From owner-chemistry@ccl.net Mon Jul 30 11:10:00 2012 From: "manish kumar upadhyay manish.d912]=[hotmail.com" To: CCL Subject: CCL: Problems on NICS calculation Using Gaussian Message-Id: <-47294-120730053250-16173-CJriOI/0y9H1Or7KgpcW1g^^^server.ccl.net> X-Original-From: "manish kumar upadhyay" Date: Mon, 30 Jul 2012 05:32:47 -0400 Sent to CCL by: "manish kumar upadhyay" [manish.d912*|*hotmail.com] Sir,I wanted to know the stepwise procedure to calculate the nuclear independent chemical shieft values at any given point of space in a molecule using a ghost atom (Bq),as were praposed by Schleyer. Kindly tell me the all steps involed the processes starting from submittin a job and analysing its output. From owner-chemistry@ccl.net Mon Jul 30 11:45:00 2012 From: "Mahmoud Ahmed Noamaan Noamaan85*gmail.com" To: CCL Subject: CCL: Strange angle Message-Id: <-47295-120730093917-16858-wRVe8VpVubvLUsgdRUDTVw[]server.ccl.net> X-Original-From: "Mahmoud Ahmed Noamaan" Date: Mon, 30 Jul 2012 09:39:15 -0400 Sent to CCL by: "Mahmoud Ahmed Noamaan" [Noamaan85!A!gmail.com] Dear All respectable CCL members, I know that it may be trivial but I was surprised with the following behavior. While doing a TS search the final output with normal termination show in the optimized Parameters section the following ! A11 A(4,5,7) 126.9034 -DE/DX = 0.0 ! ! A12 A(2,8,9) 110.5261 -DE/DX = 0.0! ! A13 L(8,9,10,6,-1) 199.1901 -DE/DX = 0.0! ! A14 L(8,9,10,6,-2) 223.1914 -DE/DX = 0.0! ! D1 D(5,1,2,3) 5.1951 -DE/DX = 0.0! The A11 and D1 are normal angles and dihedral angels but for angle A13 and A14 what is the meaning of the numbers 8,9,10,6,-1 we usually need 3 atom numbers to define an angle and 4 for dihedral so what is the need for 5 numbers and I wonder what are there meaning? Thanks From owner-chemistry@ccl.net Mon Jul 30 12:19:01 2012 From: "Chirag Vora chirag740===gmail.com" To: CCL Subject: CCL: Smartphone applications for bioinformaticians and computational chemists Message-Id: <-47296-120730113042-10387-Z+govhv+cFrGMa6Et5GKfg]|[server.ccl.net> X-Original-From: Chirag Vora Content-Type: multipart/alternative; boundary=20cf307f343e3e050c04c60dbe06 Date: Mon, 30 Jul 2012 21:00:35 +0530 MIME-Version: 1.0 Sent to CCL by: Chirag Vora [chirag740|gmail.com] --20cf307f343e3e050c04c60dbe06 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable A list of smartphone apps, especially useful for bioinformaticians and computational chemists can be found here: Most of them are available for free. Link: http://eventheodd.blogspot.com/2012/07/smartphone-apps-to-improve-your.html Applications reviewed in this post are: - SimGene - GeneticCode - Phylogram - BioGene - Bio-IT World - Esmol and NDKmol =96 Molecular Viewer If you are aware about more of such smartphone applications, please feel free to leave a comment here . Regards, Molecular Modelling Blog --20cf307f343e3e050c04c60dbe06 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable A list of smartphone apps, especially useful for bioinformaticians and comp= utational chemists can be found here:
Most of them are available for fre= e.

Link: http://eventheodd.blogspot.c= om/2012/07/smartphone-apps-to-improve-your.html


Applications reviewed in this post are:
  • SimGene
  • = GeneticCode
  • Phylogram
  • BioGene
  • Bio-IT World
  • = Esmol and NDKmol =96 Molecular Viewer

If you are aware abou= t more of such smartphone applications, please feel free to leave a comment= here.

Regards,
Molecular Modelling Blog

--20cf307f343e3e050c04c60dbe06-- From owner-chemistry@ccl.net Mon Jul 30 12:54:01 2012 From: "Chirag Vora chirag740],[gmail.com" To: CCL Subject: CCL: Smartphone applications for bioinformaticians and computational chemists Message-Id: <-47297-120730115915-29299-3QStjJbQOz83MthAqNW8yg#%#server.ccl.net> X-Original-From: Chirag Vora Content-Type: multipart/alternative; boundary=bcaec54ee2824d5ac504c60e24fb Date: Mon, 30 Jul 2012 21:29:07 +0530 MIME-Version: 1.0 Sent to CCL by: Chirag Vora [chirag740\a/gmail.com] --bcaec54ee2824d5ac504c60e24fb Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable A list of smartphone apps, especially useful for bioinformaticians and computational chemists can be found here: Most of them are available for free. Link: http://eventheodd.blogspot.com/2012/07/smartphone-apps-to-improve-your.html Applications reviewed in this post are: - SimGene - GeneticCode - Phylogram - BioGene - Bio-IT World - Esmol and NDKmol =96 Molecular Viewer If you are aware about more of such smartphone applications, please feel free to leave a comment on the link above. Thank you. ----- Regards, Molecular Modelling Blog --bcaec54ee2824d5ac504c60e24fb Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable A list of smartphone apps, especially useful for bioinformaticians and comp= utational chemists can be found here:
Most of them are available for fre= e.

Link: http://eventheodd.blogspot.c= om/2012/07/smartphone-apps-to-improve-your.html


Applications reviewed in this post are:
  • SimGene
  • = GeneticCode
  • Phylogram
  • BioGene
  • Bio-IT World
  • = Esmol and NDKmol =96 Molecular Viewer

If you are aware about mo= re of such smartphone applications, please feel free to leave a comment=A0o= n the link above.



Thank you.
-----
Regards,
Molecular Modellin= g Blog --bcaec54ee2824d5ac504c60e24fb-- From owner-chemistry@ccl.net Mon Jul 30 21:02:00 2012 From: "cina foroutan canyslopus\a/yahoo.co.uk" To: CCL Subject: CCL:G: Problems on NICS calculation Using Gaussian Message-Id: <-47298-120730170936-18825-tZy5oQnUiPuFIxSF0Biq8A,,server.ccl.net> X-Original-From: cina foroutan Content-Type: multipart/alternative; boundary="-357169082-1354380957-1343682567=:36898" Date: Mon, 30 Jul 2012 22:09:27 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: cina foroutan [canyslopus:_:yahoo.co.uk] ---357169082-1354380957-1343682567=:36898 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Manish,=0A=0AFor computing NICS you must place a Bq in or above the ri= ng center of your molecule and submit an NMR job. Then read "Isotropic shie= lding" values for isotropic NICS and the out-of-plane component of shieldin= g for NICSzz values. Be careful that NICS is negative of the shielding valu= es.=0AIn addition, it is good to know that NICS as an aromaticity index has= lots of shortcomings beside its advantages. For Shortcomings of NICS caref= ully read these papers:=0APhys. Chem. Chem. Phys., 2010, 12, 12630.=0APhys.= Chem. Chem. Phys., 2011, 13, 12655.=0AJ. Comput. Chem. 2011, 32, 2422.=0A= =0AJ. Phys. Chem. A, 2011, 115, 12708=0A=0AAlso you can consider other meth= ods for measuring magnetic aromaticity which are not based on a singlepoint= index like NICS. See for example this paper:=0AJ. Phys. Chem. A, 2011, 115= , 12555.=0A=0AGood luck,=0ACina=0A=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= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0ACina Foroutan-Nejad, Ph.D.=0Ahttp://= independent.academia.edu/CinaForoutanNejad=0A=0A=0A=0A=0A__________________= ______________=0A From: manish kumar upadhyay manish.d912]=3D[hotmail.com <= owner-chemistry^^^ccl.net>=0ATo: "Foroutan-Nejad, Cina " =0ASent: Monday, 30 July 2012, 13:32=0ASubject: CCL: Problems = on NICS calculation Using Gaussian=0A =0A=0ASent to CCL by: "manish kumar u= padhyay" [manish.d912*|*hotmail.com]=0ASir,I wanted to know the stepwise pr= ocedure to calculate the nuclear independent chemical shieft values at any = given point of space in a molecule using a ghost atom (Bq),as were praposed= by Schleyer. Kindly tell me the all steps involed the processes starting f= rom submittin a job and analysing its output.=0A=0A=0A=0A-=3D This is autom= atically added to each message by the mailing script =3D-=0ATo recover the = email address of the author of the message, please change=0Athe strange cha= racters on the top line to the ^^^ sign. You can also=0Alook up the X-Origina= l-From: line in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY^^^ccl.= net or use:=0A=A0 =A0 =A0= =0A=0A=0A=A0 =A0 = =A0=0A=0ASubscribe/Unsubscr= ibe: =0A=A0 =A0 =A0=0A=0ABefor= e posting, check wait time at: http://www.ccl.net=0A=0AJob: http://www.ccl.= net/jobs =0AConferences: http://server.ccl.net/chemistry/announcements/conf= erences/=0A=0ASearch Messages: http://www.ccl.net/chemistry/searchccl/index= .shtml=0A=0A=0A=A0 = =A0 =A0=0A=0ARTFI: http://www.ccl.net/chemi= stry/aboutccl/instructions/ ---357169082-1354380957-1343682567=:36898 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Man= ish,

For computing NICS = you must place a Bq in or above the ring center of your molecule and submit= an NMR job. Then read "Isotropic shielding" values for isotropic NICS and = the out-of-plane component of shielding for NICSzz values. Be careful that = NICS is negative of the shielding values.
In additio= n, it is good to know that NICS as an aromaticity index has lots of shortco= mings beside its advantages. For Shortcomings of NICS carefully read these = papers:
Phys. Chem. Chem. Phys., 2010, 12, 12630.
Phys. Chem. Chem. Phys., 201= 1, 13, 12655.
J. Comput. Chem. 2011, 32, 2422.
J. Phys. Chem. A, 2011, 115, 12708

Also you can cons= ider other methods for measuring magnetic aromaticity which are not based o= n a singlepoint index like NICS. See for example this paper:
J. Phys. Chem. A, 2011, 115, 12555.

Good luck,
Cina
=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=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D
Cina Foroutan-Nejad, Ph.D.
http://independent.academia.edu/CinaForoutanNejad
=


From: manish kumar= upadhyay manish.d912]=3D[hotmail.com <owner-chemistry^^^ccl.net>
To: "Foroutan-Nejad, Cina " = <canyslopus^^^yahoo.co.uk>
S= ent: Monday, 30 July 2012, 13:32
Subject: CCL: Problems on NICS calculation Using Gaus= sian


Sent to CCL by: "manish kumar upadhyay" [ma= nish.d912*|*hotmail.com]
Sir,I wanted to know the stepwise procedure to = calculate the nuclear independent chemical shieft values at any given point= of space in a molecule using a ghost atom (Bq),as were praposed by Schleye= r. Kindly tell me the all steps involed the processes starting from submitt= in a job and analysing its output.



-=3D This is automaticall= y added to each message by the mailing script =3D-
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