From owner-chemistry@ccl.net Thu Dec 16 04:39:01 2010 From: "Johannes Johansson johjo76{:}gmail.com" To: CCL Subject: CCL: geometry optimization of O2 (singlet delta) Message-Id: <-43404-101216043104-16288-wB81pc24DuBRxegz3oKD+Q\a/server.ccl.net> X-Original-From: Johannes Johansson Content-Type: multipart/alternative; boundary=0016e646a53af1f927049783b5de Date: Thu, 16 Dec 2010 10:30:55 +0100 MIME-Version: 1.0 Sent to CCL by: Johannes Johansson [johjo76{=}gmail.com] --0016e646a53af1f927049783b5de Content-Type: text/plain; charset=UTF-8 Dear Dr Jensen, I am quite sure that you will obtain the 1(Delta)g state just by setting the spin multiplicity to one, since the 1(Delta)g state is a closed-shell singlet state (and the most stable singlet state of O2). The 1(Sigma+)g state can be obtained as an open-shell singlet state. For further details on how to obtain such a state, see the CCL archive: 10 July 2009. Sincerely / Johannes -- Adam Johannes Johansson Ph.D., M.Sc. Division of Physical Chemistry KTH (Royal Institute of Technology) Teknikringen 36 SE-100 44 Stockholm Sweden Office: 087908217 Cell phone: 0708178487 E-mail:johjo76]*[gmail.com Research web page:www.physto.se/~johjo --0016e646a53af1f927049783b5de Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Dr Jensen, I am quite sure that you will obtain the 1(Delta)g state ju= st by setting the spin multiplicity to one, since the 1(Delta)g state is a = closed-shell singlet state (and the most stable singlet state of O2). The 1= (Sigma+)g state can be obtained as an open-shell singlet state. For further= details on how to obtain such a state, see the CCL archive: 10 July 2009.<= div>
Sincerely / Johannes

--
Adam Joha= nnes Johansson
Ph.D., M.Sc.
Division of Physical Chemistry
KTH (Ro= yal Institute of Technology)
Teknikringen 36
SE-100 44 Stockholm
Sweden
Office: 087908217
Cell phone: 0708178487
E-mail:johjo76]*[gmail.com
Research web page:www.physto.se/~johjo
--0016e646a53af1f927049783b5de-- From owner-chemistry@ccl.net Thu Dec 16 07:31:00 2010 From: "Johannes Johansson johjo76]-[gmail.com" To: CCL Subject: CCL:G: geometry optimization of O2 (singlet delta) Message-Id: <-43405-101216072944-14175-cuLziHBTd+H6jCbjL1fAKQ(!)server.ccl.net> X-Original-From: Johannes Johansson Content-Type: multipart/alternative; boundary=00163630f4470c31f2049786350a Date: Thu, 16 Dec 2010 13:29:38 +0100 MIME-Version: 1.0 Sent to CCL by: Johannes Johansson [johjo76 . gmail.com] --00163630f4470c31f2049786350a Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Btw, this is a nice paper on the subject of singlet O2: T. Carlton, J. Chem. Educ., 2006, 83 (3), p 477 /Johannes 2010/12/15 Roy Jensen JensenRH/./MacEwan.ca > > Sent to CCL by: Roy Jensen [JensenRH{=3D}MacEwan.ca] > I found that G03 Test Job 001 calculates the singlet delta energy of > oxygen at fixed geometry. > ******************** > #P HF/STO-3G COMPLEX > > Gaussian Test Job 01 > GROUND STATE STO-3G//STO-3G DIOXYGEN > > 0 1 > O > O 1 R > > R 1.22 > ******************** > > Whereas removing the 'COMPLEX' keyword calculates the singlet sigma > state. However, every time I attempt to do a geometry optimization, > with both OPT and COMPLEX, it crashes. > ******************** > (Enter C:\G03W\l401.exe) > Initial guess read from the read-write file: > Guess basis will be translated and rotated to current coordinates. > Unable to project occupied orbitals ! > Error termination via Lnk1e in C:\G03W\l401.exe at Mon Dec 13 > 11:23:37 2010. > ******************** > > According to the Gaussian manual, the COMPLEX keyword is very > limiting. Is there another way to optimized to the singlet delta state > of oxygen and oxygen analogues (NF specifically)? > > Thanks, > Dr. Roy Jensen > (=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D)-----------------------------------------= =C2=A4 > Chemistry, Grant MacEwan University > Room 5-172J, 10700-104 Avenue > Edmonton, AB T5J 4S2 > 780.633.3915 > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Adam Johannes Johansson Ph.D., M.Sc. Division of Physical Chemistry KTH (Royal Institute of Technology) Teknikringen 36 SE-100 44 Stockholm Sweden Office: 087908217 Cell phone: 0708178487 E-mail:johjo76{:}gmail.com Research web page:www.physto.se/~johjo --00163630f4470c31f2049786350a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Btw, this is a nice paper on the subject of singlet O2:

= T. Carlton, J. Chem. Educ., 2006,=C2=A083=C2=A0(3), p 477

/Johannes

2010/12/1= 5 Roy Jensen JensenRH/./MacEwan.ca <owner-chemistry{:}ccl.net>

Sent to CCL by: Roy Jensen [JensenRH{=3D}MacEwan.ca]
I found that G03 Test Job 001 calculates the singlet delta energy of
oxygen at fixed geometry.
********************
#P HF/STO-3G COMPLEX

Gaussian Test Job 01
GROUND STATE STO-3G//STO-3G DIOXYGEN

=C2=A00 1
=C2=A0O
=C2=A0O 1 R

R 1.22
********************

Whereas removing the 'COMPLEX' keyword calculates the singlet sigma=
state. However, every time I attempt to do a geometry optimization,
with both OPT and COMPLEX, it crashes.
********************
=C2=A0(Enter C:\G03W\l401.exe)
=C2=A0Initial guess read from the read-write file:
=C2=A0Guess basis will be translated and rotated to current coordinates. =C2=A0Unable to project occupied orbitals !
=C2=A0Error termination via Lnk1e in C:\G03W\l401.exe at Mon Dec 13
11:23:37 2010.
********************

According to the Gaussian manual, the COMPLEX keyword is very
limiting. Is there another way to optimized to the singlet delta state
of oxygen and oxygen analogues (NF specifically)?

Thanks,
=C2=A0Dr. Roy Jensen
(=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D)-----------------------------------------= =C2=A4
=C2=A0Chemistry, Grant MacEwan University
=C2=A0Room 5-172J, 10700-104 Avenue
=C2=A0Edmonton, AB =C2=A0 =C2=A0T5J 4S2
=C2=A0780.633.3915



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--
Adam Johannes Johansson=
Ph.D., M.Sc.
Division of Physical Chemistry
KTH (Royal Institute = of Technology)
Teknikringen 36
SE-100 44 Stockholm
Sweden
Offic= e: 087908217
Cell phone: 0708178487
E-m= ail:johjo76{:}gmail.com
Research web page:www.physto.se/~johjo
--00163630f4470c31f2049786350a-- From owner-chemistry@ccl.net Thu Dec 16 08:19:01 2010 From: "asp asp99-#-yandex.ru" To: CCL Subject: CCL:G: convering ORCA GBW file Message-Id: <-43406-101216041743-2841-uOoOD51suN1oDCLbTydlDw[]server.ccl.net> X-Original-From: asp Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 16 Dec 2010 12:17:34 +0300 MIME-Version: 1.0 Sent to CCL by: asp [asp99%%yandex.ru] Deal CCL users, is there a way to convet a GBW wavefunction file ganerated by ORCA program to some other format to be used for Atoms in molecules analysis (using AIMAll), for example, gaussian formated checkpoint file or AIMAll *.wfx file? I used the orca_2mkl utility to convert gbw to mkl file. Perhaps, there is a way to use that file for further conversion? Thank you in advance for your comments, Andrei From owner-chemistry@ccl.net Thu Dec 16 08:54:00 2010 From: "Sathya Perumal sathya-*-theochem.kth.se" To: CCL Subject: CCL:G: geometry optimization of O2 (singlet delta) Message-Id: <-43407-101216072021-14323-CtUua5fsnQ+ygFhnBWkBAg**server.ccl.net> X-Original-From: Sathya Perumal Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 16 Dec 2010 13:19:53 +0100 MIME-Version: 1.0 Sent to CCL by: Sathya Perumal [sathya**theochem.kth.se] Hi, The first excited singlet ^1 Delta_g (placed 0.97 eV above the ^3 Sigma_g^-1 ) is described by linear combination of two degenerate pi^* orbitals and therefore two determinants for normal iteration procedure. However it's possible to describe in a single determinant (as in RHF) by employing complex orbitals. and hence it's necessary to specify 'complex' keyword for obtaining 1^Delta_g in linear representation. I am not sure whether the analytical derivatives works for complex orbitals and so for frequencies for minimum location. But it's possible to check the instability of the obtained Complex RHF wavefunctions using the keyword stable=(crhf,1opt). Ofcourse immediate other possible alternatives would be casscf, or perhaps with guess=mix. regards Sathya --- KTH, Stockholm On 15 December 2010 21:43, Roy Jensen JensenRH/./MacEwan.ca wrote: > > Sent to CCL by: Roy Jensen [JensenRH{=}MacEwan.ca] > I found that G03 Test Job 001 calculates the singlet delta energy of > oxygen at fixed geometry. > ******************** > #P HF/STO-3G COMPLEX > > Gaussian Test Job 01 > GROUND STATE STO-3G//STO-3G DIOXYGEN > >  0 1 >  O >  O 1 R > > R 1.22 > ******************** > > Whereas removing the 'COMPLEX' keyword calculates the singlet sigma > state. However, every time I attempt to do a geometry optimization, > with both OPT and COMPLEX, it crashes. > ******************** >  (Enter C:\G03W\l401.exe) >  Initial guess read from the read-write file: >  Guess basis will be translated and rotated to current coordinates. >  Unable to project occupied orbitals ! >  Error termination via Lnk1e in C:\G03W\l401.exe at Mon Dec 13 > 11:23:37 2010. > ******************** > > According to the Gaussian manual, the COMPLEX keyword is very > limiting. Is there another way to optimized to the singlet delta state > of oxygen and oxygen analogues (NF specifically)? > > Thanks, >  Dr. Roy Jensen > (==========)-----------------------------------------¤ >  Chemistry, Grant MacEwan University >  Room 5-172J, 10700-104 Avenue >  Edmonton, AB    T5J 4S2 >  780.633.3915>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Dec 16 10:21:00 2010 From: "Gerard Pujadas gerard.pujadas:gmail.com" To: CCL Subject: CCL: How to identify duplicates for the same molecule that correspond to different tautomers or protonation states? Message-Id: <-43408-101216101931-11411-NZ4N15fAzz7dxx17EBNK2Q^^^server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=90e6ba53a69e4c0d07049788947e Date: Thu, 16 Dec 2010 16:19:26 +0100 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas#gmail.com] --90e6ba53a69e4c0d07049788947e Content-Type: text/plain; charset=ISO-8859-1 Dear CCL subscribers, I am interested in building a chemical database from different chemical suppliers databases. One of the things that I would like to avoid is the repetition of different structures in my database that correspond to the same molecule (for instance, if in the database of two different chemical suppliers the structure for the same molecule is in a different tautomer or protonation state, I would like to identify that they correspond to the same molecule). Any suggestion about how to achieve this? With many thanks in advances for your help Yours sincerely Gerard -- Gerard Pujadas http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 Nutrigenomics Research Group phone +34 977 55 (9565) Biochemistry and Biotechnology Department Universitat Rovira i Virgili Tarragona, Catalonia --90e6ba53a69e4c0d07049788947e Content-Type: text/html; charset=ISO-8859-1 Dear CCL subscribers,

I am interested in building a chemical database from different chemical suppliers databases. One of the things that I would like to avoid is the repetition of different structures in my database that correspond to the same molecule (for instance, if in the database of two different chemical suppliers the structure for the same molecule is in a different tautomer or protonation state, I would like to identify that they correspond to the same molecule). Any suggestion about how to achieve this?

With many thanks in advances for your help

Yours sincerely

Gerard


--
Gerard Pujadas
http://bioquimica.urv.cat/eng/fitxa.jsp?id=22
Nutrigenomics Research Group
phone +34 977 55 (9565)
Biochemistry and Biotechnology Department
Universitat Rovira i Virgili
Tarragona, Catalonia
--90e6ba53a69e4c0d07049788947e-- From owner-chemistry@ccl.net Thu Dec 16 10:55:00 2010 From: "Zork Zou zorkzou++gmail.com" To: CCL Subject: CCL:G: convering ORCA GBW file Message-Id: <-43409-101216104814-18675-d+ZdTwaTG3lMTXB8NZdTZg%x%server.ccl.net> X-Original-From: Zork Zou Content-Type: multipart/alternative; boundary=0016364d2c91c8a63b049788fac3 Date: Thu, 16 Dec 2010 09:48:05 -0600 MIME-Version: 1.0 Sent to CCL by: Zork Zou [zorkzou..gmail.com] --0016364d2c91c8a63b049788fac3 Content-Type: text/plain; charset=ISO-8859-1 Hi Andrei, The answer is yes. 1. generate a molden file. Please refer to the ORCA manual about how to do this. 2. edit the molden file. Add a line [Program] Orca 3. convert molden file to *.wfn file using Molden2AIM http://people.smu.edu/wzou/program/index.html Note: ECP is not supported by Molden2AIM. Zork On Thu, Dec 16, 2010 at 3:17 AM, asp asp99-#-yandex.ru < owner-chemistry+*+ccl.net> wrote: > > Sent to CCL by: asp [asp99%%yandex.ru] > Deal CCL users, > is there a way to convet a GBW wavefunction file ganerated by ORCA program > to some other format to be used for Atoms in molecules analysis (using > AIMAll), for example, gaussian formated checkpoint file or AIMAll *.wfx > file? > > I used the orca_2mkl utility to convert gbw to mkl file. Perhaps, there is > a way to use that file for further conversion? > > Thank you in advance for your comments, > Andrei> > > --0016364d2c91c8a63b049788fac3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Andrei,

The answer is yes.

<= div>1. generate a molden file. Please refer to the ORCA manual about how to= do this.

2. edit the molden file. Add a line
[Program] Orca

3. convert molden file to *.wf= n file using Molden2AIM

Note: ECP is not supported by Molden2AIM.

Zork

On Thu, Dec 16, 2010 at 3:1= 7 AM, asp asp99-#-yandex.ru <owner-chemistry+*+ccl.net<= /a>> wrote:

Sent to CCL by: asp [asp99%%= yandex.ru]
Deal CCL users,
is there a way to convet a GBW wavefunction file ganerated by ORCA program = to some other format to be used for Atoms in molecules analysis (using AIMA= ll), for example, gaussian formated checkpoint file or AIMAll *.wfx file?
I used the orca_2mkl utility to convert gbw to mkl file. Perhaps, there is = a way to use that file for further conversion?

Thank you in advance for your comments,
Andrei



-=3D This is automatically added to each message by the mailing script =3D-=
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--0016364d2c91c8a63b049788fac3-- From owner-chemistry@ccl.net Thu Dec 16 12:21:00 2010 From: "Wolf Ihlenfeldt wdi###xemistry.com" To: CCL Subject: CCL: How to identify duplicates for the same molecule that correspond to different tautomers or protonation states? Message-Id: <-43410-101216113205-17111-kU7JQLr5FgMVa4vuafCIcA|-|server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=20cf3054acddacf04204978997cf Date: Thu, 16 Dec 2010 16:31:57 +0000 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi:+:xemistry.com] --20cf3054acddacf04204978997cf Content-Type: text/plain; charset=UTF-8 Easy to do with the Cactvs toolkit (www.xemistry.com/academic, free for academic users). Use property E_NEUTRALIZED_STRUCTURE to standardize to e neutral form, then use property E_TAUTO_HASH (non-stereospecific) or E_STEREO_TAUTO_HASH (stereospecific for those structure parts which are not in any tautomer system) on that structure to find duplicates with tautomer detection. On Thu, Dec 16, 2010 at 3:19 PM, Gerard Pujadas gerard.pujadas:gmail.com < owner-chemistry() ccl.net> wrote: > Dear CCL subscribers, > > I am interested in building a chemical database from different chemical > suppliers databases. One of the things that I would like to avoid is the > repetition of different structures in my database that correspond to the > same molecule (for instance, if in the database of two different chemical > suppliers the structure for the same molecule is in a different tautomer or > protonation state, I would like to identify that they correspond to the same > molecule). Any suggestion about how to achieve this? > > With many thanks in advances for your help > > Yours sincerely > > Gerard > > > -- > Gerard Pujadas > http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 > Nutrigenomics Research Group > phone +34 977 55 (9565) > Biochemistry and Biotechnology Department > Universitat Rovira i Virgili > Tarragona, Catalonia > -- Wolf-D. Ihlenfeldt, Xemistry GmbH www.xemistry.com --20cf3054acddacf04204978997cf Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Easy to do with the Cactvs toolkit (www.xemistry.com/academic, free for academi= c users).

Use property E_NEUTRALIZED_STRUCTURE to standardize to e n= eutral form, then use property E_TAUTO_HASH (non-stereospecific) or E_STERE= O_TAUTO_HASH (stereospecific for those structure parts which are not in any= tautomer system) on that structure to find duplicates with tautomer detect= ion.



On Thu, Dec 16, 2010 at 3:19 PM, Ger= ard Pujadas gerard.pujadas:g= mail.com <owner-chemistry() ccl.net> wrote:
Dear CCL subscrib= ers,

I am interested in building a chemical database from different = chemical suppliers=20 databases. One of the things that I would like to avoid is the=20 repetition of different structures in my database that correspond to the sa= me molecule (for instance, if in the=20 database of two different chemical suppliers the structure for the same=20 molecule is in a different tautomer or protonation state, I would like to i= dentify that they correspond to the same molecule). Any suggestion about ho= w to achieve this?

With many thanks in advances for your help

Yours sincerely

Gerard


-- Gerard Pujadas
http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22Nutrigenomics Research Group
phone +34 977 55 (9565)
Biochemistry and Biotechnology Department
Uni= versitat Rovira i Virgili
Tarragona, Catalonia



--
Wolf-D. Ihlenfel= dt, Xemistry GmbH
= www.xemistry.com

--20cf3054acddacf04204978997cf-- From owner-chemistry@ccl.net Thu Dec 16 13:26:01 2010 From: "Zsolt Zsoldos zsolt~~simbiosys.ca" To: CCL Subject: CCL: How to identify duplicates for the same molecule that correspond to different tautomers or protonation states? Message-Id: <-43411-101216115858-4423-g+3iEiTj97mLdIi6YyzI3Q[-]server.ccl.net> X-Original-From: Zsolt Zsoldos Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 16 Dec 2010 11:58:49 -0500 MIME-Version: 1.0 Sent to CCL by: Zsolt Zsoldos [zsolt!^!simbiosys.ca] Dear Gerard, The convert executable in the ehits package (that you have as far as I know) will transform the input molecule to a generic protonation form and use 'aromatic' bond type instead of alternating single/double, thus after conversion all tautomeric and protonation forms become an identical (canonical) form, so a simply identity check is sufficient at that point. For processing a large library of ligands and find the identical pairs, I would suggest to use a Morgan hash code as a fast solution. Best regards, Zsolt On Thu, Dec 16, 2010 at 10:19 AM, Gerard Pujadas gerard.pujadas:gmail.com wrote: > Dear CCL subscribers, > > I am interested in building a chemical database from different chemical > suppliers databases. One of the things that I would like to avoid is the > repetition of different structures in my database that correspond to the > same molecule (for instance, if in the database of two different chemical > suppliers the structure for the same molecule is in a different tautomer or > protonation state, I would like to identify that they correspond to the same > molecule). Any suggestion about how to achieve this? > > With many thanks in advances for your help > > Yours sincerely > > Gerard > > > -- > Gerard Pujadas > http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 > Nutrigenomics Research Group > phone +34 977 55 (9565) > Biochemistry and Biotechnology Department > Universitat Rovira i Virgili > Tarragona, Catalonia > -- Zsolt Zsoldos From owner-chemistry@ccl.net Thu Dec 16 14:04:01 2010 From: "Mikko Vainio mikko.vainio||abo.fi" To: CCL Subject: CCL: How to identify duplicates for the same molecule that correspond to different tautomers or protonation states? Message-Id: <-43412-101216120225-6646-fcRFIQgMr8yUZ8OxQLZjYA.:.server.ccl.net> X-Original-From: Mikko Vainio Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 16 Dec 2010 19:02:14 +0200 MIME-Version: 1.0 Sent to CCL by: Mikko Vainio [mikko.vainio .. abo.fi] On 12/16/2010 05:19 PM, Gerard Pujadas gerard.pujadas:gmail.com wrote: > Dear CCL subscribers, > > I am interested in building a chemical database from different > chemical suppliers databases. One of the things that I would like to > avoid is the repetition of different structures in my database that > correspond to the same molecule (for instance, if in the database of > two different chemical suppliers the structure for the same molecule > is in a different tautomer or protonation state, I would like to > identify that they correspond to the same molecule). Any suggestion > about how to achieve this? > > With many thanks in advances for your help > > Yours sincerely > > Gerard > Dear Gerard, The InChI program (http://www.iupac.org/inchi/) can be used to weed out duplicates in different databases. The InChI program does normalization of tautomeric states. The resulting identifier string includes a "charge layer" that you can easily ignore when doing comparisons. See also http://www.inchi-trust.org/ Best regards, Mikko