From chemistry-request@ccl.net Wed Dec 17 02:57:03 2003
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From: ManojKumar <manojkumar_tk|at|yahoo.com>
Subject: MM parameters in Gaussian-98 and Gaussian-03: Summary
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Hello,

 

A few days back we posted a question about how to include extra MM parameters in the Gaussian input stream. 

 

Thanks for all who responded 



In G-98, link 402 should be recompiled after including 

extra parameters in the source. While G-03 has the option amber=softfirst 

to directly include extra parameters in the input stream. (test528.gjf)

 

Thanking you

 

Sincerely

 

Manoj

 

-------------------------------

T. K. Manojkumar, CSM

Dept. of Chemistry

POSTECH, Pohang, S. Korea

www.csm.postech.ac.kr

----------------------------------

 



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<DIV>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Hello,</SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN>&nbsp;</P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">A few days back we posted a question about how to include extra MM parameters in the Gaussian input stream. <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p>&nbsp;</o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Thanks for all who responded <o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p></o:p></SPAN></P><PRE><TT>In G-98, link 402 should be recompiled after including </TT></PRE><PRE><TT>extra parameters in the source. While G-03 has the option amber=softfirst </TT></PRE><PRE><TT>to directly include extra parameters in the input stream. (test528.gjf)</TT></PRE><PRE><TT><o:p>&nbsp;</o:p></TT></PRE><PRE><TT><o:p></o:p></TT><TT>Thanking you<o:p></o:p></TT></PRE><PRE><TT><o:p>&nbsp;</o:p></TT></PRE><PRE><TT>Sincerely<o:p></o:p></TT></PRE><PRE><TT><o:p>&nbsp;</o:p></TT></PRE><PRE><TT>Manoj<o:p></o:p></TT></PRE>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT face="Times New Roman" size=3>&nbsp;</FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>-------------------------------</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>T. K. Manojkumar, CSM</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>Dept. of Chemistry</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman">POSTECH, <?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:City><st1:place>Pohang</st1:place></st1:City>, <st1:place>S. Korea</st1:place></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><A href="http://www.csm.postech.ac.kr/"><FONT face="Times New Roman" size=3>www.csm.postech.ac.kr</FONT></A></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>----------------------------------</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT face="Times New Roman" size=3>&nbsp;</FONT></o:p></P></DIV><p><hr SIZE=1>
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From chemistry-request@ccl.net Tue Dec 16 23:02:29 2003
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Date: Tue, 16 Dec 2003 23:14:55 -0500 (EST)
Subject: Re: CCL:Calculations without  Born-Oppenheimer approximation '2nd Call'
From: "Steven Wheeler" <swheele2|at|hermes.ccqc.uga.edu>
To: <chemistry|at|ccl.net>
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Along the lines of Dr Sukumar's response, one can do
optimizations/frequencies via energy points utilizing BO-based energies
corrected via the Born-Oppenheimer Diagonal Correction (BODC/DBOC), which
will at least be one step closer to "non-Born-Oppenheimer"
geometries/frequencies.

Psi 3.2 (www.psicode.org) could be made to do this (using a DBOC based on
SCF or CISD wavefunctions), though currently such an approach could not be
carried out automatically.

Steven Wheeler
--------------------------------------------------------------------
Steven E. Wheeler                      | phone: 706 542-7379
Ctr. for Comp. Quantum Chem. | fax:   706 542-0406
University of Georgia     | e-mail: swheele2|at|ccqc.uga.edu
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 --------------------------------------------------------------------

> On Tue, 16 Dec 2003 15:11:47 +0100 (MET) Giju Kalathingal wrote:
>
>> Last week I had send the following message without
>> any success. So I am posting it again.
>>
>> Dear CCL-all,
>>
>> Could you please give me some info on programs
>> that let me to do quantum chemical calculations
>> (geometry optimzations and vibrational frequencies)
>> without Born-Oppenheimer approximation?
>>
>> Thanks in advance.
>>
>> Giju Kalathingal
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>
> Perhaps the reason you did not get any response was because your
> question specifically dealt with programs for geometry optimzations and
> vibrational frequencies. These concepts (molecular geometry and
> molecular vibrations) are normally understood within the
> Born-Oppenheimer approximation. I do not know of any readily available
> programs that deal with these outside of BO. However quantities such as
> bond lengths and vibrational frequencies are derivable from experiment
> and thus these concepts ARE defined beyond the Born-Oppenheimer
> approximation: equilibrium bond lengths, for instance, would be defined
> as the peaks in the two-particle radial distribution functions for the
> two bonded nuclei. See the special issue of Israel Journal of Chemistry,
> vol.19 (1980) for many papers (and much debate), e.g. those of
> R.G.Woolley, pp.30-46 and of Carl Trindle, pp.47-53. L. Lathouwers and
> P. Van Leuven (CPL 52, 439, 1977; PRA 18, 2150, 1978; IJQC S12, 371,
> 1978) demonstrated that the generator coordinate method could be
> employed to avoid the BO separation and develop a non-adiabatic
> formulation of molecular quantum theory.
>
> In a series of pioneering papers on hydrides (CPL 3, 705, 1969; PS 185,
> 90, 1969; PRA 2, 728, 1200, 1675, 1970; PRA 3, 565, 1022, 1971; PRA 4,
> 457, 1971; PRA 5, 1104, 1972), I.L.Thomas put electrons into electronic
> orbitals and protons into protonic orbitals (thereby avoiding the BO
> approximation), antisymmetrized the two kinds of orbitals separately,
> performed SCF computations and obtained molecular structures and spectra
> that
> corresponded to experiment. For instance, the microwave transition
> frequency of ammonia (conventionally explained by "umbrella flipping"
> between two structures) is now obtained as the transition frequency
> between protonic orbitals. Subsequently Thomas went on to become
> vice-president of Occidental Petroleum and did not continue his protonic
> structure studies. I wrote some programs to do similar computations as
> part of my candidacy work at Stony Brook in the early 80s, but those are
> now lost on some magnetic tape somewhere.
>
> There are now several computations and programs that go beyond the BO
> approximation by calculating the nonadiabatic coupling terms or
> performing a diabatic transformation in multi-reference CI or CASSCF
> spaces (see e.g. D.R.Yarkony in "Modern Electronic Structure Theory"
> Part I, World
> Scientific, Singapore, 1995, pp.642-721; W.Domcke, et al. CPL 216,362,
> 1993; 226, 257, 1994; Neuheuser, Sukumar and Peyerimhoff, Chem.Phys.,
> 194, 45-64, 1995; Mol.Phys. 95, 61-70, 1998) but none of these can be
> considered as truly "without Born-Oppenheimer approximation"
>
> (PRA=Phys.Rev A; CPL=Chem.Phys.Lett.; IJQC=Int.J.Quantum Chem)
>
> N. Sukumar
> RPI Department of Chemistry
>
>
>
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From chemistry-request@ccl.net Tue Dec 16 22:21:29 2003
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From: =?iso-8859-1?q?Kaliappan=20Muthukumar?= <muthukumar2k3|at|yahoo.com>
Subject: calculation of enthalpy,ZPE,entropy and gibbs free energies from the out put file
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Dear CCl ers,
Could you please explain me how to calculate enthalpy,ZPE,entropy and gibbs free energies from the out put file of gaussian-98.
I will be very thankful to you and I will summarise all at the end.
bye.
With regards,
M.k.,

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<DIV>Dear CCl ers,</DIV>
<DIV>Could you please explain me how to calculate&nbsp;enthalpy,ZPE,entropy and gibbs free energies from the out put file of gaussian-98.</DIV>
<DIV>I will be very thankful to you and I will summarise all at the end.</DIV>
<DIV>bye.</DIV>
<DIV>With regards,</DIV>
<DIV>M.k.,</DIV><p><font face=arial size=-1>
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From chemistry-request@ccl.net Tue Dec 16 21:52:14 2003
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To: "CHEMISTRY/at/ccl.net" <CHEMISTRY/at/ccl.net>
CC: "manojkumar_tk/at/yahoo.com" <manojkumar_tk/at/yahoo.com>
Subject: Re:MM type  in G03
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 Hi,
   You can add force field parameter in G03. Please see the manual of G03: the section" Molecular Mechanics Methods". You can also see the example file" test528.gjf" in G03.
  
!!!!!!!!!!!!!!!!xiongying
!!!!!!!!!!!!!!!!yxiong/at/mail.ccnu.edu.cn
!!!!!!!!
!!!!!!!!!!!!2003-12-16

Dear CCL Community,

We would like perform QM/MM (MM using amber force field) calculations of
some biological system using Gaussian package. Some of the MM atom types
are not defined in the Gaussian Programme ( for example Cl, sulphur atom
of (CH3)3S+ , atom types of NAD+/NADH ). We wish to include these atom
parameters in the input stream. We looked at the Gaussian mannual - it
does not help.

If anybody knows on how to include extra MM/amber parameters in the input
stream, please help. Your kind suggestions would be highly appreciated.

Sincerely yours,

Manoj






From chemistry-request@ccl.net Wed Dec 17 03:59:11 2003
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To: Christoph.vanWullen=at=TU-Berlin.De
Cc: chemistry=at=ccl.net
Subject: RE: Intel Fortran 8.0 bug
Date: Wed, 17 Dec 2003 08:58:36 -0000
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Christoph,

it's a long time since I've used FORTRAN, and I've not tried the intel
compilers, but I do seem to remember needing to initialise _all_ variables I
wanted to work with, unless I was happy to use random initialised states.
The fact that you are getting an index position way beyond the end of your
first string is what makes me suspicious.

I think you should try initialising str(1) and str(2) to 48-character blank
strings _first_, then go on to set values and look for targets with the
index function.

regards,

Graham


Graham Mullier
Chemoinformatics Team Leader,
Chemistry Design Group,
Syngenta, Bracknell, RG42 6EY, UK.
direct line: +44 (0) 1344 414163
mailto:Graham.Mullier=at=syngenta.com



-----Original Message-----
From: Christoph van W|llen [mailto:Christoph.vanWullen=at=TU-Berlin.De]
Sent: 16 December 2003 11:42
To: chemistry=at=ccl.net
Subject: CCL:Intel Fortran 8.0 bug


Meanwhile I have analyzed the error in the FORTRAN support library
and constructed a small test case. Try this with ifort version 8:

       program test
       character*48 str(2)
       str(1)=' 1.  this is some junk'
       str(2)=' 2.  here is the target'
       do i=1,2
       write (6,*) index(str(i), ' the')
       end do
       end

and you will see what's going wrong (I got the answers 61 and 13).
The error is in the support function for_string_index.
It is not unreasonable to assume a problem in the quality control.

+---------------------------------+----------------------------------+
| Prof. Christoph van W|llen      | Tele-Phone (+49) (0)30 314 27870 |
| Technische Universitdt Sekr. C3 | Tele-Fax   (+49) (0)30 314 23727 |
| Stra_e des 17. Juni 135         | eMail                            |
| D-10623 Berlin, Germany         | Christoph.vanWullen=at=TU-Berlin.De |
+---------------------------------+----------------------------------+
-- 




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From chemistry-request@ccl.net Wed Dec 17 12:51:29 2003
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From: "Kadir Diri" <kadir(at)visual1.chem.pitt.edu>
To: "Kaliappan Muthukumar" <muthukumar2k3(at)yahoo.com>, <chemistry(at)ccl.net>
References: <20031217032058.29834.qmail(at)web42003.mail.yahoo.com>
Subject: Re: CCL:calculation of enthalpy,ZPE,entropy and gibbs free energies from the out put file
Date: Wed, 17 Dec 2003 12:50:54 -0500
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Hello!
Gaussian will calculate and print all these by default in a frequency =
calculation (just include the freq keyword in your input).
Kadir


  ----- Original Message -----=20
  From: Kaliappan Muthukumar=20
  To: chemistry(at)ccl.net=20
  Sent: Tuesday, December 16, 2003 10:20 PM
  Subject: CCL:calculation of enthalpy,ZPE,entropy and gibbs free =
energies from the out put file


  Dear CCl ers,
  Could you please explain me how to calculate enthalpy,ZPE,entropy and =
gibbs free energies from the out put file of gaussian-98.
  I will be very thankful to you and I will summarise all at the end.
  bye.
  With regards,
  M.k.,
  Yahoo! India Mobile: Ringtones, Wallpapers, Picture Messages and more. =
Download now.

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charset=3Diso-8859-1">
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<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV>
<DIV><FONT face=3DArial size=3D2>Hello!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Gaussian will calculate and print all =
these by=20
default in a frequency calculation (just include the freq keyword in =
your=20
input).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Kadir</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV></DIV>
<BLOCKQUOTE dir=3Dltr=20
style=3D"PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; =
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
  <DIV style=3D"FONT: 10pt arial">----- Original Message ----- </DIV>
  <DIV=20
  style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
  <A title=3Dmuthukumar2k3(at)yahoo.com=20
  href=3D"mailto:muthukumar2k3(at)yahoo.com">Kaliappan Muthukumar</A> =
</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>To:</B> <A =
title=3Dchemistry(at)ccl.net=20
  href=3D"mailto:chemistry(at)ccl.net">chemistry(at)ccl.net</A> </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Tuesday, December 16, =
2003 10:20=20
  PM</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Subject:</B> CCL:calculation of=20
  enthalpy,ZPE,entropy and gibbs free energies from the out put =
file</DIV>
  <DIV><BR></DIV>
  <DIV>Dear CCl ers,</DIV>
  <DIV>Could you please explain me how to =
calculate&nbsp;enthalpy,ZPE,entropy=20
  and gibbs free energies from the out put file of gaussian-98.</DIV>
  <DIV>I will be very thankful to you and I will summarise all at the =
end.</DIV>
  <DIV>bye.</DIV>
  <DIV>With regards,</DIV>
  <DIV>M.k.,</DIV>
  <P><FONT face=3Darial size=3D-1><A href=3D"http://in.mobile.yahoo.com" =

  target=3D_blank><B>Yahoo! India Mobile</A>:</B> Ringtones, Wallpapers, =
Picture=20
  Messages and more. <FONT face=3Darial size=3D-1>Download <A=20
  href=3D"http://in.mobile.yahoo.com"=20
  =
target=3D_blank><B>now</A></B>.</FONT></FONT></P></BLOCKQUOTE></BODY></HT=
ML>

------=_NextPart_000_0502_01C3C49C.68B042B0--




From chemistry-request@ccl.net Wed Dec 17 13:29:47 2003
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Content-Type: text/plain
Content-Disposition: inline
To: dshobe(at)sud-chemieinc.com
From: "Dr. N. SUKUMAR" <nagams(at)rpi.edu>
Organization: Rensselaer Polytechnic Institute
Cc: gkalathi(at)vub.ac.be, chemistry(at)ccl.net
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Reply-To: "Dr. N. SUKUMAR" <nagams(at)rpi.edu>
Date: Wed, 17 Dec 2003 13:29:14 EST
X-Mailer: EMUmail 4.00
Subject: Re: Calculations without  Born-Oppenheimer approximation "2nd Call"
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On Wed, 17 Dec 2003 09:40:09 -0500 "Shobe, David" wrote:

> That brings up an interesting question (interesting for me anyway).  What

> Dr. Sukumar defined below is AFAIK neither r-sub-e as it's usually
> defined within the Born-Oppenheimer approximation (i.e. the internuclear
> distance with minimum electronic energy), nor r-sub-zero which is the
> *mean* of the the two-particle radial distribution function.	The
> definition below is the *mode* of the distribution.  
> 

The mean of the two-particle radial distribution function is not a
meaningful quantity. Note that when you solve for the eigenfunctions of the
Hamilronian WITHOUT making the Born-Oppenheimer separation, you do NOT get
solutions corresponding to a particular molecular structure or isomer; you
get a wave function which corresponds to ALL isomers of that stoichiometry.
Thus the two-particle distribution function for C6H6 will have peaks
corresponding to benzene, cyclobutadiene, prismane, bicyclo-propenyl, etc.
The mean of these structures makes no sense chemically.

In making the correspondance between the peaks (mode) of the two-particle 
radial distribution functions and equilibrium bond lengths, one makes the
assumption that the low-energy regions of the potential energy
hypersurfaces will be more populated in a canonical ensemble and thus will
correspond to maxima in the distribution function. This follows equally
> from Boltzman or Fermi-Dirac/Bose Einstein statistics for the nuclei. These
would then correspond to low-temperature experimental structures. For
high-temperature structures or highly fluxional molecules, of course, this
simple correspondance with experiment will not hold.

N. Sukumar
RPI Department of Chemistry

> 
> ++++++++++++++++++++++++++++
> Dr. N. SUKUMAR wrote:
> "equilibrium bond lengths, for instance,would be defined as the peaks in
> the two-particle radial distribution functions for the two bonded nuclei"

> 





From chemistry-request@ccl.net Wed Dec 17 14:07:18 2003
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Date: Thu, 18 Dec 2003 00:12:22 +0530 (IST)
From: utpal sarkar <utpal(at)cts.iitkgp.ernet.in>
To: chemistry(at)ccl.net
Subject: Chemical harness value 
Message-ID: <Pine.LNX.4.44.0311251205450.4962-100000(at)cts.iitkgp.ernet.in>
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Dear CCL users,
               I will be greatful if anybody tells me the 
relative order of chemical hardness value of alpha form, beta form 
and aldehyde form of glucose.
Is the chemical harness of aldehyde form is greater than alpha and beta 
form? Why ?
Please give me the references. 
Thanking you in advance.
With regards
Utpal sarkar




From chemistry-request@ccl.net Wed Dec 17 04:52:00 2003
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Date: Wed, 17 Dec 2003 17:48:18 +0800
From: "6!Q8@W" <dxl*at*mail.ustc.edu.cn>
Reply-To: dxl*at*mail.ustc.edu.cn
To: CCL <chemistry*at*ccl.net>
CC: "help*at*gaussian.com" <help*at*gaussian.com>
Subject: Electronic configuration of the excited state
Organization: VP9z?F4sQ!<|;/Q'J5QiJR
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Dear CCLs:

I want to know how to determine the electronic configuration of the excited state below?

Excited State   1:   ?Spin  -A"     0.3210 eV 3862.42 nm  f=0.0000
    16A -> 28A       -0.41371
    19A -> 28A        0.61820
    21A -> 28A       -0.63309
    26A -> 28A        0.72077
    27A -> 28A       -0.50063
    16B -> 28B       -0.46365
    19B -> 28B       -0.84094
    19B -> 29B       -0.17964
    21B -> 28B       -0.46319
    26B -> 28B        0.80347
    26B -> 29B        0.11637

Ground state:
Orbital Symmetries:
  Alpha Orbitals:
      Occupied  (A') (A') (A') (A') (A') (A') (A") (A') (A') (A")
                (A') (A') (A') (A') (A") (A') (A') (A") (A') (A")
                (A') (A") (A') (A') (A") (A') (A')
      Virtual   (A") (A') (A') (A") (A') (A') (A") (A') (A') (A')
                (A") (A') (A') (A") (A') (A") (A') (A') (A") (A')
                (A') (A') (A") (A') (A') (A") (A') (A") (A') (A")
                (A') (A') (A') (A") (A') (A") (A') (A') (A') (A')
                (A") (A') (A") (A") (A') (A') (A') (A") (A') (A')
                (A') (A') (A") (A') (A") (A') (A') (A") (A') (A")
                (A') (A') (A') (A") (A') (A") (A') (A') (A") (A')
                (A") (A') (A") (A') (A") (A') (A') (A") (A') (A')
                (A') (A") (A') (A") (A') (A') (A") (A') (A") (A')
                (A') (A") (A') (A') (A')
  Beta Orbitals:
      Occupied  (A') (A') (A') (A') (A') (A") (A') (A') (A") (A')
                (A') (A') (A') (A") (A') (A") (A') (A') (A") (A')
                (A") (A') (A") (A') (A') (A") (A')
      Virtual   (A') (A') (A') (A") (A') (A") (A') (A') (A') (A')
                (A") (A') (A') (A") (A') (A") (A') (A') (A") (A')
                (A') (A') (A") (A') (A') (A") (A') (A") (A') (A")
                (A') (A') (A') (A") (A') (A") (A') (A') (A') (A')
                (A") (A") (A") (A') (A') (A') (A') (A") (A') (A')
                (A') (A") (A') (A') (A") (A') (A') (A") (A") (A')
                (A') (A') (A") (A') (A") (A') (A') (A') (A") (A")
                (A') (A") (A') (A") (A') (A') (A') (A") (A') (A')
                (A") (A') (A') (A") (A') (A') (A") (A') (A") (A')
                (A") (A') (A') (A') (A')

!!!!!!!!!!!!!!!!!!!!!!!!!!!!dxl*at*mail.ustc.edu.cn
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!2003-12-17
=================================================
   Xunlei Ding
   Ph.D. Candidate
   Open Laboratory of Bond Selective Chemistry,
   University of Science and Technology of China,
   Hefei, Anhui, 230026,
   People's Republic of China
   Tel.: 86-551-3606428
   Fax.: 86-551-3602969
   http://www.bsc.ustc.edu.cn/~dxl






From chemistry-request@ccl.net Wed Dec 17 08:21:48 2003
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Date: Wed, 17 Dec 2003 08:21:17 -0500 (EST)
From: Jan Labanowski <jkl.-at-.ccl.net>
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Subject: 03.06.21 MATH/CHEM/COMP 2004 - The First Announcement (fwd)
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---------- Forwarded message ----------
Date: Wed, 17 Dec 2003 09:20:21 +0100
From: MATH/CHEM/COMP <mcc.-at-.irb.hr>
To: mcc-info <mcc-info.-at-.irb.hr>
Subject: MATH/CHEM/COMP 2004 - The First Announcement
Resent-Date: Wed, 17 Dec 2003 09:26:10 +0100
Resent-From: mcc-info.-at-.irb.hr

         The First Announcement


Home page: http://mcc.irb.hr


          MATH/CHEM/COMP 2004

The Nineteenth International Course & Conference on the
Interfaces among Mathematics, Chemistry & Computer Sciences


    June 21-26, 2004, Dubrovnik, Croatia


   will be held under the joint auspices of

Inter-University Center, Dubrovnik, Croatia,
"Rudjer Boskovic" Institute, Zagreb, Croatia,
Universities of Zagreb & Split,
International Society for Mathematical Chemistry and
International Society for Theoretical Chemical Physics



Scientific Committee

T. Braun (Budapest)
J. Brickmann (Darmstadt)
D. Butina (Cambridge)
J. Cioslowski (Tallahassee)
H. Hosoya (Tokyo)
P. Fowler (Exeter)
D. J. Klein (Galveston)
S. McGlynn (Baton Rouge)
W. A. Milne (Williston)
V. A. Ostrovskii (St. Petersburg)
R. Ponec (Prague)
M. Randic (Des Moines)
H. Sachs (Ilmenau)
I. Simon (Budapest)
D. Svrtan (Zagreb)
N. Trinajstic (Zagreb)
I. Ugi (Garching)
H. Vancik (Zagreb)
D. Veljan (Zagreb)


Organizing Committee

M. V. Diudea (Cluj)
D. Janezic (Ljubljana)
A. Graovac (Zagreb), director
E. C. Kirby (Pitlochry), co-dir.
I. Lukovits (Budapest)
T. Pisanski (Ljubljana), co-dir.
D. Plavsic (Zagreb)
B. Pokric (Zagreb)
V. Smrecki (Zagreb)
N. Stambuk (Zagreb)
D. Vikic-Topic (Zagreb), co-dir.
J. Zerovnik (Maribor)


WWW page: http://mcc.irb.hr



Venue

The Math/Chem/Comp 2004 (MCC'04) will be held in Dubrovnik from
21-26 June, 2004. Dubrovnik is situated on Adriatic Coast at the
far south of the Republic of Croatia and due to its beauty and harmony is
designated by UNESCO as a world heritage.
The MCC'04 will take place at the Inter-University Centre (IUC),
don Frana Bulica 4, which is situated near the western gate
(Vrata od Pila) of the Old City.



Conference Scope

The MCC'04 is the 19th in the series of MCC meetings which started
in 1986. Any subject pertinent in an interdisciplinary way to
mathematics and/or computer sciences and chemistry and related
sciences is a legitimate topic to be presented at the MCC'04.
The meeting is open to all aspects of current research in the
applications of computer modeling, combinatorics, graph theory
and topology to any area of chemistry, physics, material and life
sciences.



Scientific Program

The conference part will cover recent developments in mathematical
and computational chemistry and physics with a due respect to
applications in material sciences, drug and vaccine design, genetics
and protein studies, etc. The conference program includes invited
lectures, contributed oral presentations and posters. The course
part covers the introductory lectures to the topics presented in
the conference part.

A series of special sessions will be accommodated within the conference.
Up to now Sessions on Chemometrics & Drug Discovery (organized by
D. Butina, darko.butina.-at-.ntlworld.com) and Session on Bioinformatics
(organized by I. Simon, simon.-at-.enzim.hu & P. F. Stadler,
stadler.-at-.bioinf.uni-leipzig.de) are announced.

A series of Courses is also to be held. Up to now Course on RNA
Secondary Prediction Algorithms (I. Hofacker, ivo.-at-.tbi.univie.ac.at)
and Course on Philosophy of Chemistry (H. Vancik, vancik.-at-.irb.hr)
are confirmed.

Information on some further possible sessions & courses will be given
in the Second Announcement and/or MCC web page (http://mcc.irb.hr).



Registration Form & Abstract

Participants may register and submit abstracts by filling our online
entry form presented on the mcc web page.
(http://mcc.irb.hr/formular_03.html)

Registration submission deadline: April 15, 2004

Abstract submission deadline: May 1, 2004

The inclusion in the Book of Abstract is not guaranteed for abstracts
submitted after May 1, 2004.


Besides, registration form and abstract could be also sent as an e-mail
or e-mail attachment to all of the three following mailing addresses:

graovac.-at-.rudjer.irb.hr; pokric.-at-.rudjer.irb.hr; smrecki.-at-.rudjer.irb.hr

MS Word Document (any version) with the margins of 2.5 cm, Times New
Roman (12 point) font and 1.5 line spacing, is recommended for Abstract.
Please, avoid LaTex formats, or send it in both, 'tex' and 'ps'.

The name of the person presenting the contribution should be underlined.



Posters

Poster presentations will be displayed in one of the lecture rooms at
the first floor of the IUC.
The recommended dimensions of the posters are 90 x 120 cm (16.5" x 22").
Posters to be presented should include a concise title, names and complete
addresses of authors, with indication of the author presenting the poster.



Proceedings

The papers presented at the MCC'04 will be published as special issue of
Croatica Chemica Acta.
Instructions to authors can be found at the MCC'04 web
page. All contributions will be refereed. The participants are encouraged
to submit their manuscripts before meeting or at latest upon their arrival
in Dubrovnik. Those unable to attend are invited to send their manuscripts
to the Director.



Registration Fee

The conference registration fee includes the following:
* Admission to all scientific sessions
* Conference materials (program, book of abstracts, list of participants)
* Coffee or juice at breaks
* Welcome drink
* Guided sightseeing city tour
* The IUC reception party
* Excursion
* Conference dinner
* Concert
* Farewell drink



Registration fee:


before April 15, 2004:

250.00  EUR (100.00  EUR for students) + 22%VAT


after April 15, 2004:

300.00  EUR (150.00 EUR for students) + 22%VAT


accompanying persons: 100.00 EUR + 22%VAT



Payment:

Bank transfer to (EUR only!):

Zagrebacka banka, Savska c. 60, HR-10000 Zagreb, Croatia
Ruder Boskovic Institute
bank account no.: 7001-978-3270289 SWIFT=ZABAHR2X
  with *purpose of payment: for MCC'04* and
  your name being indicated!

or a personal check to be sent to the Director and being payable to:
Ante Graovac, MATH/CHEM/COMP 2003


The account for those paying in Croatian currency is:

Zagrebacka banka, Savska c. 60, 10000 Zagreb
Institut "Ruder Boskovic"
broj ziro racuna: 2360000-1101210403
*svrha uplate: za MCC'04* i
obavezno navesti ime i prezime sudionika!

The copy of the receipt should be sent to the Director.


Croatian participants who need an invoice and participants from the
R. Boskovic Institute should contact Mrs. Albina Baruskin at latest
by May 15, 2004 (phone: 45 61 034; fax: 46 80 245,
e-mail: albina.-at-.rudjer.irb.hr) for further informations and payment.



Director

All correspondence concerning the meeting should be addressed to:

Prof. Ante Graovac
Rudjer Boskovic Institute
HR-10002 Zagreb, POB 180, Croatia
phone: (385)-(1)-46-64-565; fax: (385)-(1)-46-80-245
e-mail: graovac.-at-.rudjer.irb.hr



Accommodation & Transportation

The booking of accommodation & transportation is solely on the
participants and the Director is not taking any responsibility
regarding these matters.
The participants are urged to make reservations as soon as possible.

The participants will be accommodated in Hotel *Lero*. The hotel is
within a walking distance from the Inter-University Centre.

The participants are asked to make their hotel reservations directly
by applying to:

Hotel "LERO" (AX, EC/MC, DC, VISA)
Iva Vojnovica 14, HR-20000 Dubrovnik
fax: (385)-20-332-123;   tel.: (385)-20-332-022 and (385)-20-332-122
e-mail: hotel-lero.-at-.du.tel.hr
or by filling the form given on:
http://www.laus.hr/cgi-bin/hotel-reserve1.pl?hotel=Lero


The city of Dubrovnik could be reached by air from Zagreb and some
other European cities, by (frequent) coaches from Zagreb, Rijeka and
Split, by boat from the ports of Rijeka and Split, or by boat from Italy
and Greece.



Registration & Information Desk

On Sunday, June 20, 2004, the Registration/Information Desk will be open
> from 20:00 to 23:00 in Hotel *Lero*, Dubrovnik, Iva Vojnovica 14.
After that the Registration/Information Desk will be located in the
Inter-University Centre (IUC), Dubrovnik, don Frana Bulica 4, and will be
open each day of the meeting from 8:30 to 10:00.





From chemistry-request@ccl.net Wed Dec 17 12:40:41 2003
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In-Reply-To:  <3FDB35D8.C59434A4..at..reading.ac.uk>
From: "Ray Tully" <raymond.tully3..at..mail.dcu.ie>
Subject: CCL:Frontier Orbital Coefficients
To: "Comp Chem Mailing List" <CHEMISTRY..at..server.ccl.net>
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Dear CCLers,
I am trying to calculate the Frontier Orbital Coefficients of aryl oxime
acetates involved in a number of photocyclisation reactions.

Currently I only have access to HyperChem. Can it be done using this program
or is there any software available (preferably free)that can be used?

Ray Tully.




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Subject: RE: Calculations without  Born-Oppenheimer approximation "2nd Call"
Date: Wed, 17 Dec 2003 09:40:09 -0500
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Thread-Topic: Calculations without  Born-Oppenheimer approximation "2nd Call"
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From: "Shobe, David" <dshobe)at(sud-chemieinc.com>
To: "Dr. N. SUKUMAR" <nagams)at(rpi.edu>, <gkalathi)at(vub.ac.be>
Cc: <chemistry)at(ccl.net>
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That brings up an interesting question (interesting for me anyway).  What Dr. Sukumar defined below is AFAIK neither r-sub-e as it's usually defined within the Born-Oppenheimer approximation (i.e. the internuclear distance with minimum electronic energy), nor r-sub-zero which is the *mean* of the the two-particle radial distribution function.  The definition below is the *mode* of the distribution.  

Dr. N. SUKUMAR wrote:
"equilibrium bond lengths, for instance,would be defined as the peaks in the two-particle radial distribution functions for the two bonded nuclei"

There are experimentally determined r-sub-e's, for example in the NIST Webbook databases. Is this the definition of r-sub-e used by experimentalists?  It wouldn't necessarily be equal to r-sub-e as defined by computational chemists using the Born-Oppenheimer approximation, but one could argue that this is the result of using an approximation, and not that there are two different parameters called r-sub-e.

--David Shobe

++++++++++++++++++++++++++++
Dr. N. SUKUMAR wrote:
"equilibrium bond lengths, for instance,would be defined as the peaks in the two-particle radial distribution functions for the two bonded nuclei"

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request)at(ccl.net]On
Behalf Of Dr. N. SUKUMAR
Sent: Tuesday, December 16, 2003 6:03 PM
To: gkalathi)at(vub.ac.be
Cc: chemistry)at(ccl.net
Subject: CCL:Calculations without Born-Oppenheimer approximation "2nd
Call"


On Tue, 16 Dec 2003 15:11:47 +0100 (MET) Giju Kalathingal wrote:

> Last week I had send the following message without 
> any success. So I am posting it again.
> 
> Dear CCL-all,
> 
> Could you please give me some info on programs
> that let me to do quantum chemical calculations
> (geometry optimzations and vibrational frequencies) 
> without Born-Oppenheimer approximation?
> 
> Thanks in advance.
> 
> Giju Kalathingal
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
> 

Perhaps the reason you did not get any response was because your question
specifically dealt with programs for geometry optimzations and vibrational
frequencies. These concepts (molecular geometry and molecular vibrations)
are normally understood within the Born-Oppenheimer approximation. I do not
know of any readily available programs that deal with these outside of BO.
However quantities such as bond lengths and vibrational frequencies are
derivable from experiment and thus these concepts ARE defined beyond the
Born-Oppenheimer approximation: equilibrium bond lengths, for instance,
would be defined as the peaks in the two-particle radial distribution
functions for the two bonded nuclei. See the special issue of Israel
Journal of Chemistry, vol.19 (1980) for many papers (and much debate), e.g.
those of R.G.Woolley, pp.30-46 and of Carl Trindle, pp.47-53. L. Lathouwers
and P. Van Leuven (CPL 52, 439, 1977; PRA 18, 2150, 1978; IJQC S12, 371,
1978) demonstrated that the generator coordinate method could be employed
to avoid the BO separation and develop a non-adiabatic formulation of
molecular quantum theory.

In a series of pioneering papers on hydrides (CPL 3, 705, 1969; PS 185, 90,
1969; PRA 2, 728, 1200, 1675, 1970; PRA 3, 565, 1022, 1971; PRA 4, 457,
1971; PRA 5, 1104, 1972), I.L.Thomas put electrons into electronic orbitals
and protons into protonic orbitals (thereby avoiding the BO approximation),
antisymmetrized the two kinds of orbitals separately, performed SCF
computations and obtained molecular structures and spectra that
corresponded to experiment. For instance, the microwave transition
frequency of ammonia (conventionally explained by "umbrella flipping"
between two structures) is now obtained as the transition frequency between
protonic orbitals. Subsequently Thomas went on to become vice-president of
Occidental Petroleum and did not continue his protonic structure studies. I
wrote some programs to do similar computations as part of my candidacy work
at Stony Brook in the early 80s, but those are now lost on some magnetic
tape somewhere.

There are now several computations and programs that go beyond the BO
approximation by calculating the nonadiabatic coupling terms or performing
a diabatic transformation in multi-reference CI or CASSCF spaces (see e.g.
D.R.Yarkony in "Modern Electronic Structure Theory" Part I, World
Scientific, Singapore, 1995, pp.642-721; W.Domcke, et al. CPL 216,362,
1993; 226, 257, 1994; Neuheuser, Sukumar and Peyerimhoff, Chem.Phys., 194,
45-64, 1995; Mol.Phys. 95, 61-70, 1998) but none of these can be considered
as truly "without Born-Oppenheimer approximation"

(PRA=Phys.Rev A; CPL=Chem.Phys.Lett.; IJQC=Int.J.Quantum Chem)

N. Sukumar
RPI Department of Chemistry



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