From owner-chemistry@ccl.net Sun Jul 27 15:52:00 2014 From: "Andreas Klamt klamt[A]cosmologic.de" To: CCL Subject: CCL: Unsolved Problems Message-Id: <-50366-140726042036-4054-DweIQ4W+E7gFa82h9Nsgvw:-:server.ccl.net> X-Original-From: Andreas Klamt Content-Type: multipart/alternative; boundary="------------010606030305030804090505" Date: Sat, 26 Jul 2014 10:20:37 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt._._.cosmologic.de] This is a multi-part message in MIME format. --------------010606030305030804090505 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Joe, while I doubt that our COSMO-RS based pKa method fulfills the criteria of your first point, I would clearly say that our recently published HB prediction scheme based on the COSMO polarization charge densities (PCCP 2012 and 2013) and our COSMO-RS based pKa method fulfill the criteria the second point on your wish list. Andreas Am 25.07.2014 02:57, schrieb Joe Leonard jleonard42-.-gmail.com: > Thought of two more: > > - a pka model or method good / fast enough to indicate which atoms > should or shouldn't be protonated at biological ph. Extra points if > this can be used iteratively when multiple centres are present. This > should work with drug like molecules and be extensible to peptides and > proteins. > > This of course should work generally rather than being training set > dependent etc. > > - "a qm-based pharmacophore scheme". A model for Hbond prediction and > proton donor / acceptor that's not rule based. > > Joe > On Jul 24, 2014, at 5:38 PM, Rajarshi Guha guhar]=[mail.nih.gov > > wrote: > >> One more for the list - a statistical basis for structural similarity >> (something akin to BLAST e-values that is not dependent on a specific >> sample of structures) >> >> >> On Thu, Jul 24, 2014 at 4:25 PM, Joe Leonard jleonard42 : gmail.com >> > > wrote: >> >> Hmm... How about: >> >> - A (docking) scoring function that actually worked - was >> predictive, extensible and reproducible >> - A force field that worked well for both large and small >> molecules (separately and in combination) >> >> Are these on the level of string theory? No. But there's real, >> concrete problems facing industrial (and some academic) >> researchers that should be addressed. There are others, but this >> should get things started. >> >> Joe >> >> On Jul 24, 2014, at 3:28 PM, Sebastian Kozuch >> seb.kozuch:gmail.com >> > >> wrote: >> >>> >>> Sent to CCL by: "Sebastian Kozuch" [seb.kozuch|a|gmail.com >>> ] >>> Dear CCL users, >>> Except for some bashing to a particular computational chemistry >>> journal, in the last months we have been slow on controversial >>> and/or philosophical questions (it feels like the double blind >>> reviewing and the patriarchalization of conferences debates >>> happened ages ago). >>> So here is a question. It draw my attention that there are lists >>> of unsolved problems on several topics >>> (en.wikipedia.org/wiki/List_of_unsolved_problems >>> ), >>> including chemistry. >>> >>> What would be a List of Unsolved Problems in Theoretical and >>> Computational Chemistry? >>> >>> (Please dont say something obvious like solving the relativistic >>> full CI of a protein.) >>> >>> Best, >>> Sebastian >>> >>> >>> >>> -= This is automatically added to each message by the mailing >>> script =- >>> To recover the email address of the author of the message, >>> please change >>> the strange characters on the top line to the {} sign. You can also >>> >>> >>> E-mail to subscribers: CHEMISTRY{}ccl.net >>> or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net >>> or use>>> >> Conferences: >>> http://server.ccl.net/chemistry/announcements/conferences/>>> >>> If your mail bounces > from CCL with 5.7.1 error, check:>>> >>> >> >> -- >> How self-centered do you have to be to tell yourself that >> someone else's rights aren't real, but yours are? >> >> >> >> >> >> >> -- >> Rajarshi Guha | http://blog.rguha.net >> National Center for Advancing Translational Science > > -- > How self-centered do you have to be to tell yourself that > someone else's rights aren't real, but yours are? > > > -- Prof. Dr. Andreas Klamt CEO / Geschäftsführer 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 --------------010606030305030804090505 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Joe,

while I doubt that our COSMO-RS based pKa method fulfills the criteria of your first point, I would clearly say that our recently published HB prediction scheme based on the COSMO polarization charge densities (PCCP 2012 and 2013) and our COSMO-RS based pKa method fulfill the criteria the second point on your wish list.

Andreas

Am 25.07.2014 02:57, schrieb Joe Leonard jleonard42-.-gmail.com:
Thought of two more:

- a pka model or method good / fast enough to indicate which atoms should or shouldn't be protonated at biological ph.  Extra points if this can be used iteratively when multiple centres are present.  This should work with drug like molecules and be extensible to peptides and proteins. 

This of course should work generally rather than being training set dependent etc. 

- "a qm-based pharmacophore scheme". A model for Hbond prediction and proton donor / acceptor that's not rule based. 

Joe
On Jul 24, 2014, at 5:38 PM, Rajarshi Guha guhar]=[mail.nih.gov <owner-chemistry[a]ccl.net> wrote:

One more for the list - a statistical basis for structural similarity (something akin to BLAST e-values that is not dependent on a specific sample of structures)


On Thu, Jul 24, 2014 at 4:25 PM, Joe Leonard jleonard42 : gmail.com <owner-chemistry|ccl.net> wrote:
Hmm...  How about:

- A (docking) scoring function that actually worked - was predictive, extensible and reproducible
- A force field that worked well for both large and small molecules (separately and in combination)

Are these on the level of string theory?  No.  But there's real, concrete problems facing industrial (and some academic) researchers that should be addressed.  There are others, but this should get things started.

Joe

On Jul 24, 2014, at 3:28 PM, Sebastian Kozuch seb.kozuch:gmail.com <owner-chemistry{}ccl.net> wrote:


Sent to CCL by: "Sebastian  Kozuch" [seb.kozuch|a|gmail.com]
Dear CCL users,
Except for some bashing to a particular computational chemistry journal, in the last months we have been slow on controversial and/or philosophical questions (it feels like the double blind reviewing and the patriarchalization of conferences debates happened ages ago).
So here is a question. It draw my attention that there are lists of unsolved problems on several topics (en.wikipedia.org/wiki/List_of_unsolved_problems), including chemistry.

What would be a List of Unsolved Problems in Theoretical and Computational Chemistry?

(Please dont say something obvious like solving the relativistic full CI of a protein.)

Best,
Sebastian


the strange characters on the top line to the {} sign. You can also


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--
How self-centered do you have to be to tell yourself that someone else's rights aren't real, but yours are?






--
Rajarshi Guha | http://blog.rguha.net
National Center for Advancing Translational Science

--
How self-centered do you have to be to tell yourself that someone else's rights aren't real, but yours are?





-- 
Prof. Dr. Andreas Klamt
CEO / Geschäftsführer
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
--------------010606030305030804090505-- From owner-chemistry@ccl.net Sun Jul 27 16:27:00 2014 From: "Roy Tien reypwg]|[gmail.com" To: CCL Subject: CCL:G: Spin-orbit coupling at CASSCF level by Gaussian09 Message-Id: <-50367-140726131134-14369-j6PmGBbp8XVVIT09Z0ATZA%a%server.ccl.net> X-Original-From: "Roy Tien" Date: Sat, 26 Jul 2014 13:11:33 -0400 Sent to CCL by: "Roy Tien" [reypwg#,#gmail.com] Dear CCLers, Could you provided me an example input of S-O coupling calculations at CASSCF level by using Gaussian09 program? Thank you in advance. Roy From owner-chemistry@ccl.net Sun Jul 27 17:02:00 2014 From: "Giuseppe Mallia g.mallia#%#imperial.ac.uk" To: CCL Subject: CCL:G: workshop: MSSC2014 - Ab initio Modelling in Solid State Chemistry Message-Id: <-50368-140726160457-32307-7g0sJY/SmDgupaJ2xVOi2Q(!)server.ccl.net> X-Original-From: "Giuseppe Mallia" Date: Sat, 26 Jul 2014 16:04:56 -0400 Sent to CCL by: "Giuseppe Mallia" [g.mallia ~ imperial.ac.uk] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ WORKSHOP ANNOUNCEMENT MSSC2014 - Ab initio Modelling in Solid State Chemistry ==> London Edition (New Users): Discovering quantum-mechanical simulations with CRYSTAL http://www3.imperial.ac.uk/mssc2014 London (UK), September 15-19, 2014 Directors: L. Bernasconi - N.M. Harrison - G. Mallia ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The week long school is designed for CRYSTAL users, PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis, magnetism and nano-science. It will provide both an introduction to the capabilities of quantum mechanical simulation and to the practical use of CRYSTAL (http://www.crystal.unito.it/) and CRYSCOR (http://www.cryscor.unito.it). New tutorials are available in the afternoon section. . The programme is on-line; please visit the following link: http://www3.imperial.ac.uk/mssc2014/programme Please note: Thursday 31st July - Deadline for payment of standard fees ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CRYSTAL14 The new version of CRYSTAL is available at the Crystal Solutions web site. CRYSTAL is a general-purpose program for the study of crystalline solids. It computes the electronic structure of periodic systems (3D, 2D, 1D) within Hartree Fock, density functional or various hybrid HF/DFT approximations. The Bloch functions of the periodic systems are expanded as linear combinations of atom centred Gaussian functions. Powerful screening techniques are used to exploit real space locality. Space group symmetry is also fully exploited. CRYSTAL14 is a major release and the most relevant new features are: - Static first- and second-hyperpolarizability and the corresponding electric susceptibilities tensors through a Coupled Perturbed HF/KS scheme - Improved phonon dispersion calculation (phonon band structure and DOSs, ADPs and Debye-Waller factors, ...) - Raman and IR intensities through a CPHF/KS approach - Automated calculation of the piezoelectric and photoelastic tensors of crystalline systems - New DFT functionals: mGGA, Range-separated hybrids and Double-hybrids - Automatic generation of fullerene-like structures - New tools to model low-dimensionality systems (nanorods, nanoparticles, ..) - New tools for the treatment of solid solutions - Improved Massive-parallel version (MPPcrystal - distributed memory) - Internal interface to CRYSCOR for electronic structure calculations of 1D,- 2D- and 3D-periodic non-conducting systems at the L-MP2 correlated level and Double-Hybrids - Internal interface to TOPOND for topological analysis of the charge density Binaries are available for different platforms. For an easier installation on Linux, RPM and DEB packages are now available. For further information: CRYSTAL web site: www.crystal.unito.it Crystal Solutions web site: www.crystalsolutions.eu Contacts: info~~crystalsolutions.eu ; crystal~~unito.it ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~