From owner-chemistry@ccl.net Tue Feb 21 00:11:01 2017 From: "Norrby, Per-Ola Per-Ola.Norrby_._astrazeneca.com" To: CCL Subject: CCL: aldehyde O-H bond energy smaller than (sp2)C-H bond, why ? Message-Id: <-52650-170221000905-20816-aUq3PdAMWpPjxoUrVqSE9w[#]server.ccl.net> X-Original-From: "Norrby, Per-Ola" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_HE1PR04MB2092BD77A0D474F0D8A770F4CA510HE1PR04MB2092eurp_" Date: Tue, 21 Feb 2017 05:08:57 +0000 MIME-Version: 1.0 Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby(!)astrazeneca.com] --_000_HE1PR04MB2092BD77A0D474F0D8A770F4CA510HE1PR04MB2092eurp_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SeKAmW0gYXNzdW1pbmcgeW91IG1lYW4gYWxkZWh5ZGUgQy1IIGJvbmQsIHNpbmNlIHRoZXJlIGlz IG5vIE8tSCBib25kLiBJdOKAmXMgYSBnZW5lcmFsIHBoZW5vbWVub247IGEgbmVpZ2hib3Jpbmcg bG9uZSBwYWlyIHdpbGwgc3RhYmlsaXplIGFueSByYWRpY2FsLiBEcmF3IGFuIG9yYml0YWwgY29y cmVsYXRpb24gZGlhZ3JhbSB0byBzZWUgd2h5LiBSYWRpY2FscyBhcmUgc3RhYmlsaXplZCBCT1RI IGJ5IGVsZWN0cm9uIHdpdGhkcmF3aW5nIGFuZCBkb25hdGluZyBncm91cHMuIFRoZSBwaS1zeXN0 ZW0gZG9lc27igJl0IGRvIG11Y2gsIGl04oCZcyBvcnRob2dvbmFsIHRvIGJvdGggdGhlIHJhZGlj 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Message-Id: <-52651-170221034412-18185-X6k2ZyNbmgYQ84TBomSmnQ{:}server.ccl.net> X-Original-From: Rina Dao Content-Type: multipart/alternative; boundary=94eb2c1925eefb4103054906617c Date: Tue, 21 Feb 2017 16:44:05 +0800 MIME-Version: 1.0 Sent to CCL by: Rina Dao [rina.dao%gmail.com] --94eb2c1925eefb4103054906617c Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable hi, norby! yeah, I misstyped, and it is the C-H bond. So U mean the phenomenon is both valid in the sigma and pi radicals, while both formyl and vinyl radicals are sigma? And the "pi-system" in the last sentence refer to the C=3DC double bond ? On Tue, Feb 21, 2017 at 1:08 PM, Norrby, Per-Ola Per-Ola.Norrby_._ astrazeneca.com wrote: > I=E2=80=99m assuming you mean aldehyde C-H bond, since there is no O-H bo= nd. It=E2=80=99s > a general phenomenon; a neighboring lone pair will stabilize any radical. > Draw an orbital correlation diagram to see why. Radicals are stabilized > BOTH by electron withdrawing and donating groups. The pi-system doesn=E2= =80=99t do > much, it=E2=80=99s orthogonal to both the radical and the lone pair. > > > > /Per-Ola Norrby > > > > *From:* owner-chemistry+per-ola.norrby=3D=3Dastrazeneca.com++ccl.net [mail= to: > owner-chemistry+per-ola.norrby=3D=3Dastrazeneca.com++ccl.net] *On Behalf O= f *Rina > Dao rina.dao^^^gmail.com > *Sent:* den 20 februari 2017 16:46 > *To:* Norrby, Per-Ola > *Subject:* CCL: aldehyde O-H bond energy smaller than (sp2)C-H bond, why = ? > > > > guys, why is aldehyde O-H bond dissociation energy so much smaller > (87kcal/mol) than that of an (sp2)C-H bond (around 110 kcal/mol) ? It see= ms > easy but, don=E2=80=99t have an answer right now. Along comes the questio= n of How > do we evaluate the stability of sigma radicals? Thanks~ > ------------------------------ > > *Confidentiality Notice: *This message is private and may contain > confidential and proprietary information. If you have received this messa= ge > in error, please notify us and remove it from your system and note that y= ou > must not copy, distribute or take any action in reliance on it. Any > unauthorized use or disclosure of the contents of this message is not > permitted and may be unlawful. > > --94eb2c1925eefb4103054906617c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
hi, norby! yeah, I misstyped, and it is the C-H bond. So U= mean the phenomenon is both valid in the sigma and pi radicals, while both= formyl and vinyl radicals are sigma?=C2=A0

And the &quo= t;pi-system" in the last sentence refer to the C=3DC double bond ?

On Tue, F= eb 21, 2017 at 1:08 PM, Norrby, Per-Ola Per-Ola.Norrby_._astrazeneca.com <owner-chemistry++ccl.net>= ; wrote:

I=E2=80=99m assuming you mean aldehyd= e C-H bond, since there is no O-H bond. It=E2=80=99s a general phenomenon; = a neighboring lone pair will stabilize any radical. Draw an orbital correlation diagram to see why. Radicals are stabilized BOTH by electron w= ithdrawing and donating groups. The pi-system doesn=E2=80=99t do much, it= =E2=80=99s orthogonal to both the radical and the lone pair.<= /span>

=C2=A0

/Per-Ola Norrby<= /p>

=C2=A0

From: owner-chemistry+per-ola.n= orrby=3D=3Dast= razeneca.com++ccl.net [mailto:owner-chemistry+per-ola.norrby=3D= =3Dastrazeneca= .com++ccl.net] On Behalf Of Rina Dao rina.dao^^^gmail.com
Sent: den 20 februari 2017 16:46
To: Norrby, Per-Ola <Per-Ola.Norrby++astrazeneca.com>
Subject: CCL: aldehyde O-H bond energy smaller than (sp2)C-H bond, w= hy ?

=C2=A0

guys, why is aldehyde O-H bond dissociation energy so much smaller= (87kcal/mol) than that of an (sp2)C-H bond (around 110 kcal/mol) ? It seems easy but, don=E2=80=99t have an answer right now. Along comes t= he question of How do we evaluate the stability of sigma radicals? Thanks~<= /span>

Confidentiality Notice: This message is private and may contain confidential and proprieta= ry information. If you have received this message in error, please notify u= s and remove it from your system and note that you must not copy, distribut= e or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message = is not permitted and may be unlawful.


--94eb2c1925eefb4103054906617c-- From owner-chemistry@ccl.net Tue Feb 21 10:22:01 2017 From: "John McKelvey jmmckel++gmail.com" To: CCL Subject: CCL: ORCA and OPENMPI Message-Id: <-52652-170221092219-7048-oXcxw6TW29Hpa6HCeTHAWA _ server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001a113cd9cc31278f05490b1b9f Date: Tue, 21 Feb 2017 08:22:12 -0600 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel#%#gmail.com] --001a113cd9cc31278f05490b1b9f Content-Type: text/plain; charset=UTF-8 Brian, Many thanks! John On Mon, Feb 20, 2017 at 3:23 PM, Brian Skinn bskinn(~)alum.mit.edu < owner-chemistry~~ccl.net> wrote: > John, > > Be sure you have the ORCA and OpenMPI bin directories in your %PATH%. > Yes, I use OpenMPI v1.6.2 for ORCA v3.0.x. > > Below is the launch script I use for running ORCA v3.0.2 (and v3.0.3, > FWIW) on Win7: > > () echo off > > set OMPI_MCA_btl=self,sm > > if not %1=="" ( > c:\orca\bin\orca %1.txt > %1.out > ) > > > In particular, when you make the call to ORCA for a parallel run, be sure > to include the full path to orca.exe, as I've done above. > > > Best regards, > Brian > > On Mon, Feb 20, 2017 at 2:05 PM, John McKelvey jmmckel],[gmail.com ccl.net> wrote: > >> I can run serial ORCA-302 under W-7, but running parallel crashes >> attempting to start up GTOINT. If someone has ORCA-302 running under W-7 I >> would be grateful for any advice you care to offer. Are you using OPENMPI >> 162-2? >> >> Best regards, >> >> John >> >> -- >> John McKelvey >> 545 Legacy Pointe Dr >> O'Fallon, MO 63376 >> 636-294-5203 <(636)%20294-5203> >> jmmckel|gmail.com >> > > -- John McKelvey 545 Legacy Pointe Dr O'Fallon, MO 63376 636-294-5203 jmmckel~~gmail.com --001a113cd9cc31278f05490b1b9f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Brian,

Many thanks!

Jo= hn

On Mo= n, Feb 20, 2017 at 3:23 PM, Brian Skinn bskinn(~)alum.mit.edu <owner-chemistry~~ccl.net> wrote= :
John,

Be sure you have the ORCA and OpenMPI %PATH%= .=C2=A0 Yes, I use OpenMPI v1.6.2 for ORCA v3.0.x. =C2=A0
=
Below is the launch script I use for running ORCA v3.0.2 (an= d v3.0.3, FWIW) on Win7:

() echo off

set OMPI_MC= A_btl=3Dself,sm

if not %1=3D=3D"&q= uot; (
=C2=A0 c:\orca\= bin\orca %1.txt > %1.out
=C2=A0 )

In particular,= when you make the call to ORCA for a parallel run, be sure to include the = full path to orca.exe, as I'= ve done above.


Best regards,
<= div>Brian

On Mon, Feb 20, 2017 at 2:05 PM, John McKelvey jmmckel],[gmail.com <owner-chemistry() = ccl.net> wrote:
I can run serial ORCA-302 under W-7, but running parallel crashes att= empting to start up GTOINT.=C2=A0 If someone has ORCA-302 running under W-7= I would be grateful for any advice you care to offer.=C2=A0 Are you using = OPENMPI 162-2?

Best regards,

Jo= hn

-= -
John McKelvey
545 Legacy Pointe Dr
O'Fallon, MO 63= 376
636-294-5203
jmmckel|gmail.com




--
John McKelvey
545 Legacy Pointe Dr
O'Fallon,= MO 63376
636-294-5203
jmmckel~~gmail.com
--001a113cd9cc31278f05490b1b9f-- From owner-chemistry@ccl.net Tue Feb 21 10:57:01 2017 From: "Mark Mackey mark**cresset-group.com" To: CCL Subject: CCL: Free computing resources for Molecular dynamics Simulation Message-Id: <-52653-170221100005-12324-9G+LJVIq3x8SDafclTy2jQ__server.ccl.net> X-Original-From: Mark Mackey Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 21 Feb 2017 14:59:51 +0000 MIME-Version: 1.0 Sent to CCL by: Mark Mackey [mark##cresset-group.com] Hi Mannan, If this is just for occasional use, then look at using Amazon EC2. A c4-8xlarge instance, which has 36 cores and 60GB of memory, will cost you between US$0.25 and 0.40 per hour (spot price) at the moment. You can run a week-long simulation on one of these for between $40 and $70, provided you're willing to watch over it and restart it if the spot bid price gets too high. Regards, Mark CSO, Cresset -----Original Message----- > From: owner-chemistry+mark==cresset-bmd.com|ccl.net [mailto:owner-chemistry+mark==cresset-bmd.com|ccl.net] On Behalf Of Mannan K malie_03**yahoo.co.in Sent: 18 February 2017 16:02 To: Mark Mackey Subject: CCL: Free computing resources for Molecular dynamics Simulation Sent to CCL by: "Mannan K" [malie_03-,-yahoo.co.in] Hi CCLers, I need to perform molecular dynamics simulation for a protein peptide complex. But I don't have any computing resources. and I don't have any funding as of now to set-up that facility I would be more than happy if anyone in the community share some information on free computing resources Many Thanks in Advance Mannanhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Feb 21 14:59:00 2017 From: "may abdelghani may01dz]|[yahoo.fr" To: CCL Subject: CCL: the computing resources of the Amazon EC2 Message-Id: <-52654-170221145635-1354-LdzYUJFt10z+zWplyuHsJg]^[server.ccl.net> X-Original-From: "may abdelghani" Date: Tue, 21 Feb 2017 14:56:33 -0500 Sent to CCL by: "may abdelghani" [may01dz[]yahoo.fr] Dear CLL'ers We hope for our colleagues to share us its experiences in the use of the computing resources of the Amazon EC2 (In terms of performance, cost and method of use). thank you very much