From owner-chemistry@ccl.net Fri Oct 2 01:36:00 2009 From: "arslan ali arslanali1986*_*gmail.com" To: CCL Subject: CCL: activation energy Message-Id: <-40392-091002012652-23676-3hQ1sqbLGWEkS64JajNzDQ a server.ccl.net> X-Original-From: arslan ali Content-Type: multipart/alternative; boundary=00504502b2232487e90474ebd1ba Date: Fri, 2 Oct 2009 09:01:21 +0500 MIME-Version: 1.0 Sent to CCL by: arslan ali [arslanali1986/a\gmail.com] --00504502b2232487e90474ebd1ba Content-Type: text/plain; charset=ISO-8859-1 hi i am trying to find activation energies of some reactions, i need your guidance as i am new to this field i tried the following way first i did calculation for predicting equilibrium geometry then i predicted transition state geometry then i calculated energy of both and subtracted energy of transition state from equilibrium geometry to find out activation energy... please tell me whether my approach is wright??? arslan --00504502b2232487e90474ebd1ba Content-Type: text/html; charset=ISO-8859-1 hi

i am trying to find activation energies of some reactions,
i need your guidance as i am new to this field

i tried the following way

first i did calculation for predicting equilibrium geometry
then i predicted transition state geometry
then i calculated energy of both
and subtracted energy of transition state from equilibrium geometry
to find out activation energy...

please tell me whether my approach is wright???

arslan

--00504502b2232487e90474ebd1ba-- From owner-chemistry@ccl.net Fri Oct 2 02:11:00 2009 From: "Joaquin Barroso Flores joaco_barroso : yahoo.com" To: CCL Subject: CCL:G: SAC-CI: density matrix Message-Id: <-40393-091002013030-24190-62q+mcOdTVhGie3Iq3WBzg^server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Type: multipart/alternative; boundary="0-2111658596-1254461419=:50940" Date: Thu, 1 Oct 2009 22:30:19 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso%yahoo.com] --0-2111658596-1254461419=:50940 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi George=0A=0AUsing IOp(6/8=3D1) will print the density matrix in what the= program calls 'the normal amount'. IOp(6/8=3D3) will print it verbosely if= you need all the extra info. I have tried this option only with HF calcula= tions, it should work with CI calculations as well. =0A=0AHope this helps= =0A=0AJoaquin=0A=0APS To all the participants: Please write summaries when = suitable; the usual format was to use the word SUMMARY on the subject line = along with the subject of the thread, this makes it easier to find. Thanks= =0A=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=3D=3D=0AJoaquin Barroso-Flores, Ph. D.=0AFacultatea de Chimie, Un= iversitatea Babes-Bolyai=0ACluj-Napoca, Romania=0A=0A=0A-> http://joaquinba= rroso.com=0A-> http://joaquinbarroso.wordpress.com=0A=0A=0Ajoaquinbarroso''= a''chem.ubbcluj.ro=0Ajoaquin.barroso''a''gmail.com =0A=0A=0A"Blogastronom= =EDa": http://joaquinbarroso.blogspot.com =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=3D=3D=0A=0A=0A=0A=0A_________= _______________________=0ADe: Georg Lefkidis lefkidis-.-physik.uni-kl.de =0APara: "Flores, Joaquin Barroso " =0AEnviado: jueves, 1 de octubre, 2009 10:39:58=0AAsunto: = CCL:G: SAC-CI: density matrix=0A=0A =0AHello everyone,=0A =0AI have been wo= ndering whether it is possible=0Ato extract the density matrix out of the S= AC-CI states. The keyword e.g. SINGLE=3D(NSTATES=3D(2,2,2,2),DENSITY)=0Ain = Gaussian combined with ALLPROPERTIES does Mulliken analysis and does not=0A= print the density matrix D, but the population matrix instead P. =0A =0ADoe= s anyone know of a method to extract the=0Adensity matrix?=0A =0ABest regar= ds=0AGeorge=0A =0A---------------------------------------------------------= ----------=0ADr. Georg Lefkidis=0ADept. of Physics=0AUniversity of Kaisersl= autern=0APO Box 3049=0A67653 Kaiserslautern=0Ae-mail: lefkidis(at)physik(do= t)uni(dash)kl(dot)de=0ATel.: +49 631 205 3207=0A---------------------------= ----------------------------------------=0A=0A=0A Encuentra las mejore= s recetas en Yahoo! Cocina. =0Ahttp://mx.mujer.yahoo.= com/cocina/ --0-2111658596-1254461419=:50940 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi George

Using IOp(6/8=3D1) will print the density mat= rix in what the program calls 'the normal amount'. IOp(6/8=3D3) will print = it verbosely if you need all the extra info. I have tried this option only = with HF calculations, it should work with CI calculations as well.

= Hope this helps

Joaquin

PS To all the participants: Please wr= ite summaries when suitable; the usual format was to use the word SUMMARY o= n the subject line along with the subject of the thread, this makes it easi= er to find. Thanks
 
=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=3D=3D
Joaquin Barroso-Flores, Ph= . D.
Facultatea de Chimie, Universitatea Babes-Bolyai
Cluj-Napoca, Ro= mania



joaqu= inbarroso''a''chem.ubbcluj.ro
joaquin.barroso''a''gmail.com

"Blogastronom=EDa": http://joaquinbarroso.blogspot.com
= =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= =3D=3D


<= hr size=3D"1">De: Georg Le= fkidis lefkidis-.-physik.uni-kl.de <owner-chemistry[*]ccl.net>
Para: "Flores, Joaquin Barroso = " <joaco_barroso[*]yahoo.com>
E= nviado: jueves, 1 de octubre, 2009 10:39:58
Asunto: CCL:G: SAC-CI: density matrix

=0A=0A=0A =0A =0A=0A=0A=0A=0A
=0A=0AHello everyone,

=0A=0A

&nbs= p;

=0A=0A

I have been wonder= ing whether it is possible=0Ato extract the density matrix out of the SAC-C= I states. The keyword e.g. SINGLE=3D(NSTATES=3D(2,2,2,2),DENSITY)=0Ain Gaus= sian combined with ALLPROPERTIES does Mulliken analysis and does not=0Aprin= t the density matrix D, but the population matrix instead P.

= =0A=0A

 

=0A=0A=

Does anyone know of a method to= extract the=0Adensity matrix?

=0A=0A

 

=0A=0A

Best regards

=0A=0A

George

=0A=0A

 

=0A=0A

--= ----------------------------------------------------------------- =0A=0A

Dr. Georg Lefkidis

=0A=0A

Dept. of Physics

=0A=0A

University of K= aiserslautern

=0A=0A

= PO Box 3049

=0A=0A

67653 Kaiserslautern =0A=0A

e-mail: lefkidis(at)physik(dot)uni(dash)kl(d= ot)de

=0A=0A

Tel.: +49 631 205 3207

=0A=0A

-------------------------------------------------------= ------------

=0A=0A

 

=0A=0A
=0A= =0A

=0A=0A=0A=0A

=A1Encuentra las mejores recetas
con Yahoo! Co= cina!
=0Ahttp://mx.mujer.yahoo.com/cocina/
--0-2111658596-1254461419=:50940-- From owner-chemistry@ccl.net Fri Oct 2 02:59:00 2009 From: "Inbal Tuvi-Arad inbaltu(!)openu.ac.il" To: CCL Subject: CCL: IRC calculations can not converge???? Message-Id: <-40394-091002024735-13151-DdNiNVF1h5ITXy3u3AFQxA*o*server.ccl.net> X-Original-From: "Inbal Tuvi-Arad" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 2 Oct 2009 08:47:19 +0200 MIME-Version: 1.0 Sent to CCL by: "Inbal Tuvi-Arad" [inbaltu-,-openu.ac.il] Dear Rahim, I usually solve this problem with a smaller stepsize. Try stepsize=3D5 or even less if necessary. Another option is calcall - it recalculates the force constants at each point. Good luck, Inbal -----Original Message----- > From: owner-chemistry+inbaltu=3D=3Dopenu.ac.il],[ccl.net [mailto:owner-chemistry+inbaltu=3D=3Dopenu.ac.il],[ccl.net] On Behalf Of = Rahim Ghadari r_ghadari_k ~ yahoo.com Sent: Thursday, October 01, 2009 6:57 PM To: Inbal Tuvi-Arad Subject: CCL: IRC calculations can not converge???? Sent to CCL by: "Rahim Ghadari" [r_ghadari_k-x-yahoo.com] Hi I'm trying to use IRC calculation.But after 15 steps it can not converge. I used the maxcycle=3D1000, but it didn't help me. May using "tight" or "stepsize" keywords help me or no??? Thank you in advance for your help Rahim Ghadari r_ghadari_k#%#yahoo.com -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Oct 2 03:41:01 2009 From: "Georg Lefkidis lefkidis#%#physik.uni-kl.de" To: CCL Subject: CCL: AW: G: SAC-CI: density matrix Message-Id: <-40395-091002030424-28482-zbZFQwxtfyy5pcouzVB/aA^server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Language: de Content-Type: multipart/alternative; boundary="----=_NextPart_000_001A_01CA433F.44DF3580" Date: Fri, 2 Oct 2009 09:03:54 +0200 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis+/-physik.uni-kl.de] This is a multi-part message in MIME format. ------=_NextPart_000_001A_01CA433F.44DF3580 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Joaquin, thank you for the answer, however the option IOP(6/8=3) prints the density of the preceding SCF step, and not of the SAC-CI states. Best regards George >Hi George > >Using IOp(6/8=1) will print the density matrix in what the program calls 'the normal amount'. IOp(6/8=3) will print it verbosely if you need all the extra info. I have tried this option only >with HF calculations, it should work with CI calculations as well. > >Hope this helps > >Joaquin ------------------------------------------------------------------- Dr. Georg Lefkidis Dept. of Physics University of Kaiserslautern PO Box 3049 67653 Kaiserslautern e-mail: lefkidis(at)physik(dot)uni(dash)kl(dot)de Tel.: +49 631 205 3207 ------------------------------------------------------------------- ------=_NextPart_000_001A_01CA433F.44DF3580 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = Joaquin,

 

thank = you for the answer, however the option IOP(6/8=3D3) prints the density of the = preceding SCF step, and not of the SAC-CI states.

 

Best = regards

George

 

>Hi George
>
>Using IOp(6/8=3D1) will print = the density matrix in what the program calls 'the normal amount'. =
IOp(6/8=3D3) will print it verbosely if you need all the extra info. I = have tried this option only >with HF calculations, it should work with CI calculations as well.
>
>Hope this helps
>
>Joaquin

------------------------------------------------------------= -------

Dr. Georg = Lefkidis

Dept. of = Physics

University of = Kaiserslautern

PO Box = 3049

67653 Kaiserslautern

e-mail: = lefkidis(at)physik(dot)uni(dash)kl(dot)de

Tel.: +49 631 205 3207

-------------------------------------------------------= ------------

 

------=_NextPart_000_001A_01CA433F.44DF3580-- From owner-chemistry@ccl.net Fri Oct 2 06:15:04 2009 From: "andras.borosy**givaudan.com" To: CCL Subject: CCL: Who is the best philosopher(s) of science now? Message-Id: <-40396-091002043345-5635-3NFRUlseiyP5otACz449wQ a server.ccl.net> X-Original-From: andras.borosy##givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 002B7A2AC1257643_=" Date: Fri, 2 Oct 2009 09:54:53 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy+/-givaudan.com This is a multipart message in MIME format. --=_alternative 002B7A2AC1257643_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, My favourite is (even if he is already dead): August Comte "Every attempt to employ mathematical methods in=20 the study of chemical questions must be considered profoundly irrational and contrary to the spirit=20 of chemistry.... if mathematical analysis should=20 ever hold a prominent place in chemistry -- an=20 aberration which is happily almost impossible --=20 it would occasion a rapid and widespread=20 degeneration of that science." http://home.att.net/~quotations/science.html I would happy, if someone might send me it in French! Best wishes, Andr=E1s Borosy "Dr. Dallos Andras" =20 08.07.2009 10:50 To cc Subject Re: mathematical methods in the study of chemical questions :-) Every attempt to employ mathematical methods in=20 the study of chemical questions must be considered profoundly irrational and contrary to the spirit=20 of chemistry.... if mathematical analysis should=20 ever hold a prominent place in chemistry -- an=20 aberration which is happily almost impossible --=20 it would occasion a rapid and widespread=20 degeneration of that science.=20 - Auguste Comte =20 "Sengen Sun sengensun]*[yahoo.com" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com++ccl.net 28.09.2009 21:51 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: Who is the best philosopher(s) of science now? Sent to CCL by: Sengen Sun [sengensun : yahoo.com] > > =20 > If bias is tolerated, as I am French and you are Canadian I > will suggest Hubert Reeves...=20 > VL >=20 >> =20 Reeves is indeed one of my favorite philosophers and greatest scientists.=20 But I am critical. Some of his quotes in the following paragraph should be = interesting to computational scientists: . http://science.ca/scientists/scientistprofile.php?pID=3D213&pg=3D2 . "You always need to start with an observation," says Reeves. "Mathematics=20 alone can do nothing about knowing the real world. It cannot even tell you = what is the number of dimensions you feel." First comes the observation,=20 he says, then the theory. Ultimately, the theory allows us to do=20 calculations that lead to more observations that confirm or improve the=20 theory . "Mathematics alone can do nothing about knowing the real world?" This=20 quote contradicts what I said in my ppt slides archived in CCL: http://ccl.net/cca/documents/ConcertedCycloadditons=5F2/ . I "Demonstrated solid examples that computational chemistry is useful in the understanding of chemical phenomena that=20 cannot be understood otherwise." (Page 24 in my slides)=20 . In 1998, after I played the puzzles of concerted cycloadditions for about=20 17-18 years, I discovered by computations that in many cycloadditions, one = of the reactants force the other to change its polarity during collision,=20 forming cycloadduct of "weird" regioselectivity. The "weird"=20 regioselectivity had puzzled and stimulated 2-3 generations of the=20 world-best chemists. My computational results have been rejected by many=20 journals and remain unpublishable . Polanyi would say: "either it's no good or it's too new.... You're going=20 to be tested when you suggest anything new" . One of my paper referees said: "you cannot make such a groundless claim=20 without experimental evidence." My answer to the referee is: "Why has=20 Hoffmann published many hypothetical molecules then?". I was then rejected = without any further information: "I am sorry we cannot accept your paper.=20 I hope you can understand" . I am actually very exhausted in this struggling. The suggestions I got=20 before from this list were to consult Houk, Hoffmann, Bader, Polanyi...=20 But I declined these choices as I want to be myself . I am seeking any open suggestions about a scientific experiment that can=20 be possibly used to prove the polarity reversal of a molecule caused by=20 molecular collisions . Thanks to every one for attention. Sengen -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 002B7A2AC1257643_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

My favourite is (even if he is alrea= dy dead): August Comte

"Every attempt to = employ mathematical methods in  
the study of chemical questions must be considered
profoundly irrational and contrary to the spirit  
of chemistry.... if mathematical analysis should  
ever hold a prominent place in chemistry -- an    
aberration which is happily almost impossible --  
it would occasion a rapid and widespread          =
degeneration of that science."


http://home.att.net/~quotations/scie= nce.html


I would happy, if someone might send me it in French!

Best wishes,

Andr=E1s Borosy



"Dr. Dallos Andr= as" <dallos++almos.vein.hu>

08.07.2009 10:50

To
<andras.borosy++givaudan.com>
cc
Subject
Re: mathematical methods in  the study of chemical questions :-)






Every attempt to employ mathematical methods in  
the study of chemical questions must be considered
profoundly irrational and contrary to the spirit  
of chemistry.... if mathematical analysis should  
ever hold a prominent place in chemistry -- an    
aberration which is happily almost impossible --  
it would occasion a rapid and widespread          =
degeneration of that science.    


- Auguste Comte



 




"Sengen Sun seng= ensun]*[yahoo.com" <owner-chemistry++ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com++ccl.net

28.09.2009 21:51
Please respond to
"CCL Subscribers" <chemistry++ccl.net>

To
"Borosy, Andras " <andras.borosy++givaudan.com>
cc
Subject
CCL: Who is the best philosopher(s) of science now?






Sent to CCL by: Sengen Sun [sengensun : yahoo.com]
>

> If bias is tolerated, as I am French and you are Canadian I
> will suggest Hubert Reeves...
>  VL
>
>>
 
Reeves is indeed one of my favorite philosophers and greatest scientists. But I am critical. Some of his quotes in the following paragraph should be interesting to computational scientists:
.
http://science.ca/scientists/scientistprofile.php?pID=3D213&pg=3D2
.
"You always need to start with an observation," says Reeves. "Mathematics alone can do nothing about knowing the real world. It cannot even tell you what is the number of dimensions you feel." First comes the observation, he says, then the theory. Ultimately, the theory allows us to do calculations that lead to more observations that confirm or improve the theory
.
"Mathematics alone can do nothing about knowing the real world?" This quote contradicts what I said in my ppt slides archived in CCL:
http://ccl.net/cca/documents/ConcertedCycloadditons=5F2/
.
I "Demonstrated solid examples that computational chemistry
is useful in the understanding of chemical phenomena that
cannot be understood otherwise." (Page 24 in my slides)
.
In 1998, after I played the puzzles of concerted cycloadditions for about 17-18 years, I discovered by computations that in many cycloadditions, one of the reactants force the other to change its polarity during collisio= n, forming cycloadduct of "weird" regioselectivity. The "weird&= quot; regioselectivity had puzzled and stimulated 2-3 generations of the world-be= st chemists. My computational results have been rejected by many journals and remain unpublishable
.
Polanyi would say: "either it's no good or it's too new....  You're going to be tested when you suggest anything new"
.
One of my paper referees said: "you cannot make such a groundless claim without experimental evidence." My answer to the referee is: "Why has Hoffmann published many hypothetical molecules then?". I was then rejected without any further information: "I am sorry we cannot accept your paper. I hope you can understand"
.
I am actually very exhausted in this struggling. The suggestions I got before from this list were to consult Houk, Hoffmann, Bader, Polanyi... But I declined these choices as I want to be myself
.
I am seeking any open suggestions about a scientific experiment that can be possibly used to prove the polarity reversal of a molecule caused by molecular collisions
.
Thanks to every one for attention.


Sengen










-=3D This is automatically added to each message by the mailing script =3D-=      http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage
     http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage
     http://www.ccl.net/chemistry/sub=5Funsub.shtml
     http://www.ccl.net/spammers.txt



--=_alternative 002B7A2AC1257643_=-- From owner-chemistry@ccl.net Fri Oct 2 09:03:01 2009 From: "pascal boulet pascal.boulet(0)univ-provence.fr" To: CCL Subject: CCL: Who is the best philosopher(s) of science now? Message-Id: <-40397-091002085746-17581-zhVDxiQdsVfV4ii5VEe1zA|a|server.ccl.net> X-Original-From: pascal boulet Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=ISO-8859-1 Date: Fri, 02 Oct 2009 14:24:40 +0200 MIME-Version: 1.0 Sent to CCL by: pascal boulet [pascal.boulet%%univ-provence.fr]
Dear Andras,

In French, the quotation of Auguste Comte:

"Toute tentative de faire rentrer les questions chimiques dans le domaine des doctrines mathématiques, doit être réputée jusqu'ici, et sans doute à jamais, profondément irrationnelle, comme étant antipathique à la nature des phénomènes : elle ne pourrait découler que d'hypothèses vagues et radicalement arbitraires sur la constitution intime des corps, ainsi que j'ai eu l'occasion de l'exprimer dans les prolégomènes(*) de cet ouvrage."

A closer translation than the one below is the following:

Every attempt to put chemical questions back into the domain of mathematical doctrines must be reputed up to now, and certainly forever, profoundly irrational, as being contrary to the nature of phenomena: it could only result in vague and radically arbitrary hypotheses on the close constitution of the bodies, just as I have had the opportunity to express it in the prolegomenon (=preliminary statement) of this work.

I found the quotations at: http://www.cs.uic.edu/~tj/quotes.html

Best regards
Pascal Boulet


andras.borosy**givaudan.com a écrit :
Dear Colleagues,

My favourite is (even if he is already dead): August Comte


"Every attempt to employ mathematical methods in 
the study of chemical questions must be considered
profoundly irrational and contrary to the spirit 
of chemistry.... if mathematical analysis should 
ever hold a prominent place in chemistry -- an 
aberration which is happily almost impossible -- 
it would occasion a rapid and widespread 
degeneration of that science."

http://home.att.net/~quotations/science.html


I would happy, if someone might send me it in French!

Best wishes,

András Borosy




"Dr. Dallos Andras" <dallos ~ almos.vein.hu> 
08.07.2009 10:50

To
<andras.borosy ~ givaudan.com>
cc

Subject
Re: mathematical methods in  the study of chemical questions :-)








Every attempt to employ mathematical methods in 
the study of chemical questions must be considered
profoundly irrational and contrary to the spirit 
of chemistry.... if mathematical analysis should 
ever hold a prominent place in chemistry -- an 
aberration which is happily almost impossible -- 
it would occasion a rapid and widespread 
degeneration of that science. 


- Auguste Comte



 




"Sengen Sun sengensun]*[yahoo.com" <owner-chemistry ~ ccl.net> 
Sent by: owner-chemistry+andras.borosy==givaudan.com ~ ccl.net
28.09.2009 21:51
Please respond to
"CCL Subscribers" <chemistry ~ ccl.net>


To
"Borosy, Andras " <andras.borosy ~ givaudan.com>
cc

Subject
CCL: Who is the best philosopher(s) of science now?







Sent to CCL by: Sengen Sun [sengensun : yahoo.com]
  
 
If bias is tolerated, as I am French and you are Canadian I
will suggest Hubert Reeves... 
 VL

    
  
Reeves is indeed one of my favorite philosophers and greatest scientists. 
But I am critical. Some of his quotes in the following paragraph should be 
interesting to computational scientists:
.
http://science.ca/scientists/scientistprofile.php?pID=213&pg=2
.
"You always need to start with an observation," says Reeves. "Mathematics 
alone can do nothing about knowing the real world. It cannot even tell you 
what is the number of dimensions you feel." First comes the observation, 
he says, then the theory. Ultimately, the theory allows us to do 
calculations that lead to more observations that confirm or improve the 
theory
.
"Mathematics alone can do nothing about knowing the real world?" This 
quote contradicts what I said in my ppt slides archived in CCL:
http://ccl.net/cca/documents/ConcertedCycloadditons_2/
.
I "Demonstrated solid examples that computational chemistry
is useful in the understanding of chemical phenomena that 
cannot be understood otherwise." (Page 24 in my slides) 
.
In 1998, after I played the puzzles of concerted cycloadditions for about 
17-18 years, I discovered by computations that in many cycloadditions, one 
of the reactants force the other to change its polarity during collision, 
forming cycloadduct of "weird" regioselectivity. The "weird" 
regioselectivity had puzzled and stimulated 2-3 generations of the 
world-best chemists. My computational results have been rejected by many 
journals and remain unpublishable
.
Polanyi would say: "either it's no good or it's too new....  You're going 
to be tested when you suggest anything new"
.
One of my paper referees said: "you cannot make such a groundless claim 
without experimental evidence." My answer to the referee is: "Why has 
Hoffmann published many hypothetical molecules then?". I was then rejected 
without any further information: "I am sorry we cannot accept your paper. 
I hope you can understand"
.
I am actually very exhausted in this struggling. The suggestions I got 
before from this list were to consult Houk, Hoffmann, Bader, Polanyi... 
But I declined these choices as I want to be myself
.
I am seeking any open suggestions about a scientific experiment that can 
be possibly used to prove the polarity reversal of a molecule caused by 
molecular collisions
.
Thanks to every one for attention.


Sengenhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlJob: http://www.ccl.net/jobs http://www.ccl.net/spammers.txt--=_alternative 002B7A2AC1257643_Content-Type: text/html; charset="ISO-8859-1"
Content-Transfer-Encoding: quoted-printable


<br><font size=2 face="sans-serif">Dear Colleagues,</font>
<br>
<br><font size=2 face="sans-serif">My favourite is (even if he is already
dead): <b>August Comte</b></font>
<br>
<br>
<table width=100%>
<tr>
<td width=100%><font size=2 face="sans-serif">&quot;Every attempt to employ
mathematical methods in &nbsp; <br>
the study of chemical questions must be considered<br>
profoundly irrational and contrary to the spirit &nbsp;<br>
of chemistry.... if mathematical analysis should &nbsp;<br>
ever hold a prominent place in chemistry -- an &nbsp; &nbsp;<br>
aberration which is happily almost impossible -- &nbsp;<br>
it would occasion a rapid and widespread &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br>
degeneration of that science.&quot;</font>
<br>
<br><font size=2 face="sans-serif">http://home.att.net/~quotations/science.html</font>
<br>
<br>
<br><font size=2 face="sans-serif">I would happy, if someone might send
me it in French!</font>
<br>
<br><font size=2 face="sans-serif">Best wishes,</font>
<br>
<br><font size=2 face="sans-serif">András Borosy</font>
<br>
<br>
<br>
<br>
<table width=100%>
<tr valign=top>
<td width=40%><font size=1 face="sans-serif"><b>&quot;Dr. Dallos Andras&quot;
&lt;dallos ~ almos.vein.hu&gt;</b> </font>
<p><font size=1 face="sans-serif">08.07.2009 10:50</font>
<td width=59%>
<table width=100%>
<tr valign=top>
<td>
<div align=right><font size=1 face="sans-serif">To</font></div>
<td><font size=1 face="sans-serif">&lt;andras.borosy ~ givaudan.com&gt;</font>
<tr valign=top>
<td>
<div align=right><font size=1 face="sans-serif">cc</font></div>
<td>
<tr valign=top>
<td>
<div align=right><font size=1 face="sans-serif">Subject</font></div>
<td><font size=1 face="sans-serif">Re: mathematical methods in &nbsp;the
study of chemical questions :-)</font></table>
<br>
<table>
<tr valign=top>
<td>
<td></table>
<br></table>
<br>
<br>
<br>
<br>
<table width=100%>
<tr>
<td width=100%><tt><font size=3><b>Every attempt to employ mathematical
methods in &nbsp; <br>
the study of chemical questions must be considered<br>
profoundly irrational and contrary to the spirit &nbsp;<br>
of chemistry.... if mathematical analysis should &nbsp;<br>
ever hold a prominent place in chemistry -- an &nbsp; &nbsp;<br>
aberration which is happily almost impossible -- &nbsp;<br>
it would occasion a rapid and widespread &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br>
degeneration of that science. &nbsp; &nbsp;</b></font></tt></table>
<br><font size=3><br>
</font>
<table width=100%>
<tr>
<td width=100%><tt><font size=3><b>- Auguste Comte</b></font></tt></table>
<br><font size=3><br>
</font><font size=2 face="sans-serif"><br>
</font>
<br><tt><font size=3><b>&nbsp;</b></font></tt></table>
<br>
<br>
<br>
<br>
<table width=100%>
<tr valign=top>
<td width=40%><font size=1 face="sans-serif"><b>&quot;Sengen Sun sengensun]*[yahoo.com&quot;
&lt;owner-chemistry ~ ccl.net&gt;</b> </font>
<br><font size=1 face="sans-serif">Sent by: owner-chemistry+andras.borosy==givaudan.com ~ ccl.net</font>
<p><font size=1 face="sans-serif">28.09.2009 21:51</font>
<table border>
<tr valign=top>
<td bgcolor=white>
<div align=center><font size=1 face="sans-serif">Please respond to<br>
&quot;CCL Subscribers&quot; &lt;chemistry ~ ccl.net&gt;</font></div></table>
<br>
<td width=59%>
<table width=100%>
<tr valign=top>
<td>
<div align=right><font size=1 face="sans-serif">To</font></div>
<td><font size=1 face="sans-serif">&quot;Borosy, Andras &quot;
&lt;andras.borosy ~ givaudan.com&gt;</font>
<tr valign=top>
<td>
<div align=right><font size=1 face="sans-serif">cc</font></div>
<td>
<tr valign=top>
<td>
<div align=right><font size=1 face="sans-serif">Subject</font></div>
<td><font size=1 face="sans-serif">CCL: Who is the best philosopher(s)
of science now?</font></table>
<br>
<table>
<tr valign=top>
<td>
<td></table>
<br></table>
<br>
<br>
<br><tt><font size=2><br>
Sent to CCL by: Sengen Sun [sengensun : yahoo.com]<br>
&gt;<br>
&gt;&nbsp; <br>
&gt; If bias is tolerated, as I am French and you are Canadian I<br>
&gt; will suggest Hubert Reeves... <br>
&gt;&nbsp; VL<br>
&gt; <br>
&gt;&gt;<br>
&nbsp; <br>
Reeves is indeed one of my favorite philosophers and greatest scientists.
But I am critical. Some of his quotes in the following paragraph should
be interesting to computational scientists:<br>
.<br>
http://science.ca/scientists/scientistprofile.php?pID=213&amp;pg=2<br>
.<br>
&quot;You always need to start with an observation,&quot; says Reeves.
&quot;Mathematics alone can do nothing about knowing the real world. It
cannot even tell you what is the number of dimensions you feel.&quot; First
comes the observation, he says, then the theory. Ultimately, the theory
allows us to do calculations that lead to more observations that confirm
or improve the theory<br>
.<br>
&quot;Mathematics alone can do nothing about knowing the real world?&quot;
This quote contradicts what I said in my ppt slides archived in CCL:<br>
http://ccl.net/cca/documents/ConcertedCycloadditons_2/<br>
.<br>
I &quot;Demonstrated solid examples that computational chemistry<br>
is useful in the understanding of chemical phenomena that <br>
cannot be understood otherwise.&quot; (Page 24 in my slides) <br>
.<br>
In 1998, after I played the puzzles of concerted cycloadditions for about
17-18 years, I discovered by computations that in many cycloadditions,
one of the reactants force the other to change its polarity during collision,
forming cycloadduct of &quot;weird&quot; regioselectivity. The &quot;weird&quot;
regioselectivity had puzzled and stimulated 2-3 generations of the world-best
chemists. My computational results have been rejected by many journals
and remain unpublishable<br>
.<br>
Polanyi would say: &quot;either it's no good or it's too new....&nbsp;
You're going to be tested when you suggest anything new&quot;<br>
.<br>
One of my paper referees said: &quot;you cannot make such a groundless
claim without experimental evidence.&quot; My answer to the referee is:
&quot;Why has Hoffmann published many hypothetical molecules then?&quot;.
I was then rejected without any further information: &quot;I am sorry we
cannot accept your paper. I hope you can understand&quot;<br>
.<br>
I am actually very exhausted in this struggling. The suggestions I got
before from this list were to consult Houk, Hoffmann, Bader, Polanyi...
But I declined these choices as I want to be myself<br>
.<br>
I am seeking any open suggestions about a scientific experiment that can
be possibly used to prove the polarity reversal of a molecule caused by
molecular collisions<br>
.<br>
Thanks to every one for attention.<br>
<br>
<br>
Sengen<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br><br<br<br<br>
<br<br>
 &nbsp; &nbsp; &nbsp;http://www.ccl.net/cgi-bin/ccl/send_ccl_message<br>
<br<br>
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<br<br>
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<br<br>
<br<br<br>
<br<br>
<br<br>
 &nbsp; &nbsp; &nbsp;http://www.ccl.net/spammers.txt<br>
<br<br>
<br>
<br>
</font></tt>
<br>
  

-- 
Dr. pascal Boulet, computational chemist
Laboratoire Chimie Provence, UMR 6264
University of Aix-Marseille I 
Avenue Escadrille Normandie-Niemen
13397 Marseille Cedex 20
France
**********
Tel. (+33) (0)491.63.71.17
Fax. (+33) (0)491.63.71.11
**********
http://www.lc-provence.fr
http://allos.up.univ-mrs.fr/boulet
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
From owner-chemistry@ccl.net Fri Oct 2 09:38:01 2009 From: "Konrad Hinsen hinsen^_^cnrs-orleans.fr" To: CCL Subject: CCL: Who is the best philosopher(s) of science now? Message-Id: <-40398-091002085205-1091-JreSi3nAslcdyDEdyKto3A-x-server.ccl.net> X-Original-From: Konrad Hinsen Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Date: Fri, 2 Oct 2009 14:13:03 +0200 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Konrad Hinsen [hinsen^-^cnrs-orleans.fr] On 02.10.2009, at 09:54, andras.borosy**givaudan.com wrote: > My favourite is (even if he is already dead): August Comte > > > "Every attempt to employ mathematical methods in > the study of chemical questions must be considered > profoundly irrational and contrary to the spirit > of chemistry.... if mathematical analysis should > ever hold a prominent place in chemistry -- an > aberration which is happily almost impossible -- > it would occasion a rapid and widespread > degeneration of that science." > > http://home.att.net/~quotations/science.html > > > I would happy, if someone might send me it in French! It's in his "Cours de philosophie positive": = http://books.google.com/books?id=3DX3YrAAAAYAAJ&pg=3DPA42&lpg=3DPA42&dq=3D= Auguste+Comte+math=E9matique+chimie+aberration&source=3Dbl&ots=3D-eJPQafuY= 7&sig=3DFQrAtyZnQQarEKlt3JziphSCBpM&hl=3Den&ei=3D3uzFSvLTIpyc_Aaa9eSVCA&sa= =3DX&oi=3Dbook_result&ct=3Dresult&resnum=3D6#v=20 =3Donepage&q=3D&f=3Dfalse -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Mol=E9culaire, CNRS Orl=E9ans Synchrotron Soleil - Division Exp=E9riences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research at khinsen dot fastmail dot net --------------------------------------------------------------------- From owner-chemistry@ccl.net Fri Oct 2 10:12:01 2009 From: "Michel Petitjean petitjean.chiral(!)gmail.com" To: CCL Subject: CCL: Who is the best philosopher(s) of science now? Message-Id: <-40399-091002094050-6855-lSavQdbgNqz9rAZl5pJVWQ(a)server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 2 Oct 2009 15:40:38 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral%%gmail.com] Hi, I retrieved looking-like sentences in French on the web, but not the tranlation of the first sentence you quoted: << Every attempt to employ mathematical methods in the study of chemical questions must be considered profoundly irrational and contrary to the spirit of chemistry >> If A. Compte really wrote that, I disagree: what about the "mathematical chemistry" field ? I highly prefer what Hubert Reeves said, quoted by Sengen: << "You always need to start with an observation," says Reeves. "Mathematics alone can do nothing about knowing the real world. It cannot even tell you what is the number of dimensions you feel." First comes the observation, he says, then the theory. Ultimately, the theory allows us to do calculations that lead to more observations that confirm or improve the the= ory. >> Sengen disagreed: << "Mathematics alone can do nothing about knowing the real world" This quote contradicts what I said in my ppt slides archived in CCL >> But probably the mathematical model used by Sengen to predict new results was itself build on the basis of observations and experimental data. For programmers: I would be delighted to see a program able to predict some= thing without any input data (stored in a file or stored in the program itself, not necessarily numbers). I fully agree with Reeves. All my best, Michel Petitjean, CEA/DSV/iBiTec-S/SB2SM (CNRS URA 2096), 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean{=}cea.fr, petitjean.chiral{=}gmail.com (preferred) http://petitjeanmichel.free.fr/itoweb.petitjean.html > From: andras.borosy**givaudan.com Dear Colleagues, My favourite is (even if he is already dead): August Comte "Every attempt to employ mathematical methods in the study of chemical questions must be considered profoundly irrational and contrary to the spirit of chemistry.... if mathematical analysis should ever hold a prominent place in chemistry -- an aberration which is happily almost impossible -- it would occasion a rapid and widespread degeneration of that science." http://home.att.net/~quotations/science.html I would happy, if someone might send me it in French! Best wishes, Andr=E1s Borosy From owner-chemistry@ccl.net Fri Oct 2 12:11:01 2009 From: "Roman D Gorbunov rgorbuno:+:aecom.yu.edu" To: CCL Subject: CCL: Is it possible to put dummy atoms in the center of mass? Message-Id: <-40400-091002120542-16714-R17FX30mhgMTYdONdglFaQ,+,server.ccl.net> X-Original-From: "Roman D Gorbunov" Date: Fri, 2 Oct 2009 12:05:39 -0400 Sent to CCL by: "Roman D Gorbunov" [rgorbuno**aecom.yu.edu] Dear CCL Subscribers, I want to run geometry optimization of a small molecule surrounded by water. During this optimization I want to fix the position and orientation of the optimized molecule with respect to water. In other words, optimize only the local structure of the molecule prohibiting its overall rotation and shift (position of water is also fixed). I though that desired constrains can be done in the following way. Using atomic coordinates of the optimized molecule I calculate center of mass and some axis (giving orientation of the molecule). Using the COM and the axis I define positions of dummy atoms (let say I put one dummy atom in the COM and other ones are placed on the axis). Then I can define the water position using Z-matrix and dummy atoms. In this case, if the optimized molecule rotates or moves, water follow this motion and effectively the optimized molecule does not move with respect to the water (and it is what I want). The only problem, I do not know if it is possible to specify positions of dummy atoms using Cartesian coordinates of other atoms. Does anybody know if it is possible? Or, may be, somebody can suggest another strategy to get the above described constraints? Thank you in advance for any help, Roman From owner-chemistry@ccl.net Fri Oct 2 14:27:00 2009 From: "Paul.M.Mathias#fluor.com" To: CCL Subject: CCL: Who is the best philosopher(s) of science now? Message-Id: <-40401-091002141444-8361-OPYBOhNxxiooABKVUCTQww=server.ccl.net> X-Original-From: Paul.M.Mathias- -fluor.com Content-Type: multipart/alternative; boundary="=_alternative 00612E3888257643_=" Date: Fri, 2 Oct 2009 10:41:34 -0700 MIME-Version: 1.0 Sent to CCL by: Paul.M.Mathias[a]fluor.com This is a multipart message in MIME format. --=_alternative 00612E3888257643_= Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" An interesting rebuttal to Comte quote may be the following one from=20 Leonardo da Vinci: "Vitruvius says that small models are of no avail for ascertaining the=20 behavior of big ones. I here propose to show that this conclusion is a=20 false one." Paul Mathias "Konrad Hinsen hinsen^_^cnrs-orleans.fr" Sent by: owner-chemistry+paul.m.mathias=3D=3Dfluor.com]_[ccl.net 10/02/2009 05:13 AM Please respond to "CCL Subscribers" To "Mathias, Paul M. " cc Subject CCL: Who is the best philosopher(s) of science now? Sent to CCL by: Konrad Hinsen [hinsen^-^cnrs-orleans.fr] On 02.10.2009, at 09:54, andras.borosy**givaudan.com wrote: > My favourite is (even if he is already dead): August Comte > > > "Every attempt to employ mathematical methods in > the study of chemical questions must be considered > profoundly irrational and contrary to the spirit > of chemistry.... if mathematical analysis should > ever hold a prominent place in chemistry -- an > aberration which is happily almost impossible -- > it would occasion a rapid and widespread > degeneration of that science." > > http://home.att.net/~quotations/science.html > > > I would happy, if someone might send me it in French! It's in his "Cours de philosophie positive": http://books.google.com/books?id=3DX3YrAAAAYAAJ&pg=3DPA42&lpg=3DPA42&dq=3DA= uguste+Comte+math=E9matique+chimie+aberration&source=3Dbl&ots=3D-eJPQafuY7&= sig=3DFQrAtyZnQQarEKlt3JziphSCBpM&hl=3Den&ei=3D3uzFSvLTIpyc_Aaa9eSVCA&sa=3D= X&oi=3Dbook_result&ct=3Dresult&resnum=3D6#v=20 =3Donepage&q=3D&f=3Dfalse -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Mol=E9culaire, CNRS Orl=E9ans Synchrotron Soleil - Division Exp=E9riences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research at khinsen dot fastmail dot net --------------------------------------------------------------------- -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------------------------------------------------------------ The information transmitted is intended only for the person=20 or entity to which it is addressed and may contain=20 proprietary, business-confidential and/or privileged material. =20 If you are not the intended recipient of this message you are=20 hereby notified that any use, review, retransmission, dissemination,=20 distribution, reproduction or any action taken in reliance upon=20 this message is prohibited. If you received this in error, please=20 contact the sender and delete the material from any computer. =20 Any views expressed in this message are those of the individual=20 sender and may not necessarily reflect the views of the company. =20 ------------------------------------------------------------ --=_alternative 00612E3888257643_= Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="iso-8859-1"
An interesting rebuttal to Comte quo= te may be the following one from Leonardo da Vinci:

"Vitruvius says that small mode= ls are of no avail for ascertaining the behavior of big ones.  I here propose to show that this conclusion is a false one."

Paul Mathias




"Konrad Hinsen hinsen^_^cnrs= -orleans.fr" <owner-chemistry]_[ccl.net>
Sent by:  owner-chemistry+paul.= m.mathias=3D=3Dfluor.com]_[ccl.net
10/02/2009 05:13 AM
Please respond to "CCL Subscrib= ers"
To
"Mathias, Paul M. " <paul.m.mathias]_[fluor.com>
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CCL: Who is the best philosopher(s) of science now?






Sent to CCL by: Konrad Hinsen [hinsen^-^cnrs-orleans.fr]
On 02.10.2009, at 09:54, andras.borosy**givaudan.com wrote:

> My favourite is (even if he is already dead): August Comte
>
>
> "Every attempt to employ mathematical methods in
> the study of chemical questions must be considered
> profoundly irrational and contrary to the spirit
> of chemistry.... if mathematical analysis should
> ever hold a prominent place in chemistry -- an
> aberration which is happily almost impossible --
> it would occasion a rapid and widespread
> degeneration of that science."
>
> http://home.att.net/~quotations/science.html
>
>
> I would happy, if someone might send me it in French!

It's in his "Cours de philosophie positive":

http://books.google.com/books?id=3DX3YrAAAAYAAJ&pg=3DPA42&lpg=3DPA4= 2&dq=3DAuguste+Comte+math=E9matique+chimie+aberration&source=3Dbl&a= mp;ots=3D-eJPQafuY7&sig=3DFQrAtyZnQQarEKlt3JziphSCBpM&hl=3Den&e= i=3D3uzFSvLTIpyc_Aaa9eSVCA&sa=3DX&oi=3Dbook_result&ct=3Dresult&= amp;resnum=3D6#v
=3Donepage&q=3D&f=3Dfalse

--
---------------------------------------------------------------------
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Centre de Biophysique Mol=E9culaire, CNRS Orl=E9ans
Synchrotron Soleil - Division Exp=E9riences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at khinsen dot fastmail dot net
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