From owner-chemistry@ccl.net Thu Mar 8 05:46:00 2012 From: "Reza Shojaei shojaei81[A]gmail.com" To: CCL Subject: CCL:G: incremental and nonincremental Fock matrix Message-Id: <-46435-120308054512-18164-xT08Ewhc0dMlR6bX3QmSIw#server.ccl.net> X-Original-From: "Reza Shojaei" Date: Thu, 8 Mar 2012 05:45:10 -0500 Sent to CCL by: "Reza Shojaei" [shojaei81%%gmail.com] Dear all, Do you have any idea about the exact meanning of incremental Fock matrix which is default setting for direct SCF. What's the non incremental fock matrix? here I put the Gaussian's manual which I don't understand: "IncFock: Forces use of incremental Fock matrix formation. This is the default for direct SCF. NoIncFock prevents the use of incremental Fock matrix formation, and it is the default for conventional SCF. " From owner-chemistry@ccl.net Thu Mar 8 08:02:00 2012 From: "Yaxia Yuan yxyuan#%#mdl.ipc.pku.edu.cn" To: CCL Subject: CCL: Release! LigBuilder v2.0, An Integrated De Novo Drug Design System. Message-Id: <-46436-120308034241-20797-macwAnJ9JPFxUYtEEXHzVw=-=server.ccl.net> X-Original-From: "Yaxia Yuan" Date: Thu, 8 Mar 2012 03:42:39 -0500 Sent to CCL by: "Yaxia Yuan" [yxyuan- -mdl.ipc.pku.edu.cn] Dear all: The new version of LigBuilder package for de novo drug design has been available(free for academic users) on the website "ligbuilder.org" now. It is developed to design the inhibitor of protein receptor with high binding affinity, synthesis accessibility and novelty of scaffold. LigBuilder v2.0 is an integrated system featuring: 1. Structure-based protein-ligand binding site detection 2. Receptor druggability estimation 3. De novo drug design 4. Lead discovery 5. Lead optimization 6. Fragments linking 7. Mimic inhibitor design 8. Binding affinity prediction 9. Molecule clustering 10. Molecule post-filter 11. Retro-synthesis analysis LigBuilder v2.0 will hold all necessary computational process of drug design between downloading the protein structure and synthesize the target molecules. A candidate report of designed results with the synthesis routines of each compound will be provided for user to make the final determination. This program is highly automatic and user friendly. It will provide an one-stop experience in drug design for novice and high maneuverability for expert. We have successfully designed the inhibitor of CypA applying LigBuilder v2.0 which validated the effectiveness of our program. (Shuaishuai Ni, Yaxia Yuan, Jin Huang, etc. "Discovering Potent Small Molecule Inhibitors of Cyclophilin A Using de Novo Drug Design Approach", J. Med. Chem. 2009, 52, 52955298) For additional information please refer to our website "ligbuilder.org" And any feedback will be appreciated! Sincerely, Yaxia Yuan ----------------------------------------------------------------- Molecule Design Laboratory Center of Theory Biology Academy for Advanced Interdisciplinary Studies Peking University China 100871 From owner-chemistry@ccl.net Thu Mar 8 08:37:00 2012 From: "Alcides Simao alsimao^^^gmail.com" To: CCL Subject: CCL:G: Ring pseudorotation Message-Id: <-46437-120308064913-14753-t1JGkMAGbJ/qqnPKUgG3NQ..server.ccl.net> X-Original-From: Alcides Simao Content-Type: multipart/alternative; boundary=0015174bdcd60f369304bab9ddd0 Date: Thu, 8 Mar 2012 11:49:07 +0000 MIME-Version: 1.0 Sent to CCL by: Alcides Simao [alsimao . gmail.com] --0015174bdcd60f369304bab9ddd0 Content-Type: text/plain; charset=ISO-8859-1 Hello all! I'm trying to study a pseudorotation of a substituted pyrrolidine ring using GAUSSIAN 03. Although literature exists on the theme, I haven't come across any input example of it,so I'm trying to compute it in a way that I dislike particulary, which is to set a plane made of four atoms, and set one of the atoms off-plane, which is quite unrealistic. I would ask if anyone could kindly tell me what is your way of computing pseudorotation, and if you happen to have an 'automagic' way of doing so, if you would be so kind as to share it. Best, Alcides --0015174bdcd60f369304bab9ddd0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello all!

I'm trying to study a pseudorotation of a= substituted pyrrolidine ring using GAUSSIAN 03. Although literature exists= on the theme, I haven't come across any input example of it,so I'm= trying to compute it in a way that I dislike particulary, which is to set = a plane made of four atoms, and set one of the atoms off-plane, which is qu= ite unrealistic. I would ask if anyone could kindly tell me what is your wa= y of computing pseudorotation, and if you happen to have an 'automagic&= #39; way of doing so, if you would be so kind as to share it.

Best,

Alcides
--0015174bdcd60f369304bab9ddd0-- From owner-chemistry@ccl.net Thu Mar 8 09:11:01 2012 From: "Heribert Reis hreis]![eie.gr" To: CCL Subject: CCL:G: incremental and nonincremental Fock matrix Message-Id: <-46438-120308082212-25568-WPWx1/ehrTD+y4VPnCLilQ^server.ccl.net> X-Original-From: Heribert Reis Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Thu, 08 Mar 2012 15:26:00 +0200 Mime-Version: 1.0 Sent to CCL by: Heribert Reis [hreis###eie.gr] Dear Reza, NoIncFock calculates the Fock-matrix from scratch at each SCF step, which is expensive, but accurate. IncFock approximates the Fock-matrix by adding up the changes due to the density matrix change from consecutive steps of the SCF: F(P_i) = F(P_i-1) + F(P_i - P_i-1), where P is the density. This is faster than NoIncFock, and the approximation is a good one, if the density changes are small, e.g. close to convergence, but may also fail. Heribert On Thu, 2012-03-08 at 05:45 -0500, Reza Shojaei shojaei81[A]gmail.com wrote: > Sent to CCL by: "Reza Shojaei" [shojaei81%%gmail.com] > Dear all, > > Do you have any idea about the exact meanning of incremental Fock matrix which is default setting for direct SCF. > What's the non incremental fock matrix? > here I put the Gaussian's manual which I don't understand: > "IncFock: > Forces use of incremental Fock matrix formation. This is the default for direct SCF. NoIncFock prevents the use of incremental Fock matrix formation, and it is the default for conventional SCF. "> > From owner-chemistry@ccl.net Thu Mar 8 09:59:00 2012 From: "Simen Reine simen.reine _ kjemi.uio.no" To: CCL Subject: CCL:G: incremental and nonincremental Fock matrix Message-Id: <-46439-120308080449-1411-ODEwdhEPRg9F/F013RAGhA%a%server.ccl.net> X-Original-From: Simen Reine Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 8 Mar 2012 14:04:32 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Simen Reine [simen.reine_-_kjemi.uio.no] Hi Reza, The Fock matrix F(D) consist of a one-electron, h, and a two-electron contributuion (that depends on the density-matrix D), G(D), accoring to F(D) = h + G(D). In the non-incremental Fock matrix scheme the full Fock matrix is built in each SCF iteration, whereas in the incremental Fock matrix scheme the Fock matrix is built by adding only the two-electron correction (or increment) to the Fock matrix of the previous SCF iteration F(D) = F(D') + G(D'-D) where D is the current and D' the previous density matrix. The incremental Fock matrix construction is typically much more efficient since the difference between the two densities is small - thus allowing for more efficient screening. Hope this helps! On Thu, 8 Mar 2012, Reza Shojaei shojaei81[A]gmail.com wrote: > > Sent to CCL by: "Reza Shojaei" [shojaei81%%gmail.com] > Dear all, > > Do you have any idea about the exact meanning of incremental Fock matrix > which is default setting for direct SCF. What's the non incremental fock > matrix? here I put the Gaussian's manual which I don't understand: > "IncFock: Forces use of incremental Fock matrix formation. This is the > default for direct SCF. NoIncFock prevents the use of incremental Fock > matrix formation, and it is the default for conventional SCF. "> > > ______________________________________________________________ Dr. Simen S. Reine, Researcher at the Centre for Theoretical and Computation Chemistry (CTCC) Department of Chemistry E-mail: simen.reine{=}kjemi.uio.no University of Oslo Mobile ph.: (+47) 93 07 10 96 P.O.Box 1033 Blindern Telephone : (+47) 22 85 81 49 N-0315 Oslo, Norway Fax : (+47) 22 85 54 41 ______________________________________________________________ From owner-chemistry@ccl.net Thu Mar 8 10:34:01 2012 From: "Marcin Modrzejewski modrzej.:.tiger.chem.uw.edu.pl" To: CCL Subject: CCL:G: incremental and nonincremental Fock matrix Message-Id: <-46440-120308082020-19126-i8jMrYjTsk0+0klqhf6rpA|a|server.ccl.net> X-Original-From: Marcin Modrzejewski Content-Type: multipart/alternative; boundary=00248c768f26e76ced04babb226c Date: Thu, 8 Mar 2012 14:19:54 +0100 MIME-Version: 1.0 Sent to CCL by: Marcin Modrzejewski [modrzej[*]tiger.chem.uw.edu.pl] --00248c768f26e76ced04babb226c Content-Type: text/plain; charset=UTF-8 Dear Reza, Incremental Fock matrix build means that its Coulomb and exchange components are generated from difference between the current density matrix and the density matrix from previous iteration. This matrices are then added to the Fock matrix from previous iteration. It can be done because Coulomb and exchange matrices are linear with respect to density matrix elements. Such an algorithm can significantly speed up the direct Fock matrix build thanks to extensive integral screening [Schwegler, E. et al. J.Chem.Phys. 106, 9708]. However, if large number of diffuse functions is present, this option might worsen the SCF convergence. On Thu, Mar 8, 2012 at 11:45 AM, Reza Shojaei shojaei81[A]gmail.com < owner-chemistry**ccl.net> wrote: > > Sent to CCL by: "Reza Shojaei" [shojaei81%%gmail.com] > Dear all, > > Do you have any idea about the exact meanning of incremental Fock matrix > which is default setting for direct SCF. > What's the non incremental fock matrix? > here I put the Gaussian's manual which I don't understand: > "IncFock: > Forces use of incremental Fock matrix formation. This is the default for > direct SCF. NoIncFock prevents the use of incremental Fock matrix > formation, and it is the default for conventional SCF. "> > > -- Marcin Modrzejewski Ph.D. Student Quantum Chemistry Laboratory Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland --00248c768f26e76ced04babb226c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Reza,

Incremental Fock matrix build means that its Coulomb and exchange comp= onents are generated from difference between the current density matrix and= the density matrix from previous iteration. This matrices are then added t= o the Fock matrix from previous iteration. It can be done because Coulomb a= nd exchange matrices are linear with respect to density matrix elements. Su= ch an algorithm can significantly speed up the direct Fock matrix build tha= nks to extensive integral screening [Schwegler, E. et al. J.Chem.Phys. 106, 9708]. However, if large nu= mber of diffuse functions is present, this option might worsen the SCF conv= ergence.

On Thu, Mar 8, 2012 at 11:45 AM, Reza S= hojaei shojaei81[A]gmail.com <owner-chemistry**ccl.net= > wrote:

Sent to CCL by: "Reza =C2=A0Shojaei" [shojaei81%%gmail.com]
Dear all,

Do you have any idea about the exact meanning of incremental Fock =C2=A0mat= rix which is default setting for direct SCF.
What's the non incremental fock matrix?
here I put the Gaussian's manual which I don't understand:
"IncFock:
Forces use of incremental Fock matrix formation. This is the default for di= rect SCF. NoIncFock prevents the use of incremental Fock matrix formation, = and it is the default for conventional SCF. "



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY**ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEM= ISTRY-REQUEST**ccl.net or use
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
Marcin Modrzejewski
Ph.D. Student
Quantum Chemistry Laboratory
Fac= ulty of Chemistry
University of Warsaw
Pasteura 1, 02-093 Warsaw, Poland
=
--00248c768f26e76ced04babb226c-- From owner-chemistry@ccl.net Thu Mar 8 11:09:01 2012 From: "John McKelvey jmmckel%%gmail.com" To: CCL Subject: CCL:G: Ring pseudorotation Message-Id: <-46441-120308094018-25099-uj/8LOjrRkRRvkHZCbog7A]~[server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=e89a8ff2447fba27ec04babc4009 Date: Thu, 8 Mar 2012 09:40:09 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel||gmail.com] --e89a8ff2447fba27ec04babc4009 Content-Type: text/plain; charset=ISO-8859-1 I do not know how to answer this query but I do find something quite interesting in the use of the word 'automagic.' This could be a delightful word if deliberately used, even if simply a typo.. Either way it is a delightful coinage of a very useful word. John McKelvey On Thu, Mar 8, 2012 at 6:49 AM, Alcides Simao alsimao^^^gmail.com < owner-chemistry()ccl.net> wrote: > Hello all! > > I'm trying to study a pseudorotation of a substituted pyrrolidine ring > using GAUSSIAN 03. Although literature exists on the theme, I haven't come > across any input example of it,so I'm trying to compute it in a way that I > dislike particulary, which is to set a plane made of four atoms, and set > one of the atoms off-plane, which is quite unrealistic. I would ask if > anyone could kindly tell me what is your way of computing pseudorotation, > and if you happen to have an 'automagic' way of doing so, if you would be > so kind as to share it. > > Best, > > Alcides > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel()gmail.com --e89a8ff2447fba27ec04babc4009 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I do not know how to answer this query but I do find something quite intere= sting in the use of the word 'automagic.'=A0 This could be a deligh= tful word if deliberately used, even if simply a typo..=A0 Either way it is= a delightful coinage of a very useful word.

John McKelvey

On Thu, Mar 8, 2012 at = 6:49 AM, Alcides Simao alsimao^^^gmail.com= <owner-che= mistry()ccl.net> wrote:
Hello all!

I'm trying= to study a pseudorotation of a substituted pyrrolidine ring using GAUSSIAN= 03. Although literature exists on the theme, I haven't come across any= input example of it,so I'm trying to compute it in a way that I dislik= e particulary, which is to set a plane made of four atoms, and set one of t= he atoms off-plane, which is quite unrealistic. I would ask if anyone could= kindly tell me what is your way of computing pseudorotation, and if you ha= ppen to have an 'automagic' way of doing so, if you would be so kin= d as to share it.

Best,

Alcides



--
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel()gmail.com
--e89a8ff2447fba27ec04babc4009-- From owner-chemistry@ccl.net Thu Mar 8 11:44:00 2012 From: "Saman Mandegar mandegar_saman]![yahoo.com" To: CCL Subject: CCL: G09: TDDFT frequency job Message-Id: <-46442-120308111239-22682-K2SIUHMYfUainovWkMegDg*o*server.ccl.net> X-Original-From: "Saman Mandegar" Date: Thu, 8 Mar 2012 11:12:37 -0500 Sent to CCL by: "Saman Mandegar" [mandegar_saman/a\yahoo.com] Dear All, I have optimized the geometry of a system for the first excited state using TDDFT. To assure that the found stationary point is a minimum in the excited state I have to perform frequency analysis which is prohibitively expensive for my system. I am wondered to ask a naive question. Performing the frequency calculation using the same functional but using DFT method could be a reasonable approximation for TDDFT frequencies? Thank you for your kind answer. best wishes, Saman From owner-chemistry@ccl.net Thu Mar 8 15:07:00 2012 From: "luca bertini luca.bertini---unimib.it" To: CCL Subject: CCL: G09: TDDFT frequency job Message-Id: <-46443-120308122557-26003-OFUNW9gYltZiQct4YWPq3A-$-server.ccl.net> X-Original-From: "luca bertini" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1; format="flowed" Date: Thu, 08 Mar 2012 18:25:39 +0100 MIME-Version: 1.0 Sent to CCL by: "luca bertini" [luca.bertini^unimib.it] No, becuase you are computing sencond derivatives on the ground state PES that has a different tolopogy with respect to that of the excited state. Sorry but this computation has no meaning! On Thu, 8 Mar 2012 11:12:37 -0500 "Saman Mandegar mandegar_saman]![yahoo.com" wrote: > > Sent to CCL by: "Saman Mandegar" >[mandegar_saman/a\yahoo.com] > Dear All, > > I have optimized the geometry of a system for the first >excited state using TDDFT. To assure that the found >stationary point is a minimum in the excited state I have >to perform frequency analysis which is prohibitively >expensive for my system. I am wondered to ask a naive >question. Performing the frequency calculation using the >same functional but using DFT method could be a >reasonable approximation for TDDFT frequencies? > > Thank you for your kind answer. > best wishes, > Saman > > > > -= 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 a sign. >You can also> > E-mail to administrators: CHEMISTRY-REQUEST a ccl.net or >use> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: >http://www.ccl.net/chemistry/searchccl/index.shtml> > RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/ > > From owner-chemistry@ccl.net Thu Mar 8 17:33:01 2012 From: "Mezei, Mihaly mihaly.mezei * mssm.edu" To: CCL Subject: CCL:G: Ring pseudorotation Message-Id: <-46444-120308105342-3667-DY2bnF3EoG8bQWrg9axcNg^server.ccl.net> X-Original-From: "Mezei, Mihaly" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_23B1335F43764D4EBFA3AC5C9FB1D10BB642A4EXCH2KXMBXEB1Exch_" Date: Thu, 8 Mar 2012 15:53:34 +0000 MIME-Version: 1.0 Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei(!)mssm.edu] --_000_23B1335F43764D4EBFA3AC5C9FB1D10BB642A4EXCH2KXMBXEB1Exch_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Greetings, my program Simulaid (http://inka.mssm.edu/~mezei/simulaid) can calculate pseudorotational angles, both using t= he definition specific to 5-memberd rings and the general definition of Cre= mer & Pople. Mihaly Mezei ________________________________ > From: owner-chemistry+mihaly.mezei=3D=3Dmssm.edu*o*ccl.net [owner-chemistry+m= ihaly.mezei=3D=3Dmssm.edu*o*ccl.net] on behalf of Alcides Simao alsimao^^^gma= il.com [owner-chemistry*o*ccl.net] Sent: Thursday, March 08, 2012 6:49 AM To: Mezei, Mihaly Subject: CCL:G: Ring pseudorotation Hello all! I'm trying to study a pseudorotation of a substituted pyrrolidine ring usin= g GAUSSIAN 03. Although literature exists on the theme, I haven't come acro= ss any input example of it,so I'm trying to compute it in a way that I disl= ike particulary, which is to set a plane made of four atoms, and set one of= the atoms off-plane, which is quite unrealistic. I would ask if anyone cou= ld kindly tell me what is your way of computing pseudorotation, and if you = happen to have an 'automagic' way of doing so, if you would be so kind as t= o share it. Best, Alcides --_000_23B1335F43764D4EBFA3AC5C9FB1D10BB642A4EXCH2KXMBXEB1Exch_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Greetings,

my program Simulaid (http://inka.mssm.edu/~mezei/simulaid) can calculate pseu= dorotational angles, both using the definition specific to 5-memberd rings = and the general definition of Cremer & Pople.

Mihaly Mezei
From: owner-chemistry+mihaly.mezei=3D= =3Dmssm.edu*o*ccl.net [owner-chemistry+mihaly.mezei=3D=3Dmssm.edu*o*ccl.net= ] on behalf of Alcides Simao alsimao^^^gmail.com [owner-chemistry*o*ccl.net]<= br> Sent: Thursday, March 08, 2012 6:49 AM
To: Mezei, Mihaly
Subject: CCL:G: Ring pseudorotation

Hello all!

I'm trying to study a pseudorotation of a substituted pyrrolidine ring= using GAUSSIAN 03. Although literature exists on the theme, I haven't come= across any input example of it,so I'm trying to compute it in a way that I= dislike particulary, which is to set a plane made of four atoms, and set one of the atoms off-plane, which = is quite unrealistic. I would ask if anyone could kindly tell me what is yo= ur way of computing pseudorotation, and if you happen to have an 'automagic= ' way of doing so, if you would be so kind as to share it.

Best,

Alcides
--_000_23B1335F43764D4EBFA3AC5C9FB1D10BB642A4EXCH2KXMBXEB1Exch_-- From owner-chemistry@ccl.net Thu Mar 8 18:08:01 2012 From: "Jussi Lehtola jussi.lehtola::helsinki.fi" To: CCL Subject: CCL: incremental and nonincremental Fock matrix Message-Id: <-46445-120308112746-4180-mOMfyrtmlwJMBVEnoeiIiA .. server.ccl.net> X-Original-From: Jussi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 8 Mar 2012 18:27:36 +0200 Mime-Version: 1.0 Sent to CCL by: Jussi Lehtola [jussi.lehtola- -helsinki.fi] On Thu, 08 Mar 2012 15:26:00 +0200 "Heribert Reis hreis]![eie.gr" wrote: > Sent to CCL by: Heribert Reis [hreis###eie.gr] > Dear Reza, > > NoIncFock calculates the Fock-matrix from scratch at each SCF step, > which is expensive, but accurate. > IncFock approximates the Fock-matrix by adding up the changes due to > the density matrix change from consecutive steps of the SCF: > > F(P_i) = F(P_i-1) + F(P_i - P_i-1), where P is the density. > > This is faster than NoIncFock, and the approximation is a good one, if > the density changes are small, e.g. close to convergence, but may also > fail. Well, it's not really an approximation, since in Hartree-Fock theory the Fock matrix is linear in the density matrix, and you should get the same result in both cases. When you form the matrix from scratch as G(i,j) = sum_{k,l} P(k,l) [2(ij|kl) - (ik|lj)] you screen out the elements for which the product of the density matrix elements and integrals (estimated, e.g., with the Schwarz inequality), are small. If you do incremental formation, the formation becomes much more effective as the elements that haven't changed are screened out. -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.lehtola^^^helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Jussi Lehtola, FM Tohtorikoulutettava jussi.lehtola^^^helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- From owner-chemistry@ccl.net Thu Mar 8 18:43:01 2012 From: "Rajarshi Guha rajarshi.guha(-)gmail.com" To: CCL Subject: CCL:G: Ring pseudorotation Message-Id: <-46446-120308141551-15320-neNBpr3GjQ3UURigP32EAw+*+server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: multipart/alternative; boundary=0016e6d77eee38d78204bac01ae5 Date: Thu, 8 Mar 2012 14:15:43 -0500 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha++gmail.com] --0016e6d77eee38d78204bac01ae5 Content-Type: text/plain; charset=ISO-8859-1 This term seems to originate from the 70's (and even used as far as back as 1940 in an advertisement!) http://www.outpost9.com/reference/jargon/jargon_16.html On Thu, Mar 8, 2012 at 9:40 AM, John McKelvey jmmckel%%gmail.com < owner-chemistry],[ccl.net> wrote: > I do not know how to answer this query but I do find something quite > interesting in the use of the word 'automagic.' This could be a delightful > word if deliberately used, even if simply a typo.. Either way it is a > delightful coinage of a very useful word. > > John McKelvey > > > On Thu, Mar 8, 2012 at 6:49 AM, Alcides Simao alsimao^^^gmail.com < > owner-chemistry%%ccl.net > wrote: > >> Hello all! >> >> I'm trying to study a pseudorotation of a substituted pyrrolidine ring >> using GAUSSIAN 03. Although literature exists on the theme, I haven't come >> across any input example of it,so I'm trying to compute it in a way that I >> dislike particulary, which is to set a plane made of four atoms, and set >> one of the atoms off-plane, which is quite unrealistic. I would ask if >> anyone could kindly tell me what is your way of computing pseudorotation, >> and if you happen to have an 'automagic' way of doing so, if you would be >> so kind as to share it. >> >> Best, >> >> Alcides >> > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel%%gmail.com > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science --0016e6d77eee38d78204bac01ae5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable This term seems to originate from the 70's (and even used as far as bac= k as 1940 in an advertisement!)

http://www.outpost9.com/referen= ce/jargon/jargon_16.html

On Thu, Mar 8, 2012 at 9:40 AM, John McKelve= y jmmckel%%gmail.com <= ;owner-chemistry],[ccl.net>= wrote:
I do not know how to answer this query but I= do find something quite interesting in the use of the word 'automagic.= '=A0 This could be a delightful word if deliberately used, even if simp= ly a typo..=A0 Either way it is a delightful coinage of a very useful word.=

John McKelvey


On Thu, Mar 8, 2012 at 6:49 AM, Alcides Simao alsimao^^^gmail.com <owner= -chemistry%%ccl.net> wrote:
Hello all!

I'm trying= to study a pseudorotation of a substituted pyrrolidine ring using GAUSSIAN= 03. Although literature exists on the theme, I haven't come across any= input example of it,so I'm trying to compute it in a way that I dislik= e particulary, which is to set a plane made of four atoms, and set one of t= he atoms off-plane, which is quite unrealistic. I would ask if anyone could= kindly tell me what is your way of computing pseudorotation, and if you ha= ppen to have an 'automagic' way of doing so, if you would be so kin= d as to share it.

Best,

Alcides



--
John McKelvey
10819 Middleford PlFt Wayne, IN 46818
260-489-2160
jmmckel%%gmail.= com



-- Rajarshi Guha | http:= //blog.rguha.net
NIH Center for Advancing Translational Science
<= br>
--0016e6d77eee38d78204bac01ae5-- From owner-chemistry@ccl.net Thu Mar 8 19:18:00 2012 From: "Daniel Fernando Coimbra danielfcoimbra_+_gmail.com" To: CCL Subject: CCL:G: Ring pseudorotation Message-Id: <-46447-120308142523-13342-FjCsXO60OQbd2Qvc1cO8Jg-.-server.ccl.net> X-Original-From: Daniel Fernando Coimbra Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 08 Mar 2012 16:26:13 -0300 MIME-Version: 1.0 Sent to CCL by: Daniel Fernando Coimbra [danielfcoimbra*|*gmail.com] As far as I know this term was first used by the authors of the (now discontinued) brazillian Linux distribution Kurumin. They created sets of BASH scripts that automated lots of installation proccess so that a novice user could configure non-trivial hardware with just a click on a menu item. There were said to so "automagicamente" (automagically), as it looked even easyer than simpler automatic task available at the time. Em 08-03-2012 11:40, John McKelvey jmmckel%%gmail.com escreveu: > I do not know how to answer this query but I do find something quite > interesting in the use of the word 'automagic.' This could be a > delightful word if deliberately used, even if simply a typo.. Either > way it is a delightful coinage of a very useful word. > > John McKelvey > > On Thu, Mar 8, 2012 at 6:49 AM, Alcides Simao alsimao^^^gmail.com > > wrote: > > Hello all! > > I'm trying to study a pseudorotation of a substituted pyrrolidine > ring using GAUSSIAN 03. Although literature exists on the theme, I > haven't come across any input example of it,so I'm trying to compute > it in a way that I dislike particulary, which is to set a plane made > of four atoms, and set one of the atoms off-plane, which is quite > unrealistic. I would ask if anyone could kindly tell me what is your > way of computing pseudorotation, and if you happen to have an > 'automagic' way of doing so, if you would be so kind as to share it. > > Best, > > Alcides > > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel%%gmail.com -- Daniel Fernando Coimbra Grupo de Estrutura Eletrônica Molecular Departamento de Química Universidade Federal de Santa Catarina