From owner-chemistry@ccl.net Wed Oct 1 08:04:00 2014 From: "Varun Kundi chemvarun*_*gmail.com" To: CCL Subject: CCL: Invitation to cooperate in calculations for joint article Message-Id: <-50542-140930231752-2875-UIDOJtXCe07WCFsrQ11irg^^server.ccl.net> X-Original-From: Varun Kundi Content-Type: multipart/alternative; boundary=089e01493c945ea600050453f147 Date: Wed, 1 Oct 2014 08:47:41 +0530 MIME-Version: 1.0 Sent to CCL by: Varun Kundi [chemvarun=-=gmail.com] --089e01493c945ea600050453f147 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Yes Sure On Tue, Sep 30, 2014 at 10:51 PM, Daniel Glossman-Mitnik dglossman .. gmail.com wrote: > Dear Arvydas, > > Please let me know which kind of calculations you do want to perform, to > see if I can help you. > > Best regards, > > Daniel > > > > *************************************************************************= ************************************** > Dr. Daniel Glossman-Mitnik > Laboratorio Virtual NANOCOSMOS > Centro de Investigaci=F3n en Materiales Avanzados, SC > Departamento de Medio Ambiente y Energ=EDa > Miguel de Cervantes 120 - Comp. Ind. Chihuahua - Chihuahua, Chih 31109, > Mexico > Phone: +52 614 4391151 FAX: +52 614 4394884 Lab: +52 614 4394805 > E-mail: daniel.glossman[*]cimav.edu.mx dglossman[*]gmail.com > WWW: http://www.cimav.edu.mx/cv/daniel.glossman > http://blogs.cimav.edu.mx/daniel.glossman > > *************************************************************************= ************************************** > > 2014-09-30 6:58 GMT-06:00 Arvydas Tamulis tamulis9#,#gmail.com < > owner-chemistry[*]ccl.net>: > >> Dear Colleagues, >> >> I am inviting researchers who possess computational time on powerful >> computers to participate in the calculations of the TD DFT spectrum of >> large bioorganic system. I will include you in the list of authors of my >> new writing joint article. >> >> This our new joint article will be similar to examples of my two last >> years publications: >> >> 1. Arvydas Tamulis, Mantas Grigalavicius and Jonas Baltrusaitis, (2013) >> "Phenomenon of Quantum Entanglement in a System Composed of Two Minimal >> Protocells", *Origins of Life and Evolution of Biospheres,* 43:49-66, >> DOI 10.1007/s11084-012-9323-0, available in electronic version at >> *http://link.springer.com/article/10.1007%2Fs11084%C2%AD012%C2%AD9323%C2= %AD0* >> , >> >> 2. Arvydas Tamulis and Mantas Grigalavicius, "Molecular Spintronics >> Control of Photosynthesis in Artificial Cell", "*Journal of >> Computational and Theoretical Nanoscience*", vol. 10, No 4, p.p. 989-995= , >> 2013. >> >> 3. Arvydas Tamulis, Mantas Grigalavicius, "Quantum Entanglement in >> Photoactive Prebiotic Systems. journal *Systems and Synthetic Biology",* >> vol. 8, p.p. 117-140., 2014. >> >> 4. Arvydas Tamulis, Mantas Grigalavicius, Sarunas Krisciukaitis, "Quantu= m >> Entanglement in a System Composed of Two Prebiotic Kernels with Molecula= r >> Spintronics Logic Devices for Control of Photosynthesis" *Journal of >> Computational and Theoretical Nanoscience, *vol. 11, p.p. 1597-1608, >> 2014. >> >> 5. Arvydas Tamulis and Mantas Grigalavicius, "Quantum Mechanical Origin >> of Fatty Acid Life and Correlations with Anthropic Principle and Old >> Testament", journal *Quantum Matter* of the American Scientific >> Publishers, vol. 3, p.p.460-468, 2014. >> >> 6. Tamulis A, Berteska L, Grigalavicius M, Baltrusaitis J, "Quantum Dyna= mics of Self-Assembly of Minimal Photosynthetic Cells", journal *Quantum Ma= tter* of the American Scientific Publishers*, *31 pages article accepted on= February 2014.7. Tamulis A, Grigalavicius M, Serbenta J, Plausinaitis K (2= 014) "Quantum Entangled Single BioOrganic Supramolecules as Light Absorbing= and Light Emitting Logical Devices", 32 pages research article is accepted= in the *Journal of Computational and Theoretical Nanoscience**. *June, 201= 4. >> >> >> With best regards, >> >> Arvydas Tamulis, >> >> Independent expert of European Commission >> >> http://www.itpa.lt/~tamulis/ >> > > --=20 With Regards *Varun Kundi* (Research Scholar) Theoretical Chemistry Lab, Department of Chemistry *Indian Institute of Technology, Roorkee.* Roorkee- 247 667 , UTTARAKHAND , INDIA Phone- 01332-286228 (O), 09458113440(M) Email- bmrvkdcy---iitr.ernet.in , chemvarun---gmail.com --089e01493c945ea600050453f147 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Yes Sure

On Tue, Sep 30, 2014 at 10:51 PM, Daniel Glossman-Mitnik dglo= ssman .. gmail.com <<= a href=3D"mailto:owner-chemistry---ccl.net" target=3D"_blank">owner-chemistry= ---ccl.net> wrote:
Dear Arvydas,

Please let me know which kind of = calculations you do want to perform, to see if I can help you.
Best regards,

Daniel


*********************= ***************************************************************************= ***************
Dr. Daniel Glossman-Mitnik
Laboratorio Virtual NANOC= OSMOS
Centro de Investigaci=F3n en Materiales Avanzados, SC
Departame= nto de Medio Ambiente y Energ=EDa
Miguel de Cervantes 120 - Comp. Ind. C= hihuahua - Chihuahua, Chih 31109, Mexico
Phone: +52 614 4391151   F= AX: +52 614 4394884    Lab: +52 614 4394805
E-mail:  daniel.glos= sman[*]cimav.edu.mx          dglossman[*]gmail.com
WWW:=   http://www.cimav.edu.mx/cv/daniel.glossman
     =         http://blogs.cimav.edu.mx/daniel.glossman
= ***************************************************************************= ************************************

2014-09-30 6:58 GMT-06:00 Arvydas Tamulis ta= mulis9#,#gmail.com <owner-chemistry[*]ccl.net>:
=09 =09 =09 =09

Dear Colleagues,

I am inviting researchers who possess computational time on powerful computers to partici= pate in the calculations of the TD DFT spectrum of large bioorganic system. I will include you in the list of authors of my new writing joint article.

This our new joint article will be similar to examples of my two last years publications:

1<= span style=3D"background:none repeat scroll 0% 0% rgb(255,255,255)">. Arvydas Tamulis, Mantas Grigalavicius and Jonas Baltrusaitis<= /span>, (2013) „Phenomenon of Quantum Entanglement in a System Composed of Two Minimal Protocells“, Origins of Life and Evolution of Biospheres,= = 43:49–66, DOI 10.1007/s11084-012-9323-0, available in electronic version at http://link.springer.com/article= /10.1007%2Fs11084%C2%AD012%C2%AD9323%C2%AD0= = = ,

2. Arvy= das Tamulis and Mantas Grigalavicius, “Molecular Spintronics Control of Photosynthesis in <= /span>Artificial Cell”, “Journal of Computational and Theoretical Nanoscience”, vol. 10, No 4, p.p. 989-995, 2013.

3<= /font>. Arvydas Tamulis, Mantas Grigalavicius, “Quantum Entanglement in Photoactive Prebiotic Systems. journal <= font face=3D"Times New Roman, serif">Systems and Synthetic Biology”,= vol. 8, p.p. 117-140., 2014.

4<= span lang=3D"lt-LT">. Arvydas Tamulis, Mantas Grigalavicius, Sarunas Krisciukaitis,<= /font> „Quantum Entanglement in a System Composed of Two Prebiotic Kernels with Molecular Spintronics Logic Devices for Control of Photosynthesis“ Journal of Computational and Theoretical Nanoscience, vol. 11, p.p. 1597-1608, 2014.<= /span>

5<= span lang=3D"lt-LT">. Arvyd= as Tamulis and Mantas Grigalavicius,= “Quantum Mechanical Origin of Fatty Acid Life and Correlations with Anthropic Principle and Old Testament”, journal Quantum Matter <= span style=3D"text-decoration:none">of the American Scientific Publishers, vol. 3, p.p.460-468, 2014.<= /span>

<=
span style=3D"background:none repeat scroll 0% 0% rgb(255,255,255)">6. Tamulis A, Berteska L, Grigalavic=
ius M, Baltrusaitis J, “Quantum Dynamics of Self-Assembly of Minimal =
Photosynthetic Cells”, journal <=
/span>Q=
uantum Matter =
of the American Scientific Publishers, 31=
 pages article accepted on February 2014.
7. Tamulis A, Grigalavicius M, Serbenta J, Plausinaitis K (2014) &bdquo=
;Quantum Entangled Single BioOrganic Supramolecules as Light Absorbing and =
Light Emitting Logical Devices“, 32 pages research article is accepte=
d in the Jour=
nal of Computational and Theoretical Nanoscience. June,=
 <=
/span>2014.


With best regards,

Arvydas Tamulis,

Independent expert of European Commission

http://www.itpa.lt/~tamulis/





--
= With Regards

Varun Kundi= (Research Scholar)
Theoretical Chemistry Lab,
Department of= Chemistry
Indian Institute of Technology, Roorkee.Ro= orkee- 247 667 , UTTARAKHAND , INDIA
Phone- 01332-286228 (O), 094581= 13440(M)
Email- bmrvkdcy---iitr.ernet.i= n , chemvarun---gmail.com
--089e01493c945ea600050453f147-- From owner-chemistry@ccl.net Wed Oct 1 08:39:00 2014 From: "Jan H Jensen jhjensen*|*chem.ku.dk" To: CCL Subject: CCL: Computational Chemistry Highlight: September issue Message-Id: <-50543-141001032935-25532-8ygtl/6z+5p/6aHM3afVfA]~[server.ccl.net> X-Original-From: "Jan H Jensen" Date: Wed, 1 Oct 2014 03:29:33 -0400 Sent to CCL by: "Jan H Jensen" [jhjensen++chem.ku.dk] The September issue of Computational Chemistry Highlights is out. CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here. Table of content for this issue features contributions from CCH editors Steven Bachrach and Jan Jensen: Why Bistetracenes Are Much Less Reactive Than Pentacenes in DielsAlder Reactions with Fullerenes http://www.compchemhighlights.org/2014/09/why-bistetracenes-are-much-less.html A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations http://www.compchemhighlights.org/2014/09/a-general-quantum-mechanically-derived.html Perspective: Fifty years of density-functional theory in chemical physics http://www.compchemhighlights.org/2014/09/perspective-fifty-years-of-density.html A Quantum Mechanical Jack in the Box: Rapid Rearrangement of a Tetrahedryl-Tetrahedrane via Heavy Atom Tunneling http://www.compchemhighlights.org/2014/09/a-quantum-mechanical-jack-in-box-rapid.html Fullerene Van der Waals Oligomers as Electron Traps http://www.compchemhighlights.org/2014/09/fullerene-van-der-waals-oligomers-as.html Transition State Analysis of Enantioselective Brnsted Base Catalysis Chiral Cyclopropenimines http://www.compchemhighlights.org/2014/09/transition-state-analysis-of.html 8-Electron Tautomeric Benziphthalocyanine: A Functional Near-Infrared Dye with Tunable Aromaticity http://www.compchemhighlights.org/2014/09/8-electron-tautomeric.html Interested in more? There are many ways to subscribe to CCH updates. From owner-chemistry@ccl.net Wed Oct 1 09:14:00 2014 From: "Scott Habershon S.Habershon*warwick.ac.uk" To: CCL Subject: CCL: Computational Molecular Science - University of Warwick, March 2015 Message-Id: <-50544-141001051859-30748-x68YGWakwLzuIgXNNzde1A{}server.ccl.net> X-Original-From: "Scott Habershon" Date: Wed, 1 Oct 2014 05:18:58 -0400 Sent to CCL by: "Scott Habershon" [S.Habershon:_:warwick.ac.uk] * * COMPUTATIONAL MOLECULAR SCIENCE 2015 * * 15 - 18 March 2015 * University of Warwick, UK * Registration opens: 1st October 2014 * Website: http://go.warwick.ac.uk/cms2015 * Dear Colleagues, You are warmly invited to participate in Computational Molecular Science (CMS) 2015 at the University of Warwick, Coventry, UK in March 2015. The latest in the CMS conference series, CMS2015 will highlight recent work in a wide range of topics, including: - Electronic structure; - Biomolecular simulations; - Charge transfer processes; - Coarse-grained simulations; - Quantum dynamics; - Reaction mechanisms; - Excited-state dynamics..and more.. KEYNOTE SPEAKERS: * Prof. Michael Levitt (Stanford, USA) * Prof. Sharon Hammes-Schiffer (Illinois, USA) * Prof. George Schatz (Northwestern, USA) * Prof. Cecilia Clementi (Rice, USA) * Prof. Gerhard Hummer (MPI, Germany) INVITED SPEAKERS: * Dr. Robert Paton (Oxford, UK) * Prof. Amparo Galindo (Imperial, UK) * Dr. Edina Rosta (Kings, UK) * Prof. David Manolopoulos (Oxford, UK) * Prof. David Tozer (Durham, UK) * Prof. Fred Manby (Bristol, UK) * Prof. Ian Williams (Bath, UK) * Dr. Tanja van Mourik (St. Andrews, UK) * Dr. David Willock (Cardiff, UK) * Prof. Jochen Blumberger (UCL, UK) * Prof. Ali Alavi (Cambridge, UK) * Prof. Michele Vendruscolo (Cambridge, UK) * Prof. Jonathan Hirst (Nottingham, UK) * Prof. John McGrady (Oxford, UK) * Prof. Sally Price (UCL, UK) Registration for CMS will OPEN ON 1ST OCTOBER 2014. Registration will include 3 nights ensuite accomodation, and all meals during the conference. The meeting will also include a poster session for postgraduate and postdoctoral researchers, with poster prizes available. We look forward to welcoming you to the University of Warwick in 2015! Yours sincerely, CMS organising committee: Scott Habershon, Rebecca Notman, David Quigley, Robert Deeth, Alessandro Troisi and Mark Rodger > From: Scott Habershon (S.Habershon=-=warwick.ac.uk) From owner-chemistry@ccl.net Wed Oct 1 14:40:01 2014 From: "Adam Tenderholt atenderholt * gmail.com" To: CCL Subject: CCL:G: cclib v1.3b released Message-Id: <-50545-141001143815-9601-RX/dQVlgs66aSETDwoF65g(~)server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=001a1139fdda3fe504050460cdd5 Date: Wed, 1 Oct 2014 11:37:50 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt-$-gmail.com] --001a1139fdda3fe504050460cdd5 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable On behalf of the cclib development team, we are pleased to announce the release of cclib 1.3b, which is now available for download from http://cclib.github.io. This version includes three new parsers (for NWchem, Psi and QChem), as well as a number of bug fixes and improvements (see below). cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, Firefly, GAMESS (US), GAMESS-UK, Gaussian, Jaguar, Molpro, NWChem, ORCA, Psi and QChem. Among other data, cclib extracts: * coordinates and energies * information about geometry optimization * atomic orbital information * molecular orbital information * information on vibrational modes * the results of a TD-DFT calculation * charges and mutlipole moments (For a complete list see http://cclib.github.io/data.html). cclib also provides some calculation methods for interpreting the electronic properties of molecules using analyses such as: * Mulliken and Lowdin population analyses * Overlap population analysis * Calculation of Mayer's bond orders. (For a complete list see http://cclib.github.io/methods.html). For information on how to use cclib, see http://cclib.github.io/tutorial.html If you need help, find a bug, want new features or have any questions, please send an email to our mailing list: https://lists.sourceforge.net/lists/listinfo/cclib-users If your published work uses cclib, please support its development by citing the following article: N. M. O'Boyle, A. L. Tenderholt, K. M. Langner, cclib: a library for package-independent computational chemistry algorithms, J. Comp. Chem. 29 (5), 839-845 (2008) You can also specifically reference the newest stable version of cclib as: Karol M. Langner, Noel M. O'Boyle, and Adam L. Tenderholt. Release of cclib version 1.2. 2014. http://dx.doi.org/10.5281/zenodo.11668. Regards, The cclib development team =E2=80=94=E2=80=94- Major changes since cclib 1.2: Features: * New parser: cclib can now parse NWChem files * New parser: cclib can now parse Psi (versions 3 and 4) files * New parser: cclib can now parse QChem files (by Eric Berquist) * Replace PC-GAMESS tests with Firefly versions * Many bugfixes, thanks to Martin Rahm, Russell Johnson, Matt Ernst and others --001a1139fdda3fe504050460cdd5 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
On behalf of the cclib development team, we are pleas= ed to announce the release of cclib 1.3b, which is now available for downlo= ad from http://cclib.github.io. This= version includes three new parsers (for NWchem, Psi and QChem), as well as= a number of bug fixes and improvements (see below).

cclib is an open source library, written in Python, for parsing and inte= rpreting the results of computational chemistry packages. It currently pars= es output files from ADF, Firefly, GAMESS (US), GAMESS-UK, Gaussian, Jaguar= , Molpro, NWChem, ORCA, Psi and QChem.

Among other= data, cclib extracts:

=C2=A0 =C2=A0 * coordinates= and energies
=C2=A0 =C2=A0 * information about geometry optimiza= tion
=C2=A0 =C2=A0 * atomic orbital information
=C2=A0 = =C2=A0 * molecular orbital information
=C2=A0 =C2=A0 * informatio= n on vibrational modes
=C2=A0 =C2=A0 * the results of a TD-DFT ca= lculation
=C2=A0 =C2=A0 * charges and mutlipole moments

(For a complete list see http://cclib.github.io/data.html).

= cclib also provides some calculation methods for interpreting the electroni= c properties of molecules using analyses such as:

= =C2=A0 =C2=A0 * Mulliken and Lowdin population analyses
=C2=A0 = =C2=A0 * Overlap population analysis
=C2=A0 =C2=A0 * Calculation = of Mayer's bond orders.=C2=A0

(For a complete = list see http://cclib.githu= b.io/methods.html).

For information on how to = use cclib, see

=
If you need help, find a bug, want new features or have any ques= tions, please send an email to our mailing list:

If your published work uses cclib, = please support its development by citing the following article:
= =C2=A0 =C2=A0 N. M. O'Boyle, A. L. Tenderholt, K. M. Langner, cclib: a = library for package-independent computational chemistry algorithms, J. Comp= . Chem. 29 (5), 839-845 (2008)

You can also specif= ically reference the newest stable version of cclib as:
=C2=A0 = =C2=A0 Karol M. Langner, Noel M. O'Boyle, and Adam L. Tenderholt. Relea= se of cclib version 1.2. 2014. http://dx.doi.org/10.5281/zenodo.11668.


Regards,

=C2=A0The cclib developme= nt team

=E2=80=94=E2=80=94-

Major changes since cclib 1.2:

Features:
<= div> * New parser: cclib = can now parse NWChem files
* New parser: cclib can now parse Psi (versions 3 and 4) files=
* New parser:= cclib can now parse QChem files (by Eric Berquist)
=C2=A0 =C2=A0= * Replace PC-GAMESS tests with Firefly versions
=C2=A0 =C2=A0 * = Many bugfixes, thanks to Martin Rahm, Russell Johnson, Matt Ernst and other= s

--001a1139fdda3fe504050460cdd5--