From owner-chemistry@ccl.net Sat Jun 14 03:29:01 2014 From: "Susi Lehtola susi.lehtola.++.alumni.helsinki.fi" To: CCL Subject: CCL: Exchange correlation Message-Id: <-50216-140614032234-22811-1UUDijLvccfrVJX/Tu2A2Q++server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Sat, 14 Jun 2014 10:22:26 +0300 MIME-Version: 1.0 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" 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" To: CCL Subject: CCL: Exchange correlation Message-Id: <-50217-140614032832-23059-rMhNP4/H7q/4+I5UleOElg.:.server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Sat, 14 Jun 2014 10:28:24 +0300 MIME-Version: 1.0 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" 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" To: CCL Subject: CCL: Prasenjit - Quering about Transition States Message-Id: <-50218-140614044727-13919-1fx+URo898bPntoSSJugRA(0)server.ccl.net> X-Original-From: Content-Language: en-GB Content-Type: multipart/alternative; boundary="_000_140273572980335450surreyacuk_" Date: Sat, 14 Jun 2014 08:47:16 +0000 MIME-Version: 1.0 Sent to CCL by: [p.d.jarowski_._surrey.ac.uk] --_000_140273572980335450surreyacuk_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable 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 on behalf of Victor Rosas Garcia= rosas.victor[]gmail.com 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 >: 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_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello:


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.


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.


Best,


Peter

From: 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>
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 wa= nt 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 syst= ems? 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.p= rasenjit*_*gmail.com <owner-chemistry||ccl.net>:
Hi,

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.

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? 

I would really appreciate if someone has some idea regarding this matt= er.

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_-- From owner-chemistry@ccl.net Sat Jun 14 07:26:00 2014 From: "Barry Hardy barry.hardy^^vtxmail.ch" To: CCL Subject: CCL: anti-malarial drug design Message-Id: <-50219-140614072443-15760-6QO8uY1YIAMwtr8fDcYkUA+*+server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Sat, 14 Jun 2014 13:24:32 +0200 MIME-Version: 1.0 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" 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 Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Sat, 14 Jun 2014 13:54:30 +0200 MIME-version: 1.0 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. Víctor Luaña From owner-chemistry@ccl.net Sat Jun 14 18:07:01 2014 From: "Sergio Manzetti sergio.manzetti|outlook.com" To: CCL Subject: CCL: Exchange correlation Message-Id: <-50221-140614033634-25453-eBXKVsu5nkMd4ZmAXZEk6w_._server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary="_6837bddb-9104-48ff-b874-ed3ffe8f6306_" Date: Sat, 14 Jun 2014 09:36:26 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti^^^outlook.com] --_6837bddb-9104-48ff-b874-ed3ffe8f6306_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable 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? = --_6837bddb-9104-48ff-b874-ed3ffe8f6306_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
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?
From: owner-chemistry:-:ccl.net
To: sergio.m= anzetti:-:gmx.com
Subject: CCL: Exchange correlation
Date: Fri=2C 13 Ju= n 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?
= --_6837bddb-9104-48ff-b874-ed3ffe8f6306_--