Susi Lehtola, FT Tutkijatohtori
susi.lehtola*alumni.helsinki.fi Fysiikan laitos
http://www.helsinki.fi/~jzlehtol Aalto-yliopisto
---------------------------------------------------------------
From owner-chemistry@ccl.net Sat Jun 14 04:03:01 2014
From: "Susi Lehtola susi.lehtola-x-alumni.helsinki.fi" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL: Exchange correlation
Message-Id: <-50217-140614032832-23059-rMhNP4/H7q/4+I5UleOElg.:.server.ccl.net>
X-Original-From: Susi Lehtola <susi.lehtola-,-alumni.helsinki.fi>
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Date: Sat, 14 Jun 2014 10:28:24 +0300
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Sent to CCL by: Susi Lehtola [susi.lehtola]~[alumni.helsinki.fi]
On Fri, 13 Jun 2014 09:56:14 -0700
"William McDonald pchem]=[ucsc.edu" <owner-chemistry(~)ccl.net> wrote:
> Sorry, my previous post was totally unclear. I understand what exchange and
> correlation refer to. I meant to ask "isn't the self-interaction error a
> consequence of the mean-field approximation?"
> As to Dr. Lehtola's comment that "Exchange is important even for a single
> electron, because it cancels out (or tries to) the self-Coulomb
> interaction." This seems odd, because why are two-electron (Coulomb
> repulsion) integrals being evaluated in a one-electron system? It seems to
> me that for any one-electron system, one simply evaluates the electronic
> kinetic energy and electron-nucleus attraction; there should not be a
> self-Coulomb interaction.
That depends on what you are doing. If you're only running
Hartree-Fock, then it's OK to skip evaluating the two-electron
integrals as you know they will cancel out exactly.
Exchange-correlation (at least to me) means density-functional theory.
Here, one doesn't use exact exchange. Or at least not 100% of it. So
you don't get full cancellation; only a partial cancellation.
For instance, if you run LDA/cc-pVQZ on the hydrogen atom, you'll get an
energy -0.45725 Ha, compared to HF that gives -0.4999 Ha which is 0.1mHa
away from the exact value of -0.5 due to the incomplete basis set.
--
---------------------------------------------------------------
Mr. Susi Lehtola, PhD Research Associate
susi.lehtola(~)alumni.helsinki.fi Department of Applied Physics
http://www.helsinki.fi/~jzlehtol Aalto University
Finland
---------------------------------------------------------------
Susi Lehtola, FT Tutkijatohtori
susi.lehtola(~)alumni.helsinki.fi Fysiikan laitos
http://www.helsinki.fi/~jzlehtol Aalto-yliopisto
---------------------------------------------------------------
From owner-chemistry@ccl.net Sat Jun 14 04:48:00 2014
From: "p.d.jarowski[#]surrey.ac.uk" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: Prasenjit - Quering about Transition States
Message-Id: <-50218-140614044727-13919-1fx+URo898bPntoSSJugRA(0)server.ccl.net>
X-Original-From: <p.d.jarowski],[surrey.ac.uk>
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Sent to CCL by: [p.d.jarowski_._surrey.ac.uk]
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Hello:
No. There is no software. You will have to walk through the mechanism step =
by step and try different things to find the minimum energy path. The best =
way usually is to start from the products, but in your case you have combin=
ation-fragmentation so it will be crucial to understand how the H2 is leavi=
ng. From the other direction, it would be nice to know how this is initiate=
d. You must start from somewhere. Luckily your molecules are small and you =
can get structures and energyies at a good level quickly. If you can identi=
fy stable intermediates, the transition states will be simple enough to get=
.
Remember!!!! Just cause you might find a minimum energy pathway that looks =
reasonable, does not mean you have proven the mechanism. You can't prove a =
mechanism since there is always the possibility that the transformation can=
happen a different way. If the mechanism helps you understand and design t=
he reaction than that is what you are after.
Best,
Peter
________________________________
> From: owner-chemistry+p.d.jarowski=3D=3Dsurrey.ac.uk__ccl.net <owner-chemist=
ry+p.d.jarowski=3D=3Dsurrey.ac.uk__ccl.net> on behalf of Victor Rosas Garcia=
rosas.victor[]gmail.com <owner-chemistry__ccl.net>
Sent: 14 June 2014 01:47
To: Jarowski PD Dr (Physics)
Subject: CCL: Prasenjit - Quering about Transition States
> From your message, I do not understant what your problem is. Do you want to=
know the mechanism? Do you want a transition state in particular?
You say that for some of your systems you have no idea of the reaction path=
. Does this mean that you do have a reaction path for other systems? Those=
could be a starting point for the ones that lack the information.
Victor
2014-06-13 16:56 GMT-05:00 Prasenjit Seal seal.prasenjit*_*gmail.com<http:/=
/gmail.com> <owner-chemistry||ccl.net<mailto:owner-chemistry||ccl.net>>:
Hi,
I am having a problem dealing with transition states. For some of my system=
s, I have no idea what the reaction path will look like, no idea of the tra=
nsition states, no idea of the reaction mechanism.
What I have in hand is only the structures of the reactants and products. I=
s there any software available which can solve my problem?
I would really appreciate if someone has some idea regarding this matter.
Some of these type of reactions are
1. Si2H5(-) + SiH4 ------> Si3H7(-) + H2
2. Si2H4(-) + SiH4 ------> Si3H6(-) + H2
Please note that Si2H4(-) is silylene anions and not silene. Same goes for =
Si3H6(-). Si2H5(-) and Si3H7(-) are radical anions.
Thanks and best regards,
Prasenjit
--_000_140273572980335450surreyacuk_
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und-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<p>Hello:</p>
<p><br>
</p>
<p>No. There is no software. You will have to walk through the mechanism st=
ep by step and try different things to find the minimum energy path. The be=
st way usually is to start from the products, but in your case you have com=
bination-fragmentation so it will
be crucial to understand how the H2 is leaving. From the other direction, =
it would be nice to know how this is initiated. You must start from somewhe=
re. Luckily your molecules are small and you can get structures and energyi=
es at a good level quickly. If you
can identify stable intermediates, the transition states will be simple en=
ough to get.<br>
</p>
<p><br>
</p>
<p>Remember!!!! Just cause you might find a minimum energy pathway that loo=
ks reasonable, does not mean you have proven the mechanism. You can't prove=
a mechanism since there is always the possibility that the transforma=
tion can happen a different way. If the
mechanism helps you understand and design the reaction than that is what y=
ou are after.</p>
<p><br>
</p>
<p>Best,</p>
<p><br>
</p>
<p>Peter<br>
</p>
<div style=3D"color: rgb(40, 40, 40);">
<hr tabindex=3D"-1" style=3D"display:inline-block; width:98%">
<div id=3D"divRplyFwdMsg" dir=3D"ltr"><font style=3D"font-size:11pt" color=
=3D"#000000" face=3D"Calibri, sans-serif"><b>From:</b> owner-chemistry+=
p.d.jarowski=3D=3Dsurrey.ac.uk__ccl.net <owner-chemistry+p.d.jarowski=
=3D=3Dsurrey.ac.uk__ccl.net> on behalf of Victor Rosas Garcia rosas.victo=
r[]gmail.com
<owner-chemistry__ccl.net><br>
<b>Sent:</b> 14 June 2014 01:47<br>
<b>To:</b> Jarowski PD Dr (Physics)<br>
<b>Subject:</b> CCL: Prasenjit - Quering about Transition States</font>
<div> </div>
</div>
<div>
<div dir=3D"ltr">
<div>From your message, I do not understant what your problem is. Do you wa=
nt to know the mechanism? Do you want a transition state in particular?<br>
<br>
</div>
<div>You say that for some of your systems you have no idea of the reaction=
path. Does this mean that you do have a reaction path for other syst=
ems? Those could be a starting point for the ones that lack the information=
.<br>
<br>
</div>
Victor<br>
</div>
<div class=3D"gmail_extra"><br>
<br>
<div class=3D"gmail_quote">2014-06-13 16:56 GMT-05:00 Prasenjit Seal seal.p=
rasenjit*_*<a href=3D"http://gmail.com">gmail.com</a>
<span dir=3D"ltr"><<a href=3D"mailto:owner-chemistry||ccl.net" target=3D=
"_blank">owner-chemistry||ccl.net</a>></span>:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex; border-left:1=
px #ccc solid; padding-left:1ex">
<div dir=3D"ltr">Hi,
<div><br>
</div>
<div>I am having a problem dealing with transition states. For some of my s=
ystems, I have no idea what the reaction path will look like, no idea of th=
e transition states, no idea of the reaction mechanism.</div>
<div><br>
</div>
<div>What I have in hand is only the structures of the reactants and produc=
ts. Is there any software available which can solve my problem? </div>
<div><br>
</div>
<div>I would really appreciate if someone has some idea regarding this matt=
er.</div>
<div><br>
</div>
<div>Some of these type of reactions are</div>
<div><br>
</div>
<div>1. Si2H5(-) + SiH4 ------> Si3H7(-) + H2</div>
<div><br>
</div>
<div>2. Si2H4(-) + SiH4 ------> Si3H6(-) + H2</div>
<div><br>
</div>
<div>Please note that Si2H4(-) is silylene anions and not silene. Same goes=
for Si3H6(-). Si2H5(-) and Si3H7(-) are radical anions. </div>
<div><br>
</div>
<div>Thanks and best regards,</div>
<div>Prasenjit</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
</body>
</html>
--_000_140273572980335450surreyacuk_--
From owner-chemistry@ccl.net Sat Jun 14 07:26:00 2014
From: "Barry Hardy barry.hardy^^vtxmail.ch" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: anti-malarial drug design
Message-Id: <-50219-140614072443-15760-6QO8uY1YIAMwtr8fDcYkUA+*+server.ccl.net>
X-Original-From: Barry Hardy <barry.hardy^_^vtxmail.ch>
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Date: Sat, 14 Jun 2014 13:24:32 +0200
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Sent to CCL by: Barry Hardy [barry.hardy()vtxmail.ch]
The Scientists Against Malaria (SAM) initiative was formed with the goal
of designing novel drug candidates against malaria
(http://www.scientistsagainstmalaria.net/). During its first phase
participants progressed target selection and modelling, computational
screening, biological materials and assay preparation, through to the
completion of initial experimental testing in the laboratory. The
project has been initially focused on parastic kinases as novel targets
for the potential development of a new class of anti-malaria drugs.
SAM is now being expanded as case study work supported by the eCheminfo
community of practice which brings practitioners together with interests
in the development and application of drug design methods. eCheminfo
workshops provide an opportunity for scientists to participate in the
modelling and design of libraries of molecules as potential lead candidates.
The next eCheminfo community of practice activity will involve a
hands-on drug discovery workshop taking place in Oxford the week of 21 -
25 July. This workshop activity was initiated in 2006 to provide a
setting where participants could learn and apply computational methods
to drug design.
As in previous workshops the emphasis is on problem solving, practical
hands-on use of methods and software, and working together throughout
the week. In addition to the faculty-guided learning and exercises, this
year's workshop will also offer a neglected disease case study focused
on the discovery of new inhibitors of malarial kinases. Different
methods will be applied to malarial proteins throughout the week to
build and refine protein structures, carry out virtual screening,
examine protein-drug interactions, form consensus models and include
molecular properties such as potential toxic liabilities in the decision
making framework.
More information on the program is available at
http://www.douglasconnect.com/events/echeminfo-2014
best regards
Barry Hardy
eCheminfo Community of Practice
Douglas Connect GmbH
Baermeggenweg 14
4314 Zeiningen
Switzerland
From owner-chemistry@ccl.net Sat Jun 14 08:03:01 2014
From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor^fluor.quimica.uniovi.es" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: Exchange correlation
Message-Id: <-50220-140614080106-29729-iQo1/x7CrgZ0SjSg6KDwfQ|-|server.ccl.net>
X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal <victor-.-fluor.quimica.uniovi.es>
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Date: Sat, 14 Jun 2014 13:54:30 +0200
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Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor-,-fluor.quimica.uniovi.es]
On Fri, Jun 13, 2014 at 04:48:04PM -0400, Robert Molt r.molt.chemical.physics*o*gmail.com wrote:
> Do you mean "exchange correlation" referring to a choice in an
> exchange-correlation /functional /(KS-DFT framework) or "exchange and
> correlation" referring to in a wavefunction formalism?
I use both formalisms, being initially formed on atomic, embedding and
solid state problems. However, I tend to be more confortable with the
wf method.
In a previous post I was trying to point to the different language used
by the KS-DFT and the wavefuncion community. I think that Prof. Lehtola
has done a better role in deffending my point.
As for the many outcomes of the John C. Slater role in solid state let
me remember the FP-LAPW community: wien2k, elk, ?
Best regards,
Dr. V�ctor Lua�a
From owner-chemistry@ccl.net Sat Jun 14 18:07:01 2014
From: "Sergio Manzetti sergio.manzetti|outlook.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: Exchange correlation
Message-Id: <-50221-140614033634-25453-eBXKVsu5nkMd4ZmAXZEk6w_._server.ccl.net>
X-Original-From: Sergio Manzetti <sergio.manzetti^outlook.com>
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Date: Sat, 14 Jun 2014 09:36:26 +0200
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Sent to CCL by: Sergio Manzetti [sergio.manzetti^^^outlook.com]
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I ment the principle itself of calculating the resultant on the energy fro=
m the electron exchange. Is it applied by adding a perturbation Hamiltonian=
to each electron?
> From: owner-chemistry:-:ccl.net
To: sergio.manzetti:-:gmx.com
Subject: CCL: Exchange correlation
Date: Fri=2C 13 Jun 2014 16:48:04 -0400
=0A=
=0A=
=0A=
=0A=
=0A=
Do you mean "exchange correlation" referring to a choice in an=0A=
exchange-correlation functional (KS-DFT framework) or=0A=
"exchange and correlation" referring to in a wavefunction formalism?
=
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<body class=3D'hmmessage'><div dir=3D'ltr'>I ment the =3B principle its=
elf of calculating the resultant on the energy from the electron exchange. =
Is it applied by adding a perturbation Hamiltonian to each electron?<br><br=
><div><hr id=3D"stopSpelling">From: owner-chemistry:-:ccl.net<br>To: sergio.m=
anzetti:-:gmx.com<br>Subject: CCL: Exchange correlation<br>Date: Fri=2C 13 Ju=
n 2014 16:48:04 -0400<br><br>=0A=
=0A=
=0A=
=0A=
=0A=
Do you mean "exchange correlation" referring to a choice in an=0A=
exchange-correlation <i>functional </i>(KS-DFT framework) or=0A=
"exchange and correlation" referring to in a wavefunction formalism?<br=
></div> </div></body>
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