From owner-chemistry@ccl.net Wed May 10 08:58:00 2006 From: "Weill Nathanael naweill..gmail.com" To: CCL Subject: CCL: Calculation of pka Message-Id: <-31728-060509065024-20284-Wh7ZtUHGMS9GJyBZ/PxeOw_+_server.ccl.net> X-Original-From: Weill Nathanael Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 09 May 2006 11:44:26 +0200 MIME-Version: 1.0 Sent to CCL by: Weill Nathanael [naweill^-^gmail.com] Hi , I know programs abble to calculate pka and titration curve : http://www.chemaxon.com/products.html#Marvin best regards Nathanael Weill ULP Strasbourg France Master 2 kevin abbot kevanabbot]![yahoo.com a écrit : >Sent to CCL by: kevin abbot [kevanabbot=-=yahoo.com] > >--0-147654940-1147098689=:16061 >Content-Type: text/plain; charset=iso-8859-1 >Content-Transfer-Encoding: 8bit > >Hi folks, > My question is really simple: are there some programs (free of charge) that permit to calculate pka of a determinated compound? > > Any help is appreciated > > Kevin > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com >--0-147654940-1147098689=:16061 >Content-Type: text/html; charset=iso-8859-1 >Content-Transfer-Encoding: 8bit > >
Hi folks,
My question is really simple: are there some programs (free of charge) that permit to calculate pka of a determinated compound?
 
Any help is appreciated
 
Kevin

__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com >--0-147654940-1147098689=:16061--> > > > > > From owner-chemistry@ccl.net Wed May 10 09:38:01 2006 From: "kevin abbot kevanabbot**yahoo.com" To: CCL Subject: CCL: Dihydroxyl compound Message-Id: <-31729-060510092900-21947-ZuwVP3zfieYb3xtY+atG6A[a]server.ccl.net> X-Original-From: kevin abbot Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-512180785-1147267732=:41797" Date: Wed, 10 May 2006 06:28:52 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: kevin abbot [kevanabbot::yahoo.com] --0-512180785-1147267732=:41797 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCLers, I am working on a compound which has two hydroxyl groups on the same secondary carbon atom (not primary), might someone inform me about the stability of a dihydroxyl compound and its synthetic reliability (I mean is a compound like this stable?). Some references are appreciated as I have found only a few articles on this kind of compound. Best Regards Kevin --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. --0-512180785-1147267732=:41797 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Hi CCLers,
I am working on a compound which has two hydroxyl groups on the same secondary carbon atom (not primary),
might someone inform me about the stability of a dihydroxyl compound and its synthetic reliability (I mean is a compound like this stable?).
Some references are appreciated as I have found only a few articles on this kind of compound.
 
Best Regards
 
Kevin
 

New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. --0-512180785-1147267732=:41797-- From owner-chemistry@ccl.net Wed May 10 10:13:00 2006 From: "Mark Thompson mark^-^arguslab.com" To: CCL Subject: CCL: Docking program for metalloenzymes Message-Id: <-31730-060509212243-32388-6EjN11qAwBmu2aob/t292A]|[server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 09 May 2006 17:07:18 -0700 MIME-Version: 1.0 Sent to CCL by: Mark Thompson [mark : arguslab.com] ArgusLab has good docking capabilities. It's a Windows application. http://www.arguslab.com Cheers, Mark Darryl Reid darryl.reid,gmail.com wrote: > Sent to CCL by: "Darryl Reid" [darryl.reid(a)gmail.com] > The eHiTS docking program has been successfully used to dock ligands > to metalloenzymes and it is free for academics. You can find out more > at: > > www.simbiosys.ca/ehits/ > > Darryl > > > On 5/8/06, MIRICA, LIVIU liviu]*[berkeley.edu wrote: > >> Sent to CCL by: "MIRICA, LIVIU" [liviu()berkeley.edu] >> Hi, >> I have a question regarding the application of the different docking programs to metalloenzymes. I >> am interested in analyzing the docking of small ligands to enzymes that have a metal ion in the >> active site (and the ligand may or may not bind to the metal). Given the large number of docking >> programs, what is the state-of-the-art in terms of taking into account the interactions of ligands >> and proteins with metal ions? Which program would be most successful for docking ligands to >> metalloenzymes, either for PC (preferred) or Linux platforms? >> Any advice will be appreciated. >> Thanks for your help. >> Liviu Mirica >> >> >> ------------------------------------------------------ >> Liviu Mirica, PhD >> Department of Chemistry >> University of California, Berkeley, CA 94720> > > > > > -- ------------------------ Mark Thompson mark**arguslab.com http://www.arguslab.com ------------------------ From owner-chemistry@ccl.net Wed May 10 11:02:01 2006 From: "Ramon Crehuet rcsqtc[a]iiqab.csic.es" To: CCL Subject: CCL: Dihydroxyl compound Message-Id: <-31731-060510105925-13998-VQuVDNvbAkjrLb6/gfNpGA^-^server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 10 May 2006 16:59:29 +0200 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc{=}iiqab.csic.es] Kevin, Two hydroxyl groups on the same carbon can exist, and indeed for formaldehyde, for example, this is the major form. It is true that these hydrates or geminal diols are less stable with ketones (secondary carbons) but when substituents attract electrons, they can become also the stable form as in CF3-CO-CF3. In any case, there is always an equilibrium. This is also related to the stability of hemi-acetals. You can find more examples and the reaction mechanism in an advanced organic chemistry textbook, such as "Organic chemistry", Carey, McGraw-Hill. Regards, Ramon kevin abbot kevanabbot**yahoo.com wrote: >Sent to CCL by: kevin abbot [kevanabbot::yahoo.com] >--0-512180785-1147267732=:41797 >Content-Type: text/plain; charset=iso-8859-1 >Content-Transfer-Encoding: 8bit > >Hi CCLers, > I am working on a compound which has two hydroxyl groups on the same secondary carbon atom (not primary), > might someone inform me about the stability of a dihydroxyl compound and its synthetic reliability (I mean is a compound like this stable?). > Some references are appreciated as I have found only a few articles on this kind of compound. > > Best Regards > > Kevin > > > >--------------------------------- >New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. >--0-512180785-1147267732=:41797 >Content-Type: text/html; charset=iso-8859-1 >Content-Transfer-Encoding: 8bit > >
Hi CCLers,
I am working on a compound which has two hydroxyl groups on the same secondary carbon atom (not primary),
might someone inform me about the stability of a dihydroxyl compound and its synthetic reliability (I mean is a compound like this stable?).
Some references are appreciated as I have found only a few articles on this kind of compound.
 
Best Regards
 
Kevin
 

>

New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. >--0-512180785-1147267732=:41797--> > > > > > From owner-chemistry@ccl.net Wed May 10 11:37:01 2006 From: "Shobe, David dshobe * sud-chemieinc.com" To: CCL Subject: CCL: Dihydroxyl compound Message-Id: <-31732-060510111244-27355-Phas3tJNPJ0oTVm364yr1Q.:.server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 10 May 2006 17:12:21 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe{=}sud-chemieinc.com] Normally secondary gem-dihydroxy compounds (ketone hydrates) are not stable, even less so than primary gem-dihydroxy compounds (aldehyde hydrates). But there are some exceptions: ninhydrin comes to mind. Also acetone-water mixtures have a small amount of 2,2-propanediol (acetone hydrate) by the equilibrium (CH3)2CO + H2O == (CH3)2C(OH)2. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry(a)ccl.net [mailto:owner-chemistry(a)ccl.net] Sent: Wednesday, May 10, 2006 9:50 AM To: Shobe, David Subject: CCL: Dihydroxyl compound Sent to CCL by: kevin abbot [kevanabbot::yahoo.com] --0-512180785-1147267732=:41797 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCLers, I am working on a compound which has two hydroxyl groups on the same secondary carbon atom (not primary), might someone inform me about the stability of a dihydroxyl compound and its synthetic reliability (I mean is a compound like this stable?). Some references are appreciated as I have found only a few articles on this kind of compound. Best Regards Kevin --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. --0-512180785-1147267732=:41797 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi CCLers,
I am working on a compound which has two hydroxyl groups on the same secondary carbon atom (not primary),
might someone inform me about the stability of a dihydroxyl compound and its synthetic reliability (I mean is a compound like this stable?).
Some references are appreciated as I have found only a few articles on this kind of compound.
 
Best Regards
 
Kevin
 

New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. --0-512180785-1147267732=:41797--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Wed May 10 12:12:00 2006 From: "Phil Hultin hultin .. cc.umanitoba.ca" To: CCL Subject: CCL: Dihydroxyl compound Message-Id: <-31733-060510110926-18671-kEKcGUzu402Gqrw1BGsY8A^^^server.ccl.net> X-Original-From: "Phil Hultin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 10 May 2006 10:09:15 -0500 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin(-)cc.umanitoba.ca] Kevin Abbott asked about the stability of a geminal diol. Gem-diols (also known as carbonyl hydrates) are in general NOT thermodynamically stable. The major exceptions are the hydrates of aldehydes bearing highly electronegative substituents on the alpha position. The most famous of these is chloral hydrate (a powerful sedative), which is 1,1-dihydroxy-2,2,2-trichloroethane. This is quite stable. Similarly, bis(perfluoroalkyl)ketones form very stable hydrates. For most aliphatic and aryl ketones or aldehydes, the hydrate form is thermodynamically disfavoured relative to the carbonyl plus H2O and exists only to a very small extent at equilibrium in the presence of water. Dr. Philip G. Hultin Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin:+:cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin -----Original Message----- > From: owner-chemistry:+:ccl.net [mailto:owner-chemistry:+:ccl.net] Sent: May 10, 2006 8:54 AM To: Hultin, Philip G. Subject: CCL: Dihydroxyl compound Sent to CCL by: kevin abbot [kevanabbot::yahoo.com] --0-512180785-1147267732=:41797 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCLers, I am working on a compound which has two hydroxyl groups on the same secondary carbon atom (not primary), might someone inform me about the stability of a dihydroxyl compound and its synthetic reliability (I mean is a compound like this stable?). Some references are appreciated as I have found only a few articles on this kind of compound. Best Regards Kevin --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. --0-512180785-1147267732=:41797 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi CCLers,
I am working on a compound which has two hydroxyl groups on the same secondary carbon atom (not primary),
might someone inform me about the stability of a dihydroxyl compound and its synthetic reliability (I mean is a compound like this stable?).
Some references are appreciated as I have found only a few articles on this kind of compound.
 
Best Regards
 
Kevin
 

New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. --0-512180785-1147267732=:41797--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed May 10 12:47:00 2006 From: "Dominic Ryan dominic.ryan##comcast.net" To: CCL Subject: CCL: Dihydroxyl compound Message-Id: <-31734-060510115109-12248-+gEolFXpKDC4Q7iroNOiTg*server.ccl.net> X-Original-From: "Dominic Ryan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0034_01C67421.D42539B0" Date: Wed, 10 May 2006 11:06:45 -0400 MIME-Version: 1.0 Sent to CCL by: "Dominic Ryan" [dominic.ryan/a\comcast.net] This is a multi-part message in MIME format. ------=_NextPart_000_0034_01C67421.D42539B0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Kevin, There is an equilibrium between dihydroxyl and carbonyl + water. Unless there is a strong electron withdrawing group, or significant steric strain due to a small ring, or an enzyme transition state to stabilize it, such a dihydroxyl compound will not be stable and the equilibrium lies far on the carbonyl side. Basic organic texts should cover this. Dominic Ps, direct mail to your address bounced. -----Original Message----- > From: owner-chemistry..ccl.net [mailto:owner-chemistry..ccl.net] Sent: Wednesday, May 10, 2006 8:52 AM To: Ryan, M Dominic Subject: CCL: Dihydroxyl compound Sent to CCL by: kevin abbot [kevanabbot::yahoo.com] --0-512180785-1147267732=:41797 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCLers, I am working on a compound which has two hydroxyl groups on the same secondary carbon atom (not primary), might someone inform me about the stability of a dihydroxyl compound and its synthetic reliability (I mean is a compound like this stable?). Some references are appreciated as I have found only a few articles on this kind of compound. Best Regards Kevin --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. --0-512180785-1147267732=:41797 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi CCLers,
I am working on a compound which has two hydroxyl groups on the same secondary carbon atom (not primary),
might someone inform me about the stability of a dihydroxyl compound and its synthetic reliability (I mean is a compound like this stable?).
Some references are appreciated as I have found only a few articles on this kind of compound.
 
Best Regards
 
Kevin
 

New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. --0-512180785-1147267732=:41797--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------=_NextPart_000_0034_01C67421.D42539B0 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Kevin,

 

There is an equilibrium between dihydroxyl = and carbonyl + water.  Unless there is a strong electron withdrawing = group, or significant steric strain due to a small ring, or an enzyme transition = state to stabilize it, such a dihydroxyl compound will not be stable and the = equilibrium lies far on the carbonyl side.   Basic organic texts should = cover this.

 

Dominic

 

Ps, direct mail to your address = bounced.

 

-----Original Message-----
> From: owner-chemistry..ccl.net [mailto:owner-chemistry..ccl.net]
Sent: Wednesday, May 10, 2006 8:52 AM
To: Ryan, M Dominic
Subject: CCL: Dihydroxyl compound

 

Sent to CCL by: kevin abbot = [kevanabbot::yahoo.com]

--0-512180785-1147267732=3D:41797

Content-Type: text/plain; = charset=3Diso-8859-1

Content-Transfer-Encoding: 8bit

 

Hi CCLers,

  I am working on a compound which has two hydroxyl groups = on the same secondary carbon atom (not primary),

  might someone inform me about the stability of a = dihydroxyl compound and its synthetic reliability (I mean is a compound like this = stable?).

  Some references are appreciated as I have found only a = few articles on this kind of compound.

  

  Best Regards

  

  Kevin

  

 

           = ;

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

New Yahoo! Messenger with Voice. Call regular phones from your = PC and save big.

--0-512180785-1147267732=3D:41797

Content-Type: text/html; = charset=3Diso-8859-1

Content-Transfer-Encoding: 8bit

 

<div class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN lang=3DEN-GB style=3D"mso-ansi-language: EN-GB"><FONT size=3D3><FONT face=3D"Times New Roman">Hi CCLers,<?xml:namespace prefix =3D o ns =3D = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></FONT></SPAN></d= iv>  <div class=3DMsoNormal style=3D"MARGIN: 0cm 0cm = 0pt"><SPAN lang=3DEN-GB style=3D"mso-ansi-language: EN-GB"><FONT size=3D3><FONT face=3D"Times New Roman">I&nbsp;am working&nbsp;on&nbsp;a compound which has two hydroxyl groups on = the same secondary carbon atom (not primary),<o:p></o:p></FONT></FONT></SPAN>&l= t;/div>  <div class=3DMsoNormal style=3D"MARGIN: 0cm 0cm = 0pt"><SPAN lang=3DEN-GB style=3D"mso-ansi-language: EN-GB"><FONT size=3D3><FONT face=3D"Times New Roman">might someone = inform me about the stability of a dihydroxyl compound and its synthetic = reliability (I mean is a compound like this stable?).<o:p></o:p></FONT></FONT></SPAN>&l= t;/div>  <div class=3DMsoNormal style=3D"MARGIN: 0cm 0cm = 0pt"><SPAN lang=3DEN-GB = style=3D"mso-ansi-language:

 EN-GB"><FONT size=3D3><FONT = face=3D"Times New Roman">Some references are appreciated as I have found only a few articles on this = kind of compound.<o:p></o:p></FONT></FONT></SPAN>&l= t;/div>  <div class=3DMsoNormal style=3D"MARGIN: 0cm 0cm = 0pt"><SPAN lang=3DEN-GB style=3D"mso-ansi-language: = EN-GB"><o:p><FONT face=3D"Times New Roman" size=3D3>&nbsp;</FONT></o:p></SPAN></div>&= nbsp; <div class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN = lang=3DEN-GB style=3D"mso-ansi-language: EN-GB"><FONT = size=3D3><FONT face=3D"Times New Roman">Best Regards<o:p></o:p></FONT></FONT></SPAN><= /div>  <div class=3DMsoNormal style=3D"MARGIN: 0cm 0cm = 0pt"><SPAN lang=3DEN-GB style=3D"mso-ansi-language: = EN-GB"><o:p><FONT face=3D"Times New Roman" size=3D3>&nbsp;</FONT></o:p></SPAN></div>&= nbsp; <div class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN = lang=3DEN-GB style=3D"mso-ansi-language: EN-GB"><FONT = size=3D3><FONT face=3D"Times New Roman">Kevin<o:p></o:p></FONT></FONT><= /SPAN></div>  <div>&nbsp;</div><p>

           = ; <hr size=3D1>New Yahoo! Messenger with Voice. <a href=3D"http://us.rd.yahoo.com/mail_us/taglines/postman5/*http://us.= rd.yahoo.com/evt=3D39666/*http://messenger.yahoo.com">Call regular phones from your PC</a> and save = big.

--0-512180785-1147267732=3D:41797--

 

 

 

-=3D This is automatically added to each message by the mailing = script =3D-

To recover the email address of the author of the message, = please change

the strange characters on the top line to the .. sign. You can = also

look up the X-Original-From: line in the mail = header.

 

E-mail to subscribers: CHEMISTRY..ccl.net or = use:

      =<= /p>

 

E-mail to administrators: CHEMISTRY-REQUEST..ccl.net or = use

      =<= /p>

 

      =

=

 

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

 

Conferences: = http://server.ccl.net/chemistry/announcements/conferences/

 

Search Messages: http://www.ccl.net/htdig  (login: ccl, = Password: search)

 

If your mail bounces from CCL with 5.7.1 error, = check:

      =

 

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

 

-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= +-+-+-+

 

 

------=_NextPart_000_0034_01C67421.D42539B0-- From owner-chemistry@ccl.net Wed May 10 13:22:02 2006 From: "Victor Manuel Rosas-Garcia quimico69[]yahoo.com" To: CCL Subject: CCL: Dihydroxyl compound Message-Id: <-31735-060510113400-4260-KdzIrYpOt9ShTJchp6vsRw(0)server.ccl.net> X-Original-From: Victor Manuel Rosas-Garcia Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 10 May 2006 07:33:54 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Victor Manuel Rosas-Garcia [quimico69-$-yahoo.com] Dear Kevin, For a compound like this: HO OH \ / C / \ R R' Such a compound is called a ketal. Any organic chemistry textbook will give you the mechanism of formation. With two hydroxyl groups, we are talking about a hydrated ketone and they are not very stable, but it is common in organic synthesis to protect keto groups by making the ketal with an alcohol such as methanol or even better with ethylene glycol (1,2-ethanediol) Hope this helps --- "kevin abbot kevanabbot**yahoo.com" wrote: > Sent to CCL by: kevin abbot [kevanabbot::yahoo.com] > --0-512180785-1147267732=:41797 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Hi CCLers, > I am working on a compound which has two hydroxyl groups on the same > secondary carbon atom (not primary), > might someone inform me about the stability of a dihydroxyl compound and > its synthetic reliability (I mean is a compound like this stable?). > Some references are appreciated as I have found only a few articles on this > kind of compound. > > Best Regards > > Kevin > > > > Victor M. Rosas García, PhD Coordinador del Posgrado en Ciencias Facultad de Ciencias Quimicas, UANL e-mail: quimico69^^yahoo.com Tel: (81) 8329-4010 ext. 6253 Fax: (81) 8376-5375 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Wed May 10 13:57:00 2006 From: "Boyd, D. boyd*|*chem.iupui.edu" To: CCL Subject: CCL: Gordon Conference on Computational Chemistry Message-Id: <-31736-060510123625-14375-o8CW68VLV4InJgBD5nYXWg(a)server.ccl.net> X-Original-From: "Boyd, D." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 10 May 2006 11:31:36 -0400 MIME-Version: 1.0 Sent to CCL by: "Boyd, D." [boyd**chem.iupui.edu] Computational chemists meet this October in Switzerland for the 2006 biennial Gordon Research Conference on Computational Chemistry. Register soon. For more information, see http://chem.iupui.edu/rcc/grccc.html and http://www.grc.org From owner-chemistry@ccl.net Wed May 10 14:32:00 2006 From: "Gunda Tamás tgunda2005%x%puma.unideb.hu" To: CCL Subject: CCL: Dihydroxyl compound Message-Id: <-31737-060510140503-15925-SjXKadwOWugm3TVqtdhirQ]|[server.ccl.net> X-Original-From: "Gunda Tamás" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 10 May 2006 19:06:28 +0200 MIME-Version: 1.0 Sent to CCL by: "Gunda Tamás" [tgunda2005%x%puma.unideb.hu] Kevin, Geminal diols >C(OH)2 are very rarely stable enough to put them onto the table in pure crystalline form. An example is chloralhydrate CCl3-CH(OH)2 or the reagent ninhydrine. They are stable only if strong electron attracting groups are attached to the carbon atom. However, in aqueous solution they can exist in equilibrium form with the corresponding keton or aldehyde. Tamas E. Gunda ----- Original Message ----- > From: "kevin abbot kevanabbot**yahoo.com" To: "Gunda, Tamas E " Sent: Wednesday, May 10, 2006 15:50 Subject: CCL: Dihydroxyl compound > Sent to CCL by: kevin abbot [kevanabbot::yahoo.com] > --0-512180785-1147267732=:41797 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Hi CCLers, > I am working on a compound which has two hydroxyl groups on the same secondary carbon atom (not primary), > might someone inform me about the stability of a dihydroxyl compound and its synthetic reliability (I mean is a > compound like this stable?). > Some references are appreciated as I have found only a few articles on this kind of compound. > > Best Regards > > Kevin > > > > --------------------------------- > New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. > --0-512180785-1147267732=:41797 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
face="Times New Roman">Hi CCLers, />
style="mso-ansi-language: EN-GB">I am working on a compound > which has two hydroxyl groups on the same secondary carbon atom (not primary),
>
face="Times New Roman">might someone inform me about the stability of a dihydroxyl compound and its synthetic > reliability (I mean is a compound like this stable?).
style="MARGIN: 0cm 0cm 0pt">Some references are appreciated as I have found only a few articles > on this kind of compound.
size=3> 
style="mso-ansi-language: EN-GB">Best > Regards
style="mso-ansi-language: EN-GB"> 
class=MsoNormal style="MARGIN: 0cm 0cm 0pt"> face="Times New Roman">Kevin
 

>

New Yahoo! Messenger with Voice. href="http://us.rd.yahoo.com/mail_us/taglines/postman5/*http://us.rd.yahoo.com/evt=39666/*http://messenger.yahoo.com">Call > regular phones from your PC and save big. > --0-512180785-1147267732=:41797--> > > From owner-chemistry@ccl.net Wed May 10 15:08:02 2006 From: "Anderson Coser Gaudio anderson-$-npd.ufes.br" To: CCL Subject: CCL: Program for similarity index calculation Message-Id: <-31738-060510141038-18200-Paqy4B0AJyvhjUzD5FR5rg%x%server.ccl.net> X-Original-From: "Anderson Coser Gaudio" Date: Wed, 10 May 2006 14:10:34 -0400 Sent to CCL by: "Anderson Coser Gaudio" [anderson__npd.ufes.br] Dear Colleagues, I have a series of compounds that have the same backbone of chloroquine molecule, differing from it by some substituents placed here and there on the structure. I would like to get a measure of the similarity between each one of the molecules in the series and the chloroquine molecule, by using Carbo or Hodgkin indices. Does anyone know a public domain computer program (Windows, if possible...) that can reliably perform such a calculation. I acknowledge any help. Anderson From owner-chemistry@ccl.net Wed May 10 15:42:01 2006 From: "Amiram Goldblum amiram]^[vms.huji.ac.il" To: CCL Subject: CCL: Dihydroxyl compound Message-Id: <-31739-060510141618-20017-8q6PEwwI/YYSVc51x9NtTQ[]server.ccl.net> X-Original-From: Amiram Goldblum Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Wed, 10 May 2006 19:15:30 +0100 Mime-Version: 1.0 Sent to CCL by: Amiram Goldblum [amiram[*]vms.huji.ac.il] Hi Kevin, Compounds with two hydroxyls on the same carbon are known as "gem diols" and are actually hydrates of ketones or carbonyls. They are very unstable unless you have strong electron attractors on the neighboring carbon/s, such as difluoromethylene and others. With some electron attractors you may stabilize the ketone ===== hydrate equilibrium to the hydrate side up to 90%. Gem diols are supposed to be close to tetrahedral intermediates in the attack on amide carbonyls by water. They have been interesting as potential inhibitors of aspartic proteinases and other enzymes. With kind regards, Amiram From owner-chemistry@ccl.net Wed May 10 16:17:02 2006 From: "Eduard Matito ematito..gmail.com" To: CCL Subject: CCL: Program for similarity index calculation Message-Id: <-31740-060510154158-22503-oKVz50rHkQRry6MDf1ml2g[-]server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Wed, 10 May 2006 21:39:17 +0200 MIME-Version: 1.0 Sent to CCL by: Eduard Matito [ematito*gmail.com] Dear Anderson, MEssEM program is given for free, check out this link: http://iqc.udg.es/~miquel/mike.html Take care, Eduard ------------------------------------------------------------- Anderson Coser Gaudio anderson-$-npd.ufes.br wrote: >Sent to CCL by: "Anderson Coser Gaudio" [anderson__npd.ufes.br] > > >Dear Colleagues, > >I have a series of compounds that have the same backbone of chloroquine molecule, differing from it by some substituents placed here and there on the structure. I would like to get a measure of the similarity between each one of the molecules in the series and the chloroquine molecule, by using Carbo or Hodgkin indices. Does anyone know a public domain computer program (Windows, if possible...) that can reliably perform such a calculation. > >I acknowledge any help. > >Anderson> > > > > > From owner-chemistry@ccl.net Wed May 10 17:28:00 2006 From: "=?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= jvilla#%#imim.es" To: CCL Subject: CCL: Program for similarity index calculation Message-Id: <-31741-060510164138-28343-SDmXg4waXONCGSOANS/uoQ*server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 10 May 2006 21:54:10 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= [jvilla[]imim.es] Dear Anderson, MIPSim can do that and it is free for academia, although it is only for linux and IRIX. It is based on the potentials calculated by GAMESS (quantum electrostatic potential) and GRID (classical MIPs) http://diana.imim.es/software/mipsim/index.php *"Towards a MIP-based alignment and docking in computer-aided drug design"* Montserrat Barbany, Hugo Gutiérrez de Terán, Ferran Sanz, and Jordi Villà-Freixa. PROTEINS: Structure, Function and Bioinformatics, 2004, 56, 585-594, 18. * "MIPSIM: Similarity analysis of Molecular Interaction Potentials"* Miquel de Cáceres, Jordi Villà, Juan J. Lozano and Ferran Sanz. Bioinformatics, 2000, 16, 568-569 Best wishes Jordi En/na Anderson Coser Gaudio anderson-$-npd.ufes.br ha escrit: > Sent to CCL by: "Anderson Coser Gaudio" [anderson__npd.ufes.br] > > > Dear Colleagues, > > I have a series of compounds that have the same backbone of chloroquine molecule, differing from it by some substituents placed here and there on the structure. I would like to get a measure of the similarity between each one of the molecules in the series and the chloroquine molecule, by using Carbo or Hodgkin indices. Does anyone know a public domain computer program (Windows, if possible...) that can reliably perform such a calculation. > > I acknowledge any help. > > Anderson> > > > > -- Jordi Villà i Freixa Computational Biochemistry and Biophysics lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF C/ Doctor Aiguader, 80; 08003 Barcelona (Spain) Tel: +34 93 221 1009 ext 2619 // Fax: +34 93 221 3237 e-mail: jvilla .. imim.es http://diana.imim.es MSc on Bioinformatics for Health Sciences http://diana.imim.es/mbio http://www.idec.upf.edu/mbio From owner-chemistry@ccl.net Wed May 10 18:02:01 2006 From: "Steven Bachrach sbachrach[a]trinity.edu" To: CCL Subject: CCL: Large scale DNA/RNA computations Message-Id: <-31742-060510150833-29755-+DaUbu0hRhIbMC+bKOHl2g^server.ccl.net> X-Original-From: "Steven Bachrach" Date: Wed, 10 May 2006 15:08:25 -0400 Sent to CCL by: "Steven Bachrach" [sbachrach::trinity.edu] I am interested in finding any computations at the ab initio/DFT level on DNA or RNA. I am aware of the paper by Scuseria (JPCA, 1999, 103, 4782) on a 1026 atom RNA fragment and the paper by Chen and Zhang (JPC, 2004, 120, 11386) on the DNA fragment (dCGT/dGCA). Is anyone aware of other examples? Please note that I am not looking for work on individual nucleic acid bases, but rather on DNA/RNA oligomers. Many thanks in advance! Steven Bachrach -- Steven Bachrach ph: (210)999-7379 Department of Chemistry fax: (210)999-7569 Trinity University 1 Trinity Place San Antonio, TX 78212 steven.bachrach-#-trinity.edu From owner-chemistry@ccl.net Wed May 10 19:20:00 2006 From: "Bo Li liboqd]|[gmail.com" To: CCL Subject: CCL: Ask help for launching autodock tools in Vmware Message-Id: <-31743-060510185159-3081-Ovk+MVqsl0l6ZmSugkDIhw{:}server.ccl.net> X-Original-From: "Bo Li" Date: Wed, 10 May 2006 18:51:57 -0400 Sent to CCL by: "Bo Li" [liboqd .. gmail.com] Hi: I installed Redhat 9 in Vmware 5, in order to run Autodock on it. I have successfully installed Autodock Tools(ADT), but everytime I launched PMV, I received the following message and PMV paused: Run PMV from /usr/local/lib/python2.4/site-packages/Pmv Xlib: extension "XFree86-DRI" missing on display ":0.0". MSMSLIB 1.3 started on localhost.localdomain Copyright M.F. Sanner (March 2000) Compilation flags Traceback (most recent call last): File "/usr/local/lib/python2.4/site-packages/MolKit/APBSParameters.py", line 114, in __init__ self.APBS_Path = getBinary("apbs", 'binaries') File "/usr/local/lib/python2.4/site-packages/mglutil/util/packageFilePath.py", line 28, in getBinary pgmfullpath = findFilePath(name, package) File "/usr/local/lib/python2.4/site-packages/mglutil/util/packageFilePath.py", line 37, in findFilePath mod = __import__(packageName) ImportError: No module named binaries Any suggestion for this problem? Thanks a lot! Bo