From owner-chemistry@ccl.net Tue Jan 18 04:26:00 2011
From: "sobereva sobjubao|*|yahoo.com.cn" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: Looking for a source code for calculating Rys Roots and Weights
Message-Id: <-43676-110118042150-2711-h2pJNHhM45N0B78AA3Oj6g%server.ccl.net>
X-Original-From: sobereva <sobjubao(-)yahoo.com.cn>
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Sent to CCL by: sobereva [sobjubao|*|yahoo.com.cn]
Hi, Lan

You can make use of subroutines in ryspol.f of GAMESS(US) to generate Rys roots and weights.

Tian Lu

--- On Tue, 1/18/11, Youzhao Lan lyzhao(0)zjnu.cn <owner-chemistry|*|ccl.net> wrote:

> From: Youzhao Lan lyzhao(0)zjnu.cn <owner-chemistry|*|ccl.net>
> Subject: CCL: Looking for a source code for calculating Rys Roots and Weights
> To: "Lu, Tian " <sobjubao|*|yahoo.com.cn>
> Date: Tuesday, January 18, 2011, 8:48 AM
> 
> Sent to CCL by: "Youzhao  Lan" [lyzhao|a|zjnu.cn]
> Dear All,
>    Is there a source code for calculating
> the roots and weights of Rys polynomial?
> 
> Thanks for your help.
> 
> Lan
> 
> 
> 
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From owner-chemistry@ccl.net Tue Jan 18 06:50:00 2011
From: "Lukman Olawale Olasunkanmi waleolasunkanmi ~ gmail.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: geometry optimization help
Message-Id: <-43677-110118064731-20334-X9knLBMk2/AS8YmuSFjSVQ^server.ccl.net>
X-Original-From: Lukman Olawale Olasunkanmi <waleolasunkanmi^^^gmail.com>
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Sent to CCL by: Lukman Olawale Olasunkanmi [waleolasunkanmi:+:gmail.com]
--0016e64c1e765a10b9049a1d7654
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{:} Victor Rosas & others,
Thank you for your earlier reply to my mail on how to build complexes.
I discover that optimization with Avogadro gives varying coordinates and
energies of the molecule with continuous click on the optimization option.
How do I know when to stop optimizing? Because the coordinates I use in
MOPAC calculations is the determinant of the accuracy of my results.
I will really appreciate your contributions on this.
Thank you.

-- 
Olasunkanmi Lukman Olawale
+234-08052401564

--0016e64c1e765a10b9049a1d7654
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{:} Victor Rosas &amp; others,<br>Thank you for your earlier reply to my mail on how to build complexes.<br>I
 discover that optimization with Avogadro gives varying coordinates and 
energies of the molecule with continuous click on the optimization 
option.<br>
How do I know when to stop optimizing? Because the coordinates I use in 
MOPAC calculations is the determinant of the accuracy of my results.<br>I will really appreciate your contributions on this.<br>Thank you.<br clear="all"><br>-- <br>Olasunkanmi Lukman Olawale<br>+234-08052401564<br>

--0016e64c1e765a10b9049a1d7654--


From owner-chemistry@ccl.net Tue Jan 18 07:25:00 2011
From: "P.D.Jarowski^surrey.ac.uk" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: TD Errors
Message-Id: <-43678-110118071511-12632-S5jOet1eALF4GYQDvYxv2w,+,server.ccl.net>
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Sent to CCL by: [P.D.Jarowski:-:surrey.ac.uk]
--_000_C95B34BFC49pj0013surreyacuk_
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Hello,

Anyone have a reference for the error bars in a TD calculation in the lamba=
 max and oscillator strengths?

Thanks in Advance.

Peter

--_000_C95B34BFC49pj0013surreyacuk_
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<HTML>
<HEAD>
<TITLE>TD Errors</TITLE>
</HEAD>
<BODY>
<FONT FACE=3D"Calibri, Verdana, Helvetica, Arial"><SPAN STYLE=3D'font-size:=
11pt'>Hello,<BR>
<BR>
Anyone have a reference for the error bars in a TD calculation in the lamba=
 max and oscillator strengths?<BR>
<BR>
Thanks in Advance.<BR>
<BR>
Peter</SPAN></FONT>
</BODY>
</HTML>


--_000_C95B34BFC49pj0013surreyacuk_--


From owner-chemistry@ccl.net Tue Jan 18 08:20:00 2011
From: "Andreas Klamt klamt(!)cosmologic.de" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL: Pioglitazone Tautomers
Message-Id: <-43679-110118014940-12219-0RTv1Dgtf/qJeL5CIAe0hA|,|server.ccl.net>
X-Original-From: Andreas Klamt <klamt^^cosmologic.de>
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Sent to CCL by: Andreas Klamt [klamt]![cosmologic.de]
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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  <head>
    <meta content="text/html; charset=ISO-8859-1"
      http-equiv="Content-Type">
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    Nancy,<br>
    <br>
    although I find Gabriele's reply a bit to harsh, I also was a bit
    frustrated when I read your last entry, which essentially repeats
    the initial question after you got a number of replies. You now
    should draw your own conclusions on this. <br>
    <br>
    What you can learns from the diverse answers is that tautomerism is
    still a complicated and quite unsolved question. This was also shown
    in the special issue of <a title="Journal of computer-aided
      molecular design.">J Comput Aided Mol Des.</a> 2010 Jun,24 on
    tautomerism edited by Yvonne Martin and by the outcome of the
    SAMPLE2 blindtest (see <a title="Journal of computer-aided
      molecular design.">Journal of Computer-Aided Molecular Design,
      Volume 24, Number 4</a>).<br>
    <br>
    For your case of Pioglitazone I would conclude that the quantum
    chemical results for the tautomer energy differences are so large,
    that a rather unique answer can be given: The diketonic form
    (neutral and deprotonated) are absolutely predominant. This is a
    lucky case: There are many cases of tatuomerism where the DFT energy
    differences are in the range of a few kcal/mol, i.e. within the
    error bars of DFT,&nbsp; and then no such clear answer can be given. <br>
    <br>
    I would go so far to conclude that the huge energy differences of ~
    12 kcal/mol to the other forms also makes the other forms rather
    unlikely in any protein docked form. I cannot see how the local
    environment of the protein can be so much more favoring the enolic
    forms to compensate such penalty.<br>
    <br>
    If the pKa of 6.3 reported by Gabriele is an experimental one, I
    have no problem to admit that most likely his 85% deprotonated is
    the better answer than my answer based on DFT/COSMO-RS prediction of
    pKa=6.55. The difference of 0.25 pKa units is far within the error
    bars (~ 0.5) of our pKa prediction.<br>
    <br>
    Good luck in going on from here. Perhaps you can send me your final
    paper, or thesis or what ever kind of document you will produce on
    this case.<br>
    <br>
    Andreas<br>
    <br>
    <br>
    <br>
    Am 17.01.2011 22:14, schrieb Gabriele Cruciani gabri-
    -chemiome.chm.unipg.it:
    <blockquote
cite="mid:-id%234nd-43669-110117161457-22980-kC3jADUAzy4UQ8MwUVg%2FHA]*[server.ccl.net"
      type="cite">
      <br>
      Sent to CCL by: Gabriele Cruciani [gabri|a|chemiome.chm.unipg.it]
      <br>
      Nancy,
      <br>
      you get the same answer from different people, with different
      background, using different methods, and you keep asking the same
      question.
      <br>
      <br>
      I think CCL list should be used 'with caution' especially after
      you get all the answers.
      <br>
      <br>
      What you summarized is not correct. The two forms are not
      tautomeric forms. They refer to ONE tautomeric form that is in
      equilibrium with two species, one protonated and one neutral. The
      percentages you reported refer to the solvent pH and to the specie
      pKa. Since the pKa of the pioglitazone is 6.3, the relative
      abundance at pH 7.4 is
      <br>
      85% for the charged and 15% for the neutral one.
      <br>
      <br>
      As told in previous mails, this has nothing to do with the docking
      into a protein, where the local environment, dielectric, 3D
      interactions may change the 'form' of the interacting ligand. In
      this specific case, you cannot say that the charge form may
      interact better because is more abundant, since the equilibrium
      between the two forms can be modified by the protein.
      <br>
      <br>
      Precise pKa calculations are very relevant for pharmacokinetic and
      metabolism studies, but for docking to receptors is better to
      produce the 'relevant' structures. Do not use too simple methods
      (like those you reported) since the problem is very complex and
      require good approaches. Often using the brain is better than
      using free available software.
      <br>
      <br>
      Gabriele Cruciani
      <br>
      <br>
      <br>
      <br>
      <blockquote type="cite">Thus, the two major tautomers of
        pioglitazone are as shown in the attached
        <br>
        figure?
        <br>
        <br>
        Also, is there a published article, or other evidence that would
        confirm
        <br>
        that this is indeed the correct tautomeric distribution at pH 7?
        <br>
        <br>
        Thanks you,
        <br>
        Nancy
        <br>
        <br>
        <br>
        <br>
        On Mon, Jan 17, 2011 at 6:17 AM, Andreas Klamt
        klamt#cosmologic.de&lt;
        <br>
        owner-chemistry/a\ccl.net&gt;&nbsp; wrote:
        <br>
        <br>
        <blockquote type="cite">Sent to CCL by: Andreas Klamt
          [klamt-x-cosmologic.de]
          <br>
          I was just pointed by Leif N&oslash;rskov-Lauritsen to a stupid error
          which I made
          <br>
          in my first entry on this topic. I wrote that at pH=7 25%
          would be
          <br>
          deprotonated, 75% neutral. That was obviously wrong. It is the
          other way
          <br>
          round: 72% is ionic, 25% neutral. The total amount of
          zwitterions is then
          <br>
          ~3%.
          <br>
          <br>
          Sorry for my mistake. But the basic message about the most
          stable neutral
          <br>
          form stays valid.
          <br>
          The most stable anionic form is the di-keto anion.
          <br>
          <br>
          Andreas
          <br>
          <br>
          Am 16.01.2011 19:29, schrieb Nancy nancy5villa**gmail.com:
          <br>
          <br>
          Using quantum chemical calculations, you found that the
          diketone form is
          <br>
          dominant; does this mean that the enol form predicted by
          MarvinSketch v3.5.4
          <br>
          in the published article is wrong?
          <br>
          <br>
          "Structure-based design of a thiazolidinedione which targets
          the
          <br>
          mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb
          <br>
          1;20(3):819-23
          <br>
          <br>
          Thanks,
          <br>
          Nancy
          <br>
          <br>
          <br>
          On Thu, Jan 13, 2011 at 10:31 PM, Andreas Klamt
          klamt(a)cosmologic.de&lt;
          <br>
          owner-chemistry(~)ccl.net&lt;owner-chemistry%28%7E%29ccl.net&gt;&gt;&nbsp;
          wrote:
          <br>
          <br>
          <blockquote type="cite">&nbsp; Sent to CCL by: Andreas Klamt
            [klamt,cosmologic.de]
            <br>
            &nbsp; Hi Nancy,
            <br>
            <br>
            as I wrote in the previous message, we find by quantum
            chemical
            <br>
            calculations within the COSMO-RS solvation that the diketone
            form is more
            <br>
            stable by abot 12 kcal/mol, that means it absolutely
            dominates!
            <br>
            <br>
            Andreas
            <br>
            <br>
            Am 13.01.2011 22:25, schrieb Nancy nancy5villa~!~gmail.com:
            <br>
            <br>
            &nbsp; Hi All,
            <br>
            <br>
            I happened to find a published article where molecular
            docking simulations
            <br>
            of TZDs against a novel protein is detailed:
            <br>
            <br>
            "Structure-based design of a thiazolidinedione which targets
            the
            <br>
            mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010
            Feb
            <br>
            1;20(3):819-23
            <br>
            <br>
            In this paper, the authors, using MarvinSketch v3.5.4,
            determined that the
            <br>
            TZDs would exist predominantly in the enol form at pH 7.4,
            as opposed to the
            <br>
            diketone form (see attached figure).&nbsp; It appears that the
            article's tautomer
            <br>
            prediction was based only on the pH prior to docking, and
            had nothing to do
            <br>
            with ligand-protein interactions.
            <br>
            <br>
            Does anyone know if the diketone or enol, or perhaps a
            different tautomer,
            <br>
            would be predominant at pH 7.4?
            <br>
            <br>
            Thanks in advance.
            <br>
            Nancy
            <br>
            <br>
            <br>
            <br>
            &nbsp;&nbsp; On Wed, Jan 12, 2011 at 9:53 AM, Andreas Klamt
            klamt-*-cosmologic.de&lt;
            <br>
            owner-chemistry(_)ccl.net&lt;owner-chemistry%28_%29ccl.net&gt;&gt;&nbsp;
            wrote:
            <br>
            <br>
            <blockquote type="cite">
              <br>
              Sent to CCL by: Andreas Klamt [klamt[*]cosmologic.de]
              <br>
              Hi All,
              <br>
              <br>
              let me put my 5 cents into the game:
              <br>
              We have done quantum calculations for the heterocyclic
              ring, with just a
              <br>
              methyl group, since electronically the remainder of the
              compound should have
              <br>
              almost no influence on the heterocycle.
              <br>
              DFT/COSMO-RS calculations prove the neutral species
              <br>
              SMILES:CC1C(=O)[NH]C(=O)S1 of the Pioglitazone heterocycle
              to be favored
              <br>
              by 11.3 kcal/mol compared to all other neutral species of
              the heterocycle,
              <br>
              which means that there is no other relvant neutral form.
              <br>
              <br>
              We find with COSMOtherm that the pka of the heterocycle is
              6.55, i.e. at
              <br>
              pH=7 it should be deprotonated with about 25%.
              <br>
              Since the pka of the conj. acid of the pyridine ring
              according to
              <br>
              COSMOtherm (we calculated diethylpyridine) is ~5.6 there
              should be ~10% in
              <br>
              the zwitterionic form.
              <br>
              <br>
              It will be hard to decide this finally, unless someone
              measures it, but
              <br>
              we are quite confident to be qualitatively right here,
              because the energy
              <br>
              differences for the tautomers should not have more than 5
              kcal/mol erro, as
              <br>
              we learned in in the SAMPL2 tautomer contest:
              <br>
              see Andreas Klamt and Michael Diedenhofen, Some
              conclusions regarding the
              <br>
              predictions of tautomeric equilibria in solution based on
              the SAMPL2
              <br>
              challenge,
              <a class="moz-txt-link-freetext" href="http://www.springerlink.com/content/l577667th758n6h1/">http://www.springerlink.com/content/l577667th758n6h1/</a>
              <br>
              <br>
              Andreas
              <br>
              <br>
              <br>
              <br>
              <br>
              <br>
              <br>
              <blockquote type="cite">
                <br>
                Hi All,
                <br>
                <br>
                Using MarvinSketch v5.3.3 (ChemAxon software), the
                predicted pKa value
                <br>
                of the acidic hydrogen on the thiazolidinedione ring of
                pioglitazone is
                <br>
                4.57 (see attached "Figure_1.gif"). Therefore, the
                predominant species
                <br>
                at pH 7.0 predicted by MarvinSketch is the one depicted
                in
                <br>
                "Figure_2.gif". The different tautomeric forms predicted
                by MarvinSketch
                <br>
                are shown in "Figure_3.gif".
                <br>
                <br>
                Can anyone explain where these predictions come from,
                and if they are
                <br>
                correct?
                <br>
                <br>
                Thanks,
                <br>
                Nancy
                <br>
                <br>
                <br>
                On Mon, Jan 10, 2011 at 4:16 AM, Gabriele Cruciani
                <br>
                &nbsp;
                gabri(0)chemiome.chm.unipg.it<a class="moz-txt-link-rfc2396E" href="http://chemiome.chm.unipg.it">&lt;http://chemiome.chm.unipg.it&gt;</a>
                <br>
                <br>
                &lt;owner-chemistry[a]ccl.net<a class="moz-txt-link-rfc2396E" href="mailto:owner-chemistry[a]ccl.net">&lt;mailto:owner-chemistry[a]ccl.net&gt;</a>&gt;&nbsp;
                wrote:
                <br>
                <br>
                <br>
                &nbsp;&nbsp;&nbsp; Sent to CCL by: Gabriele Cruciani
                [gabri##chemiome.chm.unipg.it
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp; <a class="moz-txt-link-rfc2396E" href="http://chemiome.chm.unipg.it">&lt;http://chemiome.chm.unipg.it&gt;</a>]
                <br>
                <br>
                &nbsp;&nbsp;&nbsp; Nancy,
                <br>
                &nbsp;&nbsp;&nbsp; the first form you reported is the most stable in
                water at pH 7.0.
                <br>
                &nbsp;&nbsp;&nbsp; However, the fact that one form is more stable than
                another in water
                <br>
                &nbsp;&nbsp;&nbsp; does not help you to understand which form will be
                more 'relevant'
                <br>
                &nbsp;&nbsp;&nbsp; for docking. In protein the tautomeric equilibria
                may produce and
                <br>
                &nbsp;&nbsp;&nbsp; stabilize different forms according to the
                complementary site. There
                <br>
                &nbsp;&nbsp;&nbsp; are examples of tautomeric form in protein not
                stable in water,
                <br>
                &nbsp;&nbsp;&nbsp; where the energy difference is more than 5 Kcal/mol.
                <br>
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp; MoKa software
                (<a class="moz-txt-link-abbreviated" href="http://www.moldiscovery.com">www.moldiscovery.com</a><a class="moz-txt-link-rfc2396E" href="http://www.moldiscovery.com">&lt;http://www.moldiscovery.com&gt;</a>)
                <br>
                <br>
                &nbsp;&nbsp;&nbsp; is fast and accurate to produce tautomer stable in
                water, but it can
                <br>
                &nbsp;&nbsp;&nbsp; produce also all the (plausible) tautomeric forms.
                <br>
                <br>
                &nbsp;&nbsp;&nbsp; Then, a possibility is to dock them into your
                protein, to see if
                <br>
                &nbsp;&nbsp;&nbsp; docking methods may differentiate their binding.
                <br>
                <br>
                &nbsp;&nbsp;&nbsp; Gabriele Cruciani
                <br>
                <br>
                <br>
                <br>
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Hi All,
                <br>
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I am performing molecular docking and molecular
                dynamics
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; simulations of the
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; thiazolidinedione pioglitazone binding to the
                PPAR-gamma
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; receptor protein
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (PDB ID: 1ZGY). The thiazolidinedione ring can
                exist in numerous
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; different
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; tautomeric states; I have attached a figure
                depicting several of
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; them.
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Which tautomer would be dominant at the
                physiological pH of ~7.0?
                <br>
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Also, are there any software programs that can
                predict which
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; tautomer would
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; be correct?
                <br>
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Thanks in advance,
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Nancy&gt;
                <br>
                <br>
                <br>
                &nbsp;&nbsp;&nbsp;&nbsp; E-mail to subscribers: CHEMISTRY[a]ccl.net
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                <br>
                <br>
                <br>
                <br>
              </blockquote>
              --
              <br>
              Dr. Jens Reinisch
              <br>
              Chemist / Customer Support
              <br>
              COSMOlogic GmbH&amp;&nbsp; Co. KG
              <br>
              Burscheider Strasse 515
              <br>
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              <br>
              <br>
              phone&nbsp;&nbsp; +49-2171-363664
              <br>
              mobile&nbsp; +49-163-7337310
              <br>
              fax&nbsp;&nbsp;&nbsp;&nbsp; +49-2171-731689
              <br>
              e-mail&nbsp; reinisch[*]cosmologic.de
              <br>
              web&nbsp;&nbsp;&nbsp;&nbsp; <a class="moz-txt-link-abbreviated" href="http://www.cosmologic.de">www.cosmologic.de</a>
              <br>
              <br>
              HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
              <br>
              Komplementaer: COSMOlogic Verwaltungs GmbH
              <br>
              HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
              <br>
              <br>
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              <br>
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              &nbsp; E-mail to subscribers:
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PD. Dr. Andreas Klamt
CEO / Gesch&auml;ftsf&uuml;hrer
COSMOlogic GmbH &amp; Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
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web    	<a class="moz-txt-link-abbreviated" href="http://www.cosmologic.de">www.cosmologic.de</a>

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
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</pre>
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From owner-chemistry@ccl.net Tue Jan 18 08:55:00 2011
From: "sumit kumar sumitkumar!^!iiserpune.ac.in" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL:G: About negative frequency for stable conformers in NWCHEM
Message-Id: <-43680-110118021527-18801-w0OTmlK8tzb5w6a91DEmag[#]server.ccl.net>
X-Original-From: "sumit  kumar" <sumitkumar[A]iiserpune.ac.in>
Date: Tue, 18 Jan 2011 02:14:46 -0500


Sent to CCL by: "sumit  kumar" [sumitkumar---iiserpune.ac.in]
Dear Sir,
 
We have performed geometry optimization of mixed dimer of indole and pyridine at m05-2x/6-31+g* level using Gaussian 03 and NWCHEM softwares. In case of gaussian calculation we have obtained three sable conformers,where all of them have positive frequency only. But when same three conformers were run using NWCHEM, we have found that two of them are giving few negative frequency. Also NH stretch frequency of one of the conformers is  very much different in NWCHEM (3730cm-1)  than that obtained in gaussian (3636cm-1)
 
We don't understand how same theory and same basis set using two softwares are giving this different result.
I have attached here both gaussian and NWCHEM files.

These three conformers when were run also at higher level of theory ( MP2 ) as well as higher basis set ( cc-pVDZ,aug-cc-pVDZ ), using gaussian, don't give any negative frequency. But when they are run in NWCHEM gives negative frequency.
 
Using both Gaussian and NWCHEM, DFT level calculations are done using Grid=Ultrafine command.
 
I will appreciate help us for solving this problem in NWCHEM .
 
sincerely Yours
 
-- 
 
-- 
              Sumit Kumar
              Research Scholar
              (laser spectroscopy)
              Indian Institutes of Science
              Education and Research,
              (iiser,pune)
              mobile no:-9579450484


From owner-chemistry@ccl.net Tue Jan 18 09:30:00 2011
From: "Olasunkanmi Lukman Olawale walecomuk ~ yahoo.co.uk" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: complexes
Message-Id: <-43681-110118045051-8397-rIOMkiC5z4nv1eQeEmh0GQ ~ server.ccl.net>
X-Original-From: Olasunkanmi Lukman Olawale <walecomuk*o*yahoo.co.uk>
Content-Type: multipart/alternative; boundary="0-747588781-1295344236=:94901"
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Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk-.-yahoo.co.uk]
--0-747588781-1295344236=:94901
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,+, Victor Rosas & others,=0AThank you for your earlier reply to my mail on h=
ow to build complexes.=0AI  discover that optimization with Avogadro gives =
varying coordinates and  =0Aenergies of the molecule with continuous click =
on the optimization  option.=0AHow do I know when to stop optimizing? Becau=
se the coordinates I use in  MOPAC =0Acalculations is the determinant of th=
e accuracy of my results.=0AI will really appreciate your contributions on =
this.=0AThank you.=0A=0A Olasunkanmi Lukman Olawale=0A_____________________=
___________=0ACurrent Address:=0ADepartment of Chemistry,=0AObafemi Awolowo=
 University,=0AIle-Ife, Osun State.=0ANigeria.=0A=0A+234-0-80-52401564 Or +=
234-0-80-67161091=0A________________________________=0A =0A=0A=0A=0A=0A____=
____________________________=0AFrom: Victor Rosas Garcia rosas.victor##gmai=
l.com <owner-chemistry,+,ccl.net>=0ATo: "Olasunkanmi, Olawale Lukman =
" <walecomuk,+,yahoo.co.uk>=0ASent: Thu, 13 January, 2011 15:38:39=0ASubject:=
 CCL: complexes=0A=0AWell, if you are able to sketch the structure in a pie=
ce of paper, you should be =0Aable to build the molecule in Avogadro.  Buil=
ding mode is the default when =0AAvogadro starts.  Personally I tick off th=
e option of adjusting hydrogens, as I =0Afind it annoying most of the time.=
 Of course whatever you sketch will have lots =0Aof strained bonds and angl=
es so you will have to "clean" your structure by =0Aenergy minimization (un=
der the "Extensions" menu).  You may have to resort to a =0Adifferent force=
 field than the default, because the Fe(II) bonding may not be =0Awell repr=
esented by the MMFF94 forcefield.  Probably UFF will work, or some =0Asemie=
mpirical method (if you have mopac installed).  That will give you a =0Area=
sonable starting structure for higher level treatment.=0A=0AAlternatively, =
if you can get the XYZ coordinates from the crystal structure, =0AAvogadro =
will read those and you will get a reasonable structure in one step.=0A=0AH=
ope this helps=0A=0AVictor=0A=0A=0A2011/1/13 Olawale Lukman Olasunkanmi wal=
eolasunkanmi:_:gmail.com =0A<owner-chemistry*ccl.net>=0A=0A=0A>Sent to CCL =
by: "Olawale Lukman Olasunkanmi" [waleolasunkanmi^_^gmail.com]=0A>Thank you=
 all for your earlier contributions. I am getting there.=0A>I have got Avog=
adro installed and have started using it.=0A>Please, can anyone put me thro=
ugh how to build complexes like =0A>iron(II)phenanthroline complex with the=
 package? There is no procedure for such =0A>molecules in the manual.=0A>Th=
ank you.=0A>=0A>=0A>=0A>-=3D This is automatically added to each message by=
 the mailing script =3D-=0A>=0A>E-mail to subscribers: CHEMISTRY*ccl.net or=
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.net/cgi-bin/ccl/send_ccl_message=0A>=0A>Subscribe/Unsubscribe:=0A>     htt=
p://www.ccl.net/chemistry/sub_unsub.shtml=0A>=0A>Before posting, check wait=
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nces: http://server.ccl.net/chemistry/announcements/conferences/=0A>=0A>Sea=
rch Messages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A>=0A>   ==0A>=0A>RTFI: http://www.ccl.net/chemistry=
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--0-747588781-1295344236=:94901
Content-Type: text/html; charset=utf-8
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<html><head><style type=3D"text/css"><!-- DIV {margin:0px;} --></style></he=
ad><body><div style=3D"font-family:times new roman,new york,times,serif;fon=
t-size:10pt">,+, Victor Rosas &amp; others,<br>Thank you for your earlier rep=
ly to my mail on how to build complexes.<br>I=0A discover that optimization=
 with Avogadro gives varying coordinates and =0Aenergies of the molecule wi=
th continuous click on the optimization =0Aoption.<br>=0AHow do I know when=
 to stop optimizing? Because the coordinates I use in =0AMOPAC calculations=
 is the determinant of the accuracy of my results.<br>I will really appreci=
ate your contributions on this.<br>Thank you.<br><div>&nbsp;</div><span sty=
le=3D"color: rgb(0, 0, 127); font-weight: bold;">Olasunkanmi Lukman Olawale=
</span><br><hr style=3D"width: 100%; height: 2px;"><span style=3D"font-weig=
ht: bold;">Current Address:</span><br><span style=3D"color: rgb(0, 0, 191);=
 font-weight: bold;">Department of Chemistry,</span><br style=3D"color: rgb=
(0, 0, 191); font-weight: bold;"><span style=3D"color: rgb(0, 0, 191); font=
-weight: bold;">Obafemi Awolowo University,</span><br style=3D"color: rgb(0=
, 0, 191); font-weight: bold;"><span style=3D"color: rgb(0, 0, 191); font-w=
eight: bold;">Ile-Ife, Osun State.</span><br style=3D"color: rgb(0, 0, 191)=
; font-weight: bold;"><span style=3D"color: rgb(0, 0, 191); font-weight: bo=
ld;">Nigeria.</span><br style=3D"color: rgb(0, 0, 191); font-weight: bold;"=
><div style=3D"text-align: left;"><span style=3D"color: rgb(0, 0, 191);
 font-weight: bold;">+</span><span style=3D"color: rgb(0, 0, 191);">2</span=
><span style=3D"color: rgb(0, 0, 191); font-weight: bold;">34-0-80-52401564=
 Or +234-0-80-67161091</span><br><hr style=3D"width: 100%; height: 2px;"> <=
/div><div><br></div><div style=3D"font-family: times new roman,new york,tim=
es,serif; font-size: 10pt;"><br><div style=3D"font-family: times new roman,=
new york,times,serif; font-size: 12pt;"><font face=3D"Tahoma" size=3D"2"><h=
r size=3D"1"><b><span style=3D"font-weight: bold;">From:</span></b> Victor =
Rosas Garcia rosas.victor##gmail.com &lt;owner-chemistry,+,ccl.net&gt;<br><b>=
<span style=3D"font-weight: bold;">To:</span></b> "Olasunkanmi, Olawale Luk=
man " &lt;walecomuk,+,yahoo.co.uk&gt;<br><b><span style=3D"font-weigh=
t: bold;">Sent:</span></b> Thu, 13 January, 2011 15:38:39<br><b><span style=
=3D"font-weight: bold;">Subject:</span></b> CCL: complexes<br></font><br><m=
eta http-equiv=3D"x-dns-prefetch-control" content=3D"off">Well, if you are =
able to sketch the
 structure in a piece of paper, you should be able to build the molecule in=
 Avogadro.&nbsp; Building mode is the default when Avogadro starts.&nbsp; P=
ersonally I tick off the option of adjusting hydrogens, as I find it annoyi=
ng most of the time. Of course whatever you sketch will have lots of strain=
ed bonds and angles so you will have to "clean" your structure by energy mi=
nimization (under the "Extensions" menu).&nbsp; You may have to resort to a=
 different force field than the default, because the Fe(II) bonding may not=
 be well represented by the MMFF94 forcefield.&nbsp; Probably UFF will work=
, or some semiempirical method (if you have mopac installed).&nbsp; That wi=
ll give you a reasonable starting structure for higher level treatment.<br>=
=0A<br>Alternatively, if you can get the XYZ coordinates from the crystal s=
tructure, Avogadro will read those and you will get a reasonable structure =
in one step.<br><br>Hope this helps<br><br>Victor<br><br><div class=3D"gmai=
l_quote">=0A2011/1/13 Olawale Lukman Olasunkanmi waleolasunkanmi:_:<a rel=
=3D"nofollow" target=3D"_blank" href=3D"http://gmail.com">gmail.com</a> <sp=
an dir=3D"ltr">&lt;<a rel=3D"nofollow" ymailto=3D"mailto:owner-chemistry*cc=
l.net" target=3D"_blank" href=3D"mailto:owner-chemistry*ccl.net">owner-chem=
istry*ccl.net</a>&gt;</span><br><blockquote class=3D"gmail_quote" style=3D"=
margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); paddi=
ng-left: 1ex;">=0A<br>=0ASent to CCL by: "Olawale Lukman Olasunkanmi" [wale=
olasunkanmi^_^<a rel=3D"nofollow" target=3D"_blank" href=3D"http://gmail.co=
m">gmail.com</a>]<br>=0AThank you all for your earlier contributions. I am =
getting there.<br>=0AI have got Avogadro installed and have started using i=
t.<br>=0APlease, can anyone put me through how to build complexes like iron=
(II)phenanthroline complex with the package? There is no procedure for such=
 molecules in the manual.<br>=0AThank you.<br>=0A<br>=0A<br>=0A<br>=0A-=3D =
This is automatically added to each message by the mailing script =3D-<br>=
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From owner-chemistry@ccl.net Tue Jan 18 10:04:00 2011
From: "Eduard Matito ematito()gmail.com" <owner-chemistry!A!server.ccl.net>
To: CCL
Subject: CCL:G: Energy decomposition programs, such as SAPT
Message-Id: <-43682-110118083717-8716-Ot1ZYHIXyWKeIkAhrqneBg!A!server.ccl.net>
X-Original-From: Eduard Matito <ematito~~gmail.com>
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Date: Tue, 18 Jan 2011 14:36:58 +0100
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Sent to CCL by: Eduard Matito [ematito.:.gmail.com]
Istvan Mayer and Pedro Salvador have some programs to perform an  
energy decomposition
analysis. They are for free. Most of them use gaussian files (fchk or  
similar).
http://occam.chemres.hu/programs/

Eduard

On Jan 17, 2011, at 11:15 PM, Victor Rosas Garcia  
rosas.victor(!)gmail.com wrote:

> There is Natural Energy Decomposition Analysis, in NBO 5.0.  Not  
> free but very cheap.
>
> Victor
>
> 2011/1/17 Tapas Kar tapas.kar|*|usu.edu <owner-chemistry,ccl.net>
>
> Sent to CCL by: "Tapas  Kar" [tapas.kar[#]usu.edu]
> Hello,
>
> Is MOLPRO the standard QM program that runs SAPT and SAPT-DFT, or  
> are there others?
>
> Also any other Energy decomposition method, besides SAPT (Symmetry- 
> adapted perturbation theory) and Morokuma Energy decomposition  
> method (implemented in GAMESS-US), are developed?
>
> Thanks
> Tapas
>
>
>
> -= This is automatically added to each message by the mailing script  
> =-
>
>
>
> E-mail to subscribers: CHEMISTRY,ccl.net or use:>
> E-mail to administrators: CHEMISTRY-REQUEST,ccl.net or use> Conferences: http://server.ccl.net/chemistry/announcements/ 
> conferences/>
>
>

--
Eduard Matito
Postdoctoral researcher
Institute of Physics
University of Szczecin
Wielkopolska 15
70451 Szczecin (Poland)
Phone: +48914441436
http://ematito.webs.com


From owner-chemistry@ccl.net Tue Jan 18 10:40:00 2011
From: "Victor Rosas Garcia rosas.victor**gmail.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: geometry optimization help
Message-Id: <-43683-110118090436-8982-ATFRtM6U9SIKoNCZnEShYQ .. server.ccl.net>
X-Original-From: Victor Rosas Garcia <rosas.victor .. gmail.com>
Content-Type: multipart/alternative; boundary=0015174c43e215695c049a1f604b
Date: Tue, 18 Jan 2011 08:04:13 -0600
MIME-Version: 1.0


Sent to CCL by: Victor Rosas Garcia [rosas.victor/a\gmail.com]
--0015174c43e215695c049a1f604b
Content-Type: text/plain; charset=ISO-8859-1

Yes.  Avogadro does minimization mostly as a "clean up" of the structure.
It yields chemically reasonable structures but it is not really a thorough
optimization.  The good thing is that, once you feed those coordinates to
MOPAC, the optimizer in MOPAC will look for an energetic stationary point.
That is, if you start from similar but not identical geometries, MOPAC will
still find the same local stationary point.

Hope this helps

Victor

2011/1/18 Lukman Olawale Olasunkanmi waleolasunkanmi ~ gmail.com <
owner-chemistry-.-ccl.net>

> (0) Victor Rosas & others,
> Thank you for your earlier reply to my mail on how to build complexes.
> I discover that optimization with Avogadro gives varying coordinates and
> energies of the molecule with continuous click on the optimization option.
> How do I know when to stop optimizing? Because the coordinates I use in
> MOPAC calculations is the determinant of the accuracy of my results.
> I will really appreciate your contributions on this.
> Thank you.
>
> --
> Olasunkanmi Lukman Olawale
> +234-08052401564
>

--0015174c43e215695c049a1f604b
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Yes.=A0 Avogadro does minimization mostly as a &quot;clean up&quot; of the =
structure.=A0 It yields chemically reasonable structures but it is not real=
ly a thorough optimization.=A0 The good thing is that, once you feed those =
coordinates to MOPAC, the optimizer in MOPAC will look for an energetic sta=
tionary point.=A0 That is, if you start from similar but not identical geom=
etries, MOPAC will still find the same local stationary point.<br>
<br>Hope this helps<br><br>Victor<br><br><div class=3D"gmail_quote">2011/1/=
18 Lukman Olawale Olasunkanmi waleolasunkanmi ~ <a href=3D"http://gmail.com=
">gmail.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry-.-ccl=
.net">owner-chemistry-.-ccl.net</a>&gt;</span><br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">(0) Victor Rosas =
&amp; others,<br>Thank you for your earlier reply to my mail on how to buil=
d complexes.<br>
I
 discover that optimization with Avogadro gives varying coordinates and=20
energies of the molecule with continuous click on the optimization=20
option.<br>
How do I know when to stop optimizing? Because the coordinates I use in=20
MOPAC calculations is the determinant of the accuracy of my results.<br>I w=
ill really appreciate your contributions on this.<br>Thank you.<br clear=3D=
"all"><font color=3D"#888888"><br>-- <br>Olasunkanmi Lukman Olawale<br>+234=
-08052401564<br>

</font></blockquote></div><br>

--0015174c43e215695c049a1f604b--


From owner-chemistry@ccl.net Tue Jan 18 11:26:00 2011
From: "Ol Ga eurisco1 _ pochta.ru" <owner-chemistry_-_server.ccl.net>
To: CCL
Subject: CCL:G: About negative frequency for stable conformers in NWCHEM
Message-Id: <-43684-110118112532-18268-EjjkVOMaJJhYl8vZB4KiOw_-_server.ccl.net>
X-Original-From: "Ol  Ga" <eurisco1 ~ pochta.ru>
Date: Tue, 18 Jan 2011 11:25:30 -0500


Sent to CCL by: "Ol  Ga" [eurisco1_._pochta.ru]
Dear Sumit Kumar,

I would suggest to optimize conformers by means of NWChem with convergence 
criteria of stationary point search similar to Tight in Gaussian and 
calculate frequencies again. I hope it will solve the problem.
How large is difference of geometries for conformers optimized by means of 
Gaussian and NWChem?


Sincerely,
Ol Ga


----- ----- 
> From: sumit kumar sumitkumar!^!iiserpune.ac.in
Sent: Tuesday, January 18, 2011 10:14 AM
To: Ga, Ol 
Subject: CCL:G: About negative frequency for stable conformers in NWCHEM


Sent to CCL by: "sumit  kumar" [sumitkumar---iiserpune.ac.in]
Dear Sir,

We have performed geometry optimization of mixed dimer of indole and 
pyridine at m05-2x/6-31+g* level using Gaussian 03 and NWCHEM softwares. In 
case of gaussian calculation we have obtained three sable conformers,where 
all of them have positive frequency only. But when same three conformers 
were run using NWCHEM, we have found that two of them are giving few 
negative frequency. Also NH stretch frequency of one of the conformers is 
very much different in NWCHEM (3730cm-1)  than that obtained in gaussian 
(3636cm-1)

We don't understand how same theory and same basis set using two softwares 
are giving this different result.
I have attached here both gaussian and NWCHEM files.

These three conformers when were run also at higher level of theory ( MP2 ) 
as well as higher basis set ( cc-pVDZ,aug-cc-pVDZ ), using gaussian, don't 
give any negative frequency. But when they are run in NWCHEM gives negative 
frequency.

Using both Gaussian and NWCHEM, DFT level calculations are done using 
Grid=Ultrafine command.

I will appreciate help us for solving this problem in NWCHEM .

sincerely Yours

-- 

-- 
              Sumit Kumar
              Research Scholar
              (laser spectroscopy)
              Indian Institutes of Science
              Education and Research,
              (iiser,pune)
              mobile no:-9579450484



-=


From owner-chemistry@ccl.net Tue Jan 18 12:57:00 2011
From: "Pietro Ottati pietro.ottati-.-gmail.com" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL: Hello list... Help me first time.
Message-Id: <-43685-110118095736-29056-7qYS4o1cQqV8XrgTJXNjBA===server.ccl.net>
X-Original-From: Pietro Ottati <pietro.ottati .. gmail.com>
Content-Type: multipart/alternative; boundary=0016e64dda762e59af049a201ebe
Date: Tue, 18 Jan 2011 15:57:22 +0100
MIME-Version: 1.0


Sent to CCL by: Pietro Ottati [pietro.ottati|a|gmail.com]
--0016e64dda762e59af049a201ebe
Content-Type: text/plain; charset=ISO-8859-1

Hi all, I'm a Junior Researcher in these days I'm starting my first time work
in Computational Chemistry. My job will base on QM/MM the software that I have
to use is Qsite Schrodinger Suite. Unfortunately there aren't a lot of guide,
tutorial etc... about this software... Can you help me to learn? Do you have
some links, books, articles, wiky etc? Anybody use it?

Please take in account that I'm newbie and this is my first time.

Thanks in advance

Pietro

--0016e64dda762e59af049a201ebe
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<meta http-equiv=3D"content-type" content=3D"text/html; charset=3Dutf-8"><s=
pan class=3D"Apple-style-span" style=3D"font-family: &#39;Times New Roman&#=
39;; font-size: medium; "><pre>Hi all, I&#39;m a Junior Researcher in these=
 days I&#39;m starting my first time work=20
in Computational Chemistry. My job will base on QM/MM the software that I h=
ave=20
to use is Qsite Schrodinger Suite. Unfortunately there aren&#39;t a lot of =
guide,=20
tutorial etc... about this software... Can you help me to learn? Do you hav=
e=20
some links, books, articles, wiky etc? Anybody use it?

Please take in account that I&#39;m newbie and this is my first time.

Thanks in advance=20

Pietro</pre></span>

--0016e64dda762e59af049a201ebe--


From owner-chemistry@ccl.net Tue Jan 18 13:32:00 2011
From: "Markus Reiher stc2011(0)ethz.ch" <owner-chemistry!A!server.ccl.net>
To: CCL
Subject: CCL: Conference Announcement: Designing Molecular Functionality: Challenges
Message-Id: <-43686-110118075718-29479-rzScLnB16JK1ng4xaeSNwg!A!server.ccl.net>
X-Original-From: "Markus  Reiher" <stc2011|,|ethz.ch>
Date: Tue, 18 Jan 2011 07:57:16 -0500


Sent to CCL by: "Markus  Reiher" [stc2011|,|ethz.ch]
Dear colleague,

we are happy to announce the international conference
"47th Symposium on Theoretical Chemistry - Designing Molecular Functionality: Challenges for Theoretical Approaches"
which will be held in Sursee, Switzerland from August 21st to 
August 25th, 2011.

The following invited speakers will cover the conference topic:

A. Aspuru-Guzik ( Cambridge, MA)
J. Autschbach  (Buffalo, NY)
P.W. Ayers (Hamilton)
D.N. Beratan (Durham, NC)
D. Crawford (Blacksburg, VA)
A. Dreuw (Frankfurt)
G. Frenking (Marburg)
P. Geerlings (Brussels)
L. De Gioia (Milano-Bicocca)
S. Grimme (Mnster)
W.F. van Gunsteren (Zurich)
P. Hnenberger (Zurich)
B. Kuhlman (Chapel Hill, NC)
O.A. von Lilienfeld (Albuquerque, NM)
R. Lindh (Uppsala)
M. Parrinello (Lugano)
A. Rizzo (Pisa)
K. Ruud (Troms)
T. Saue (Toulouse)
F. Schoenebeck (Zurich)
S. Shaik (Jerusalem)
G.C. Solomon (Copenhagen)
H. Su (Singapore)
W. Thiel (Mlheim)
L. Visscher (Amsterdam)
H.J. Werner (Stuttgart)

Experimental keynote lecture:
F. Diederich (Zurich)

Contributed Talks and an expected number of about 250 posters will cover
all topics of Theoretical Chemistry.
On August 23rd, the Hellmann Prize will be awarded to a young theoretical chemist.

Young researchers are especially invited to present their contributions.

Sursee  is located in the heart of Switzerland close to the lake of Sempach
and near Lucerne. The location can be reached via Zurich Airport and 
EuroAirport Basel Mulhouse Freiburg, by train or by car. The conference 
venue is at Campus Sursee which is about a 15 minutes walk from Sursee. A 
bus service is available from Sursee train station to Campus Sursee.

For further information please visit the conference website:
http://www.stc2011.ethz.ch/

Early bird registration is open until March 15th, 2011.
http://www.stc2011.ethz.ch/registration

Please note that the number of participants is restricted to 250.
Early registration is therefore recommended.

We are looking forward to welcoming you among many scientists working in the 
field of theoretical and computer-assisted chemistry, presenting and 
discussing their latest research results.

Best regards,

Markus Reiher

ETH Zurich
Laboratory for Physical Chemistry
Wolfgang-Pauli-Strasse 10
CH-8093 Zurich/Switzerland
email: stc2011*ethz.ch
http://www.stc2011.ethz.ch


P.S.: The 2nd circular will only be distributed to those who have registered 
for the conference.


From owner-chemistry@ccl.net Tue Jan 18 14:43:00 2011
From: "Jans Alzate-Morales jalzate()utalca.cl" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: Hello list... Help me first time.
Message-Id: <-43687-110118140005-22248-hIpLNh51mGC+FRYbN9Gk/g-x-server.ccl.net>
X-Original-From: Jans Alzate-Morales <jalzate%%utalca.cl>
Content-Type: multipart/alternative; boundary=Apple-Mail-23--757596058
Date: Tue, 18 Jan 2011 15:59:43 -0300
Mime-Version: 1.0 (Apple Message framework v1082)


Sent to CCL by: Jans Alzate-Morales [jalzate++utalca.cl]

--Apple-Mail-23--757596058
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset=iso-8859-1

Dear Pietro,

If you are planning to use QSite, there is a lot of information in the =
Schrodinger web page (https://www.schrodinger.com/supportfaq/18/19/).
Also, you can search the User manual in the documentation folder which =
is available when you make the software installation.

Best regards,

Jans


El Jan 18, 2011, a las 11:57 AM, Pietro Ottati pietro.ottati-.-gmail.com =
escribi=F3:

> Hi all, I'm a Junior Researcher in these days I'm starting my first =
time work=20
> in Computational Chemistry. My job will base on QM/MM the software =
that I have=20
> to use is Qsite Schrodinger Suite. Unfortunately there aren't a lot of =
guide,=20
> tutorial etc... about this software... Can you help me to learn? Do =
you have=20
> some links, books, articles, wiky etc? Anybody use it?
>=20
> Please take in account that I'm newbie and this is my first time.
>=20
> Thanks in advance=20
>=20
> Pietro

-----------------------------------------------------------
Jans Alzate-Morales
Pharmaceutical Chemist, PhD. in Chemistry
Centre for Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile =20
Tel=E9fono: 56-71-201 798,=20
Fax: 56-71-201 561
jalzate,utalca.cl





--Apple-Mail-23--757596058
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html;
	charset=iso-8859-1

<html><head></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear =
Pietro,<div><br></div><div>If you are planning to use QSite, there is a =
lot of information in the Schrodinger web page (<a =
href=3D"https://www.schrodinger.com/supportfaq/18/19/">https://www.schrodi=
nger.com/supportfaq/18/19/</a>).</div><div>Also, you can search the User =
manual in the documentation folder which is available when you make the =
software installation.</div><div><br></div><div>Best =
regards,</div><div><br></div><div>Jans</div><div><br></div><div><br><div><=
div>El Jan 18, 2011, a las 11:57 AM, Pietro Ottati <a =
href=3D"http://pietro.ottati-.-gmail.com">pietro.ottati-.-gmail.com</a> =
escribi=F3:</div><br class=3D"Apple-interchange-newline"><blockquote =
type=3D"cite"><meta http-equiv=3D"content-type" content=3D"text/html; =
charset=3Dutf-8"><span class=3D"Apple-style-span" style=3D"font-family: =
'Times New Roman'; font-size: medium; "><pre>Hi all, I'm a Junior =
Researcher in these days I'm starting my first time work=20
in Computational Chemistry. My job will base on QM/MM the software that =
I have=20
to use is Qsite Schrodinger Suite. Unfortunately there aren't a lot of =
guide,=20
tutorial etc... about this software... Can you help me to learn? Do you =
have=20
some links, books, articles, wiky etc? Anybody use it?

Please take in account that I'm newbie and this is my first time.

Thanks in advance=20

Pietro</pre></span>
</blockquote></div><br><div>
<span class=3D"Apple-style-span" style=3D"border-collapse: separate; =
color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; =
font-variant: normal; font-weight: normal; letter-spacing: normal; =
line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; =
text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; =
-webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: =
0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span =
class=3D"Apple-style-span" style=3D"border-collapse: separate; color: =
rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: =
normal; font-weight: normal; letter-spacing: normal; line-height: =
normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: =
normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: =
0px; -webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; font-size: medium; =
"><div>-----------------------------------------------------------<br =
class=3D"Apple-interchange-newline">Jans =
Alzate-Morales</div><div>Pharmaceutical Chemist, PhD. in =
Chemistry</div><div>Centre for Bioinformatics and Molecular Simulations =
(CBSM)</div><div>Universidad de Talca<br>2 Norte 685, Casilla 721, Talca =
- Chile &nbsp;<br>Tel=E9fono: 56-71-201 798,&nbsp;<br>Fax: 56-71-201 =
561</div><div><a =
href=3D"mailto:jalzate,utalca.cl">jalzate,utalca.cl</a></div><div><br></di=
v></span><br class=3D"Apple-interchange-newline"></span><br =
class=3D"Apple-interchange-newline">
</div>
<br></div></body></html>=

--Apple-Mail-23--757596058--


From owner-chemistry@ccl.net Tue Jan 18 15:21:00 2011
From: "Nancy nancy5villa++gmail.com" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: Pioglitazone Tautomers
Message-Id: <-43688-110118135433-16548-gnj+5L9ixXE0dGg0NMHGlQ . server.ccl.net>
X-Original-From: Nancy <nancy5villa+/-gmail.com>
Content-Type: multipart/alternative; boundary=00248c11dcc9d1e3e5049a236c84
Date: Tue, 18 Jan 2011 13:54:07 -0500
MIME-Version: 1.0


Sent to CCL by: Nancy [nancy5villa.^-^.gmail.com]
--00248c11dcc9d1e3e5049a236c84
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Thank you very much; that answers all my questions.

Nancy



On Tue, Jan 18, 2011 at 1:49 AM, Andreas Klamt klamt(!)cosmologic.de <
owner-chemistry^-^ccl.net> wrote:

> Sent to CCL by: Andreas Klamt [klamt]![cosmologic.de]
> Nancy,
>
> although I find Gabriele's reply a bit to harsh, I also was a bit
> frustrated when I read your last entry, which essentially repeats the
> initial question after you got a number of replies. You now should draw y=
our
> own conclusions on this.
>
> What you can learns from the diverse answers is that tautomerism is still=
 a
> complicated and quite unsolved question. This was also shown in the speci=
al
> issue of J Comput Aided Mol Des. 2010 Jun,24 on tautomerism edited by
> Yvonne Martin and by the outcome of the SAMPLE2 blindtest (see Journal of
> Computer-Aided Molecular Design, Volume 24, Number 4).
>
> For your case of Pioglitazone I would conclude that the quantum chemical
> results for the tautomer energy differences are so large, that a rather
> unique answer can be given: The diketonic form (neutral and deprotonated)
> are absolutely predominant. This is a lucky case: There are many cases of
> tatuomerism where the DFT energy differences are in the range of a few
> kcal/mol, i.e. within the error bars of DFT,  and then no such clear answ=
er
> can be given.
>
> I would go so far to conclude that the huge energy differences of ~ 12
> kcal/mol to the other forms also makes the other forms rather unlikely in
> any protein docked form. I cannot see how the local environment of the
> protein can be so much more favoring the enolic forms to compensate such
> penalty.
>
> If the pKa of 6.3 reported by Gabriele is an experimental one, I have no
> problem to admit that most likely his 85% deprotonated is the better answ=
er
> than my answer based on DFT/COSMO-RS prediction of pKa=3D6.55. The differ=
ence
> of 0.25 pKa units is far within the error bars (~ 0.5) of our pKa
> prediction.
>
> Good luck in going on from here. Perhaps you can send me your final paper=
,
> or thesis or what ever kind of document you will produce on this case.
>
> Andreas
>
>
>
> Am 17.01.2011 22:14, schrieb Gabriele Cruciani gabri- -
> chemiome.chm.unipg.it:
>
>
> Sent to CCL by: Gabriele Cruciani [gabri|a|chemiome.chm.unipg.it]
> Nancy,
> you get the same answer from different people, with different background,
> using different methods, and you keep asking the same question.
>
> I think CCL list should be used 'with caution' especially after you get a=
ll
> the answers.
>
> What you summarized is not correct. The two forms are not tautomeric form=
s.
> They refer to ONE tautomeric form that is in equilibrium with two species=
,
> one protonated and one neutral. The percentages you reported refer to the
> solvent pH and to the specie pKa. Since the pKa of the pioglitazone is 6.=
3,
> the relative abundance at pH 7.4 is
> 85% for the charged and 15% for the neutral one.
>
> As told in previous mails, this has nothing to do with the docking into a
> protein, where the local environment, dielectric, 3D interactions may cha=
nge
> the 'form' of the interacting ligand. In this specific case, you cannot s=
ay
> that the charge form may interact better because is more abundant, since =
the
> equilibrium between the two forms can be modified by the protein.
>
> Precise pKa calculations are very relevant for pharmacokinetic and
> metabolism studies, but for docking to receptors is better to produce the
> 'relevant' structures. Do not use too simple methods (like those you
> reported) since the problem is very complex and require good approaches.
> Often using the brain is better than using free available software.
>
> Gabriele Cruciani
>
>
>
> Thus, the two major tautomers of pioglitazone are as shown in the attache=
d
> figure?
>
> Also, is there a published article, or other evidence that would confirm
> that this is indeed the correct tautomeric distribution at pH 7?
>
> Thanks you,
> Nancy
>
>
>
> On Mon, Jan 17, 2011 at 6:17 AM, Andreas Klamt klamt#cosmologic.de<
> owner-chemistry/a\ccl.net>  wrote:
>
> Sent to CCL by: Andreas Klamt [klamt-x-cosmologic.de]
> I was just pointed by Leif N=F8rskov-Lauritsen to a stupid error which I =
made
>
> in my first entry on this topic. I wrote that at pH=3D7 25% would be
> deprotonated, 75% neutral. That was obviously wrong. It is the other way
> round: 72% is ionic, 25% neutral. The total amount of zwitterions is then
> ~3%.
>
> Sorry for my mistake. But the basic message about the most stable neutral
> form stays valid.
> The most stable anionic form is the di-keto anion.
>
> Andreas
>
> Am 16.01.2011 19:29, schrieb Nancy nancy5villa**gmail.com:
>
> Using quantum chemical calculations, you found that the diketone form is
> dominant; does this mean that the enol form predicted by MarvinSketch
> v3.5.4
> in the published article is wrong?
>
> "Structure-based design of a thiazolidinedione which targets the
> mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb
> 1;20(3):819-23
>
> Thanks,
> Nancy
>
>
> On Thu, Jan 13, 2011 at 10:31 PM, Andreas Klamt klamt(a)cosmologic.de<
> owner-chemistry(~)ccl.net<owner-chemistry%28%7E%29ccl.net>>  wrote:
>
>   Sent to CCL by: Andreas Klamt [klamt,cosmologic.de]
>   Hi Nancy,
>
> as I wrote in the previous message, we find by quantum chemical
> calculations within the COSMO-RS solvation that the diketone form is more
> stable by abot 12 kcal/mol, that means it absolutely dominates!
>
> Andreas
>
> Am 13.01.2011 22:25, schrieb Nancy nancy5villa~!~gmail.com:
>
>   Hi All,
>
> I happened to find a published article where molecular docking simulation=
s
> of TZDs against a novel protein is detailed:
>
> "Structure-based design of a thiazolidinedione which targets the
> mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb
> 1;20(3):819-23
>
> In this paper, the authors, using MarvinSketch v3.5.4, determined that th=
e
> TZDs would exist predominantly in the enol form at pH 7.4, as opposed to
> the
> diketone form (see attached figure).  It appears that the article's
> tautomer
> prediction was based only on the pH prior to docking, and had nothing to =
do
>
> with ligand-protein interactions.
>
> Does anyone know if the diketone or enol, or perhaps a different tautomer=
,
> would be predominant at pH 7.4?
>
> Thanks in advance.
> Nancy
>
>
>
>    On Wed, Jan 12, 2011 at 9:53 AM, Andreas Klamt klamt-*-cosmologic.de<
> owner-chemistry(_)ccl.net<owner-chemistry%28_%29ccl.net>>  wrote:
>
>
> Sent to CCL by: Andreas Klamt [klamt[*]cosmologic.de]
> Hi All,
>
> let me put my 5 cents into the game:
> We have done quantum calculations for the heterocyclic ring, with just a
> methyl group, since electronically the remainder of the compound should
> have
> almost no influence on the heterocycle.
> DFT/COSMO-RS calculations prove the neutral species
> SMILES:CC1C(=3DO)[NH]C(=3DO)S1 of the Pioglitazone heterocycle to be favo=
red
> by 11.3 kcal/mol compared to all other neutral species of the heterocycle=
,
> which means that there is no other relvant neutral form.
>
> We find with COSMOtherm that the pka of the heterocycle is 6.55, i.e. at
> pH=3D7 it should be deprotonated with about 25%.
> Since the pka of the conj. acid of the pyridine ring according to
> COSMOtherm (we calculated diethylpyridine) is ~5.6 there should be ~10% i=
n
> the zwitterionic form.
>
> It will be hard to decide this finally, unless someone measures it, but
> we are quite confident to be qualitatively right here, because the energy
> differences for the tautomers should not have more than 5 kcal/mol erro, =
as
>
> we learned in in the SAMPL2 tautomer contest:
> see Andreas Klamt and Michael Diedenhofen, Some conclusions regarding the
> predictions of tautomeric equilibria in solution based on the SAMPL2
> challenge, http://www.springerlink.com/content/l577667th758n6h1/
>
> Andreas
>
>
>
>
>
>
>
> Hi All,
>
> Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value
> of the acidic hydrogen on the thiazolidinedione ring of pioglitazone is
> 4.57 (see attached "Figure_1.gif"). Therefore, the predominant species
> at pH 7.0 predicted by MarvinSketch is the one depicted in
> "Figure_2.gif". The different tautomeric forms predicted by MarvinSketch
> are shown in "Figure_3.gif".
>
> Can anyone explain where these predictions come from, and if they are
> correct?
>
> Thanks,
> Nancy
>
>
> On Mon, Jan 10, 2011 at 4:16 AM, Gabriele Cruciani
>   gabri(0)chemiome.chm.unipg.it<http://chemiome.chm.unipg.it><http://chem=
iome.chm.unipg.it>
>
> <owner-chemistry[a]ccl.net<mailto:owner-chemistry[a]ccl.net><owner-chemis=
try[a]ccl.net>>
> wrote:
>
>
>     Sent to CCL by: Gabriele Cruciani [gabri##chemiome.chm.unipg.it
>      <http://chemiome.chm.unipg.it> <http://chemiome.chm.unipg.it>]
>
>     Nancy,
>     the first form you reported is the most stable in water at pH 7.0.
>     However, the fact that one form is more stable than another in water
>     does not help you to understand which form will be more 'relevant'
>     for docking. In protein the tautomeric equilibria may produce and
>     stabilize different forms according to the complementary site. There
>     are examples of tautomeric form in protein not stable in water,
>     where the energy difference is more than 5 Kcal/mol.
>
>      MoKa software (www.moldiscovery.com<http://www.moldiscovery.com><htt=
p://www.moldiscovery.com>)
>
>
>     is fast and accurate to produce tautomer stable in water, but it can
>     produce also all the (plausible) tautomeric forms.
>
>     Then, a possibility is to dock them into your protein, to see if
>     docking methods may differentiate their binding.
>
>     Gabriele Cruciani
>
>
>
>
>         Hi All,
>
>         I am performing molecular docking and molecular dynamics
>         simulations of the
>         thiazolidinedione pioglitazone binding to the PPAR-gamma
>         receptor protein
>         (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous
>         different
>         tautomeric states; I have attached a figure depicting several of
>         them.
>         Which tautomer would be dominant at the physiological pH of ~7.0?
>
>         Also, are there any software programs that can predict which
>         tautomer would
>         be correct?
>
>         Thanks in advance,
>         Nancy>
>
>
>      E-mail to subscribers: CHEMISTRY[a]ccl.net
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r
> useConferences:
>
>     http://server.ccl.net/chemistry/announcements/conferences/>
>
>
>
>
>  --
> Dr. Jens Reinisch
> Chemist / Customer Support
> COSMOlogic GmbH&  Co. KG
> Burscheider Strasse 515
> D-51381 Leverkusen, Germany
>
> phone   +49-2171-363664
> mobile  +49-163-7337310
> fax     +49-2171-731689
> e-mail  reinisch[*]cosmologic.de
> web     www.cosmologic.de
>
> HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
> Komplementaer: COSMOlogic Verwaltungs GmbH
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>
>
>
>
>
>
>   E-mail to subscribers: CHEMISTRY(_)ccl.net<CHEMISTRY%28_%29ccl.net>  or
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>
>
> --
> PD. Dr. Andreas Klamt
> CEO / Gesch=E4ftsf=FChrer
> COSMOlogic GmbH&  Co. KG
> Burscheider Strasse 515
> D-51381 Leverkusen, Germany
>
> phone      +49-2171-731681
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>
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>
> HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
> Komplementaer: COSMOlogic Verwaltungs GmbH
> HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
>
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> CEO / Gesch=E4ftsf=FChrer
> COSMOlogic GmbH&  Co. KG
> Burscheider Strasse 515
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>
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>
> HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
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> --
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> CEO / Gesch=E4ftsf=FChrer
> COSMOlogic GmbH & Co. KG
> Burscheider Strasse 515
> D-51381 Leverkusen, Germany
>
> phone  	+49-2171-731681
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>
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>
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> Komplementaer: COSMOlogic Verwaltungs GmbH
> HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
>
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Content-Transfer-Encoding: quoted-printable

Thank you very much; that answers all my questions.<br><br>Nancy<br><br><br=
><br><div class=3D"gmail_quote">On Tue, Jan 18, 2011 at 1:49 AM, Andreas Kl=
amt klamt(!)<a href=3D"http://cosmologic.de">cosmologic.de</a> <span dir=3D=
"ltr">&lt;<a href=3D"mailto:owner-chemistry^-^ccl.net">owner-chemistry^-^ccl.ne=
t</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class=3D"im"=
>
Sent to CCL by: Andreas Klamt [klamt]![<a href=3D"http://cosmologic.de" tar=
get=3D"_blank">cosmologic.de</a>]


 =20
   =20
   =20
 =20
  </div><div text=3D"#000000" bgcolor=3D"#ffffff">
    Nancy,<br>
    <br>
    although I find Gabriele&#39;s reply a bit to harsh, I also was a bit
    frustrated when I read your last entry, which essentially repeats
    the initial question after you got a number of replies. You now
    should draw your own conclusions on this. <br>
    <br>
    What you can learns from the diverse answers is that tautomerism is
    still a complicated and quite unsolved question. This was also shown
    in the special issue of <a title=3D"Journal of computer-aided
      molecular design.">J Comput Aided Mol Des.</a> 2010 Jun,24 on
    tautomerism edited by Yvonne Martin and by the outcome of the
    SAMPLE2 blindtest (see <a title=3D"Journal of computer-aided
      molecular design.">Journal of Computer-Aided Molecular Design,
      Volume 24, Number 4</a>).<br>
    <br>
    For your case of Pioglitazone I would conclude that the quantum
    chemical results for the tautomer energy differences are so large,
    that a rather unique answer can be given: The diketonic form
    (neutral and deprotonated) are absolutely predominant. This is a
    lucky case: There are many cases of tatuomerism where the DFT energy
    differences are in the range of a few kcal/mol, i.e. within the
    error bars of DFT,=A0 and then no such clear answer can be given. <br>
    <br>
    I would go so far to conclude that the huge energy differences of ~
    12 kcal/mol to the other forms also makes the other forms rather
    unlikely in any protein docked form. I cannot see how the local
    environment of the protein can be so much more favoring the enolic
    forms to compensate such penalty.<br>
    <br>
    If the pKa of 6.3 reported by Gabriele is an experimental one, I
    have no problem to admit that most likely his 85% deprotonated is
    the better answer than my answer based on DFT/COSMO-RS prediction of
    pKa=3D6.55. The difference of 0.25 pKa units is far within the error
    bars (~ 0.5) of our pKa prediction.<br>
    <br>
    Good luck in going on from here. Perhaps you can send me your final
    paper, or thesis or what ever kind of document you will produce on
    this case.<br>
    <br>
    Andreas<br>
    <br>
    <br>
    <br>
    Am 17.01.2011 22:14, schrieb Gabriele Cruciani gabri-
    -<a href=3D"http://chemiome.chm.unipg.it" target=3D"_blank">chemiome.ch=
m.unipg.it</a>:
    <blockquote type=3D"cite"><div><div></div><div class=3D"h5">
      <br>
      Sent to CCL by: Gabriele Cruciani [gabri|a|<a href=3D"http://chemiome=
.chm.unipg.it" target=3D"_blank">chemiome.chm.unipg.it</a>]
      <br>
      Nancy,
      <br>
      you get the same answer from different people, with different
      background, using different methods, and you keep asking the same
      question.
      <br>
      <br>
      I think CCL list should be used &#39;with caution&#39; especially aft=
er
      you get all the answers.
      <br>
      <br>
      What you summarized is not correct. The two forms are not
      tautomeric forms. They refer to ONE tautomeric form that is in
      equilibrium with two species, one protonated and one neutral. The
      percentages you reported refer to the solvent pH and to the specie
      pKa. Since the pKa of the pioglitazone is 6.3, the relative
      abundance at pH 7.4 is
      <br>
      85% for the charged and 15% for the neutral one.
      <br>
      <br>
      As told in previous mails, this has nothing to do with the docking
      into a protein, where the local environment, dielectric, 3D
      interactions may change the &#39;form&#39; of the interacting ligand.=
 In
      this specific case, you cannot say that the charge form may
      interact better because is more abundant, since the equilibrium
      between the two forms can be modified by the protein.
      <br>
      <br>
      Precise pKa calculations are very relevant for pharmacokinetic and
      metabolism studies, but for docking to receptors is better to
      produce the &#39;relevant&#39; structures. Do not use too simple meth=
ods
      (like those you reported) since the problem is very complex and
      require good approaches. Often using the brain is better than
      using free available software.
      <br>
      <br>
      Gabriele Cruciani
      <br>
      <br>
      <br>
      <br>
      <blockquote type=3D"cite">Thus, the two major tautomers of
        pioglitazone are as shown in the attached
        <br>
        figure?
        <br>
        <br>
        Also, is there a published article, or other evidence that would
        confirm
        <br>
        that this is indeed the correct tautomeric distribution at pH 7?
        <br>
        <br>
        Thanks you,
        <br>
        Nancy
        <br>
        <br>
        <br>
        <br>
        On Mon, Jan 17, 2011 at 6:17 AM, Andreas Klamt
        klamt#<a href=3D"http://cosmologic.de" target=3D"_blank">cosmologic=
.de</a>&lt;
        <br>
        owner-chemistry/a\<a href=3D"http://ccl.net" target=3D"_blank">ccl.=
net</a>&gt;=A0 wrote:
        <br>
        <br>
        <blockquote type=3D"cite">Sent to CCL by: Andreas Klamt
          [<a href=3D"http://klamt-x-cosmologic.de" target=3D"_blank">klamt=
-x-cosmologic.de</a>]
          <br>
          I was just pointed by Leif N=F8rskov-Lauritsen to a stupid error
          which I made
          <br>
          in my first entry on this topic. I wrote that at pH=3D7 25%
          would be
          <br>
          deprotonated, 75% neutral. That was obviously wrong. It is the
          other way
          <br>
          round: 72% is ionic, 25% neutral. The total amount of
          zwitterions is then
          <br>
          ~3%.
          <br>
          <br>
          Sorry for my mistake. But the basic message about the most
          stable neutral
          <br>
          form stays valid.
          <br>
          The most stable anionic form is the di-keto anion.
          <br>
          <br>
          Andreas
          <br>
          <br>
          Am 16.01.2011 19:29, schrieb Nancy nancy5villa**<a href=3D"http:/=
/gmail.com" target=3D"_blank">gmail.com</a>:
          <br>
          <br>
          Using quantum chemical calculations, you found that the
          diketone form is
          <br>
          dominant; does this mean that the enol form predicted by
          MarvinSketch v3.5.4
          <br>
          in the published article is wrong?
          <br>
          <br>
          &quot;Structure-based design of a thiazolidinedione which targets
          the
          <br>
          mitochondrial protein mitoNEET&quot; Bioorg Med Chem Lett. 2010 F=
eb
          <br>
          1;20(3):819-23
          <br>
          <br>
          Thanks,
          <br>
          Nancy
          <br>
          <br>
          <br>
          On Thu, Jan 13, 2011 at 10:31 PM, Andreas Klamt
          klamt(a)<a href=3D"http://cosmologic.de" target=3D"_blank">cosmol=
ogic.de</a>&lt;
          <br>
          owner-chemistry(~)<a href=3D"http://ccl.net" target=3D"_blank">cc=
l.net</a>&lt;owner-chemistry%28%7E%<a href=3D"http://29ccl.net" target=3D"_=
blank">29ccl.net</a>&gt;&gt;=A0
          wrote:
          <br>
          <br>
          <blockquote type=3D"cite">=A0 Sent to CCL by: Andreas Klamt
            [klamt,<a href=3D"http://cosmologic.de" target=3D"_blank">cosmo=
logic.de</a>]
            <br>
            =A0 Hi Nancy,
            <br>
            <br>
            as I wrote in the previous message, we find by quantum
            chemical
            <br>
            calculations within the COSMO-RS solvation that the diketone
            form is more
            <br>
            stable by abot 12 kcal/mol, that means it absolutely
            dominates!
            <br>
            <br>
            Andreas
            <br>
            <br>
            Am 13.01.2011 22:25, schrieb Nancy nancy5villa~!~<a href=3D"htt=
p://gmail.com" target=3D"_blank">gmail.com</a>:
            <br>
            <br>
            =A0 Hi All,
            <br>
            <br>
            I happened to find a published article where molecular
            docking simulations
            <br>
            of TZDs against a novel protein is detailed:
            <br>
            <br>
            &quot;Structure-based design of a thiazolidinedione which targe=
ts
            the
            <br>
            mitochondrial protein mitoNEET&quot; Bioorg Med Chem Lett. 2010
            Feb
            <br>
            1;20(3):819-23
            <br>
            <br>
            In this paper, the authors, using MarvinSketch v3.5.4,
            determined that the
            <br>
            TZDs would exist predominantly in the enol form at pH 7.4,
            as opposed to the
            <br>
            diketone form (see attached figure).=A0 It appears that the
            article&#39;s tautomer
            <br>
            prediction was based only on the pH prior to docking, and
            had nothing to do
            <br>
            with ligand-protein interactions.
            <br>
            <br>
            Does anyone know if the diketone or enol, or perhaps a
            different tautomer,
            <br>
            would be predominant at pH 7.4?
            <br>
            <br>
            Thanks in advance.
            <br>
            Nancy
            <br>
            <br>
            <br>
            <br>
            =A0=A0 On Wed, Jan 12, 2011 at 9:53 AM, Andreas Klamt
            klamt-*-<a href=3D"http://cosmologic.de" target=3D"_blank">cosm=
ologic.de</a>&lt;
            <br>
            owner-chemistry(_)<a href=3D"http://ccl.net" target=3D"_blank">=
ccl.net</a>&lt;owner-chemistry%28_%<a href=3D"http://29ccl.net" target=3D"_=
blank">29ccl.net</a>&gt;&gt;=A0
            wrote:
            <br>
            <br>
            <blockquote type=3D"cite">
              <br>
              Sent to CCL by: Andreas Klamt [klamt[*]<a href=3D"http://cosm=
ologic.de" target=3D"_blank">cosmologic.de</a>]
              <br>
              Hi All,
              <br>
              <br>
              let me put my 5 cents into the game:
              <br>
              We have done quantum calculations for the heterocyclic
              ring, with just a
              <br>
              methyl group, since electronically the remainder of the
              compound should have
              <br>
              almost no influence on the heterocycle.
              <br>
              DFT/COSMO-RS calculations prove the neutral species
              <br>
              SMILES:CC1C(=3DO)[NH]C(=3DO)S1 of the Pioglitazone heterocycl=
e
              to be favored
              <br>
              by 11.3 kcal/mol compared to all other neutral species of
              the heterocycle,
              <br>
              which means that there is no other relvant neutral form.
              <br>
              <br>
              We find with COSMOtherm that the pka of the heterocycle is
              6.55, i.e. at
              <br>
              pH=3D7 it should be deprotonated with about 25%.
              <br>
              Since the pka of the conj. acid of the pyridine ring
              according to
              <br>
              COSMOtherm (we calculated diethylpyridine) is ~5.6 there
              should be ~10% in
              <br>
              the zwitterionic form.
              <br>
              <br>
              It will be hard to decide this finally, unless someone
              measures it, but
              <br>
              we are quite confident to be qualitatively right here,
              because the energy
              <br>
              differences for the tautomers should not have more than 5
              kcal/mol erro, as
              <br>
              we learned in in the SAMPL2 tautomer contest:
              <br>
              see Andreas Klamt and Michael Diedenhofen, Some
              conclusions regarding the
              <br>
              predictions of tautomeric equilibria in solution based on
              the SAMPL2
              <br>
              challenge,
              <a href=3D"http://www.springerlink.com/content/l577667th758n6=
h1/" target=3D"_blank">http://www.springerlink.com/content/l577667th758n6h1=
/</a>
              <br>
              <br>
              Andreas
              <br>
              <br>
              <br>
              <br>
              <br>
              <br>
              <br>
              <blockquote type=3D"cite">
                <br>
                Hi All,
                <br>
                <br>
                Using MarvinSketch v5.3.3 (ChemAxon software), the
                predicted pKa value
                <br>
                of the acidic hydrogen on the thiazolidinedione ring of
                pioglitazone is
                <br>
                4.57 (see attached &quot;Figure_1.gif&quot;). Therefore, th=
e
                predominant species
                <br>
                at pH 7.0 predicted by MarvinSketch is the one depicted
                in
                <br>
                &quot;Figure_2.gif&quot;. The different tautomeric forms pr=
edicted
                by MarvinSketch
                <br>
                are shown in &quot;Figure_3.gif&quot;.
                <br>
                <br>
                Can anyone explain where these predictions come from,
                and if they are
                <br>
                correct?
                <br>
                <br>
                Thanks,
                <br>
                Nancy
                <br>
                <br>
                <br>
                On Mon, Jan 10, 2011 at 4:16 AM, Gabriele Cruciani
                <br>
                =A0
                gabri(0)<a href=3D"http://chemiome.chm.unipg.it" target=3D"=
_blank">chemiome.chm.unipg.it</a><a href=3D"http://chemiome.chm.unipg.it" t=
arget=3D"_blank">&lt;http://chemiome.chm.unipg.it&gt;</a>
                <br>
                <br>
                &lt;owner-chemistry[a]<a href=3D"http://ccl.net" target=3D"=
_blank">ccl.net</a><a href=3D"mailto:owner-chemistry[a]ccl.net" target=3D"_=
blank">&lt;mailto:owner-chemistry[a]ccl.net&gt;</a>&gt;=A0
                wrote:
                <br>
                <br>
                <br>
                =A0=A0=A0 Sent to CCL by: Gabriele Cruciani
                [gabri##<a href=3D"http://chemiome.chm.unipg.it" target=3D"=
_blank">chemiome.chm.unipg.it</a>
                <br>
                =A0=A0=A0=A0 <a href=3D"http://chemiome.chm.unipg.it" targe=
t=3D"_blank">&lt;http://chemiome.chm.unipg.it&gt;</a>]
                <br>
                <br>
                =A0=A0=A0 Nancy,
                <br>
                =A0=A0=A0 the first form you reported is the most stable in
                water at pH 7.0.
                <br>
                =A0=A0=A0 However, the fact that one form is more stable th=
an
                another in water
                <br>
                =A0=A0=A0 does not help you to understand which form will b=
e
                more &#39;relevant&#39;
                <br>
                =A0=A0=A0 for docking. In protein the tautomeric equilibria
                may produce and
                <br>
                =A0=A0=A0 stabilize different forms according to the
                complementary site. There
                <br>
                =A0=A0=A0 are examples of tautomeric form in protein not
                stable in water,
                <br>
                =A0=A0=A0 where the energy difference is more than 5 Kcal/m=
ol.
                <br>
                <br>
                =A0=A0=A0=A0 MoKa software
                (<a href=3D"http://www.moldiscovery.com" target=3D"_blank">=
www.moldiscovery.com</a><a href=3D"http://www.moldiscovery.com" target=3D"_=
blank">&lt;http://www.moldiscovery.com&gt;</a>)
                <br>
                <br>
                =A0=A0=A0 is fast and accurate to produce tautomer stable i=
n
                water, but it can
                <br>
                =A0=A0=A0 produce also all the (plausible) tautomeric forms=
.
                <br>
                <br>
                =A0=A0=A0 Then, a possibility is to dock them into your
                protein, to see if
                <br>
                =A0=A0=A0 docking methods may differentiate their binding.
                <br>
                <br>
                =A0=A0=A0 Gabriele Cruciani
                <br>
                <br>
                <br>
                <br>
                <br>
                =A0=A0=A0=A0=A0=A0=A0 Hi All,
                <br>
                <br>
                =A0=A0=A0=A0=A0=A0=A0 I am performing molecular docking and=
 molecular
                dynamics
                <br>
                =A0=A0=A0=A0=A0=A0=A0 simulations of the
                <br>
                =A0=A0=A0=A0=A0=A0=A0 thiazolidinedione pioglitazone bindin=
g to the
                PPAR-gamma
                <br>
                =A0=A0=A0=A0=A0=A0=A0 receptor protein
                <br>
                =A0=A0=A0=A0=A0=A0=A0 (PDB ID: 1ZGY). The thiazolidinedione=
 ring can
                exist in numerous
                <br>
                =A0=A0=A0=A0=A0=A0=A0 different
                <br>
                =A0=A0=A0=A0=A0=A0=A0 tautomeric states; I have attached a =
figure
                depicting several of
                <br>
                =A0=A0=A0=A0=A0=A0=A0 them.
                <br>
                =A0=A0=A0=A0=A0=A0=A0 Which tautomer would be dominant at t=
he
                physiological pH of ~7.0?
                <br>
                <br>
                =A0=A0=A0=A0=A0=A0=A0 Also, are there any software programs=
 that can
                predict which
                <br>
                =A0=A0=A0=A0=A0=A0=A0 tautomer would
                <br>
                =A0=A0=A0=A0=A0=A0=A0 be correct?
                <br>
                <br>
                =A0=A0=A0=A0=A0=A0=A0 Thanks in advance,
                <br>
                =A0=A0=A0=A0=A0=A0=A0 Nancy&gt;
                <br>
                <br>
                <br>
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              --
              <br>
              Dr. Jens Reinisch
              <br>
              Chemist / Customer Support
              <br>
              COSMOlogic GmbH&amp;=A0 Co. KG
              <br>
              Burscheider Strasse 515
              <br>
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            <br>
            PD. Dr. Andreas Klamt
            <br>
            CEO / Gesch=E4ftsf=FChrer
            <br>
            COSMOlogic GmbH&amp;=A0 Co. KG
            <br>
            Burscheider Strasse 515
            <br>
            D-51381 Leverkusen, Germany
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            HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
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          PD. Dr. Andreas Klamt
          <br>
          CEO / Gesch=E4ftsf=FChrer
          <br>
          COSMOlogic GmbH&amp;=A0 Co. KG
          <br>
          Burscheider Strasse 515
          <br>
          D-51381 Leverkusen, Germany
          <br>
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          <br>
          <br>
          HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
          <br>
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          <br>
          HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas KlamtTo
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    <br>
    <br>
    <pre cols=3D"72">--=20
PD. Dr. Andreas Klamt
CEO / Gesch=E4ftsf=FChrer
COSMOlogic GmbH &amp; Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	<a href=3D"mailto:klamt%25cosmologic.de" target=3D"_blank">klamt%co=
smologic.de</a><div class=3D"im">
web    	<a href=3D"http://www.cosmologic.de" target=3D"_blank">www.cosmolog=
ic.de</a>

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
</div></pre>
  </div><div><div></div><div class=3D"h5">




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</div></div></blockquote></div><br>

--00248c11dcc9d1e3e5049a236c84--


From owner-chemistry@ccl.net Tue Jan 18 15:56:00 2011
From: "Vincent Leroux vincent.leroux _ loria.fr" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: Hello list... Help me first time.
Message-Id: <-43689-110118150104-30541-ukWNFQhoqDNVhaM7hzydHQ|*|server.ccl.net>
X-Original-From: Vincent Leroux <vincent.leroux%%loria.fr>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Tue, 18 Jan 2011 21:00:24 +0100
MIME-Version: 1.0


Sent to CCL by: Vincent Leroux [vincent.leroux[*]loria.fr]
Hi,

"schrodinger qsite manual" on Google gives you the pdf manual in the top
answers...

"schrodinger qsite" on Google Scholar gives you plenty of published
papers that made use of this software...

Ok, you are a newbie, but come on...

VL



Le 18/01/11 15:57, Pietro Ottati pietro.ottati-.-gmail.com a écrit :
> Hi all, I'm a Junior Researcher in these days I'm starting my first time work 
> in Computational Chemistry. My job will base on QM/MM the software that I have 
> to use is Qsite Schrodinger Suite. Unfortunately there aren't a lot of guide, 
> tutorial etc... about this software... Can you help me to learn? Do you have 
> some links, books, articles, wiky etc? Anybody use it?
> 
> Please take in account that I'm newbie and this is my first time.
> 
> Thanks in advance 
> 
> Pietro
>


From owner-chemistry@ccl.net Tue Jan 18 17:23:00 2011
From: "Pietro Ottati pietro.ottati,,gmail.com" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: Hello list... Help me first time.
Message-Id: <-43690-110118171953-4436-9286R8MfinECTAe7UrbDWQ:-:server.ccl.net>
X-Original-From: Pietro Ottati <pietro.ottati_-_gmail.com>
Content-Type: multipart/alternative; boundary=0015175ca7bca9e4c0049a264b9e
Date: Tue, 18 Jan 2011 23:19:35 +0100
MIME-Version: 1.0


Sent to CCL by: Pietro Ottati [pietro.ottati(-)gmail.com]
--0015175ca7bca9e4c0049a264b9e
Content-Type: text/plain; charset=ISO-8859-1

Oh come on people do you think that I post here and I didn't read the
manual? I've just read it... But Qsite manual is really uncomplete.... I've
just studied Qsite manual, jaguar quick guide, Maestro quick guide, maestro
installation guide and some more articles... But this is really not enough I
need a complete manual to understand my new work. This is my actual
position: I graduated in Medicinal chemistry in Italy (5 years degree) my
thesis work was about organic synthesis but now I'm moving to computational
chemistry because I love Computers, I'm good at operating system, network
administration and a little bit at programming. Now I need some basis in
quantum mechanics chemistry applied in computational work.

For me now QM/MM is a parallel world and I need to discover it...

I'm sorry if my discussion is not so clear...

Thanks in advance

byebye

--0015175ca7bca9e4c0049a264b9e
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Oh come on people do you think that I post here and I didn&#39;t read the m=
anual? I&#39;ve just read it... But Qsite manual is really uncomplete.... I=
&#39;ve just studied Qsite manual, jaguar quick guide, Maestro quick guide,=
 maestro installation guide and some more articles... But this is really no=
t enough I need a complete manual to understand my new work. This is my act=
ual position: I graduated in Medicinal chemistry in Italy (5 years degree) =
my thesis work was about organic synthesis but now I&#39;m moving to comput=
ational chemistry because I love Computers, I&#39;m good at operating syste=
m, network administration and a little bit at programming. Now I need some =
basis in quantum mechanics chemistry applied in computational work.<br>
<br>For me now QM/MM is a parallel world and I need to discover it... <br><=
br>I&#39;m sorry if my discussion is not so clear...<br><br>Thanks in advan=
ce<br><br>byebye<br>

--0015175ca7bca9e4c0049a264b9e--


From owner-chemistry@ccl.net Tue Jan 18 20:07:00 2011
From: "Jun Zhang coolrainbow{:}yahoo.cn" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: Looking for a source code for calculating Rys Roots and Weights
Message-Id: <-43691-110118200621-16038-R8K9N5rHGN6PotM3Y4j8wA|-|server.ccl.net>
X-Original-From: Jun Zhang <coolrainbow^^yahoo.cn>
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Date: Wed, 19 Jan 2011 09:06:04 +0800 (CST)
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Sent to CCL by: Jun Zhang [coolrainbow a yahoo.cn]
Hello:

It seems that GAMESS can only compute the roots of rys polynomial up to 13 degree. If you need a general one(such as computing ERIs up to i angular), you can refer to Dalton's Hermite module.

Cheers up!

Jun Zhang
Nankai University
coolrainbow++yahoo.cn


From owner-chemistry@ccl.net Tue Jan 18 20:42:00 2011
From: "Vincent Leroux vincent.leroux(~)loria.fr" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL: Hello list... Help me first time.
Message-Id: <-43692-110118185407-28184-QmQDXrXaqrJcdlE9K+OPLw:_:server.ccl.net>
X-Original-From: Vincent Leroux <vincent.leroux[-]loria.fr>
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Date: Wed, 19 Jan 2011 00:53:50 +0100
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Sent to CCL by: Vincent Leroux [vincent.leroux_+_loria.fr]
Hi Pietro,

Sorry if I was a little bit rude.

If you have some experience with computer science you might be used to
large, extensive documentation. Most of the times, this simply does not
exist in the computational chemistry field. Welcome a parallel world!

If you are into programming, you probably dislike working with
undocumented code from others. Better get used to it. And more often
than you think, this will be old-school Fortran code, to add insult to
injury  ;-)

QSite, with its 80-page incomplete manual and plenty of published papers
that made use of it, is indeed, IMHO, above average regarding the level
of documentation you usually get.

So if you encounter some obscure option you have no idea of the purpose
or effects, this is all normal. You can ask Schrödinger support for
explanations but do not expect much. You have nothing to lose here if
you have specific questions. Another option is to contact the
corresponding authors of some QSite-using papers you find the most
interesting. This might pay the most in the long term.

I can certify you that your current skills will not be useless if you go
forward into computer-aided chemistry. You can also try to get used to
strategies closer to your past expertise, like QSAR and other
ligand-based drug design techniques, before jumping into more difficult,
low-level theoretical playing grounds.

Good luck
VL



Le 18/01/11 23:19, Pietro Ottati pietro.ottati,,gmail.com a écrit :
> Oh come on people do you think that I post here and I didn't read the
> manual? I've just read it... But Qsite manual is really uncomplete....
> I've just studied Qsite manual, jaguar quick guide, Maestro quick guide,
> maestro installation guide and some more articles... But this is really
> not enough I need a complete manual to understand my new work. This is
> my actual position: I graduated in Medicinal chemistry in Italy (5 years
> degree) my thesis work was about organic synthesis but now I'm moving to
> computational chemistry because I love Computers, I'm good at operating
> system, network administration and a little bit at programming. Now I
> need some basis in quantum mechanics chemistry applied in computational
> work.
> 
> For me now QM/MM is a parallel world and I need to discover it...
> 
> I'm sorry if my discussion is not so clear...
> 
> Thanks in advance
> 
> byebye


From owner-chemistry@ccl.net Tue Jan 18 21:17:00 2011
From: "Brian Austin brianmaustin*gmail.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: Hello list... Help me first time.
Message-Id: <-43693-110118182714-6488-9286R8MfinECTAe7UrbDWQ{=}server.ccl.net>
X-Original-From: Brian Austin <brianmaustin]~[gmail.com>
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Date: Tue, 18 Jan 2011 15:26:40 -0800
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Sent to CCL by: Brian Austin [brianmaustin#gmail.com]
Hello Pietro,

I haven't used QSite for about ten years, but I do remember that
Schrodinger's customer support is friendly and generous.
Consider contacting them directly
http://www.schrodinger.com/supportcenter/

They also have training sessions fairly regularly.
http://www.schrodinger.com/events/

-Brian

On Tue, Jan 18, 2011 at 2:19 PM, Pietro Ottati
pietro.ottati,,gmail.com <owner-chemistry ~ ccl.net> wrote:
> Oh come on people do you think that I post here and I didn't read the
> manual? I've just read it... But Qsite manual is really uncomplete.... I've
> just studied Qsite manual, jaguar quick guide, Maestro quick guide, maestro
> installation guide and some more articles... But this is really not enough I
> need a complete manual to understand my new work. This is my actual
> position: I graduated in Medicinal chemistry in Italy (5 years degree) my
> thesis work was about organic synthesis but now I'm moving to computational
> chemistry because I love Computers, I'm good at operating system, network
> administration and a little bit at programming. Now I need some basis in
> quantum mechanics chemistry applied in computational work.
>
> For me now QM/MM is a parallel world and I need to discover it...
>
> I'm sorry if my discussion is not so clear...
>
> Thanks in advance
>
> byebye
>