From owner-chemistry@ccl.net Thu Jan 24 03:42:01 2013
From: "Andreas Klamt klamt]![cosmologic.de" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL: Why Chlorine atom is more hydrophobic than Hydrogen
Message-Id: <-48121-130123233056-21722-Dz/DSR6zbs1p1wuH+j+Abw(~)server.ccl.net>
X-Original-From: Andreas Klamt <klamt{:}cosmologic.de>
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Sent to CCL by: Andreas Klamt [klamt%%cosmologic.de]
Hi Mannan,
this can be quite nicely explained within COSMO-RS theory. Basically
the interactions in liquids are surface contacts. Hydrophobicity is
sloppy expression for the fact that water does not like to make contayts
to non- or slightly polar surface area. By the way, this is an entropic
effect, because the really polar parts of water essentially will make no
contacts to slightly polar surfaces, and the free high free energy of
contact results from the entropy loss which goes along with placing the
few "green" (in COMSO-RS the non-polar surface is colored in green)
surface pieces of water on the non-polar solute surface area.
Anyway, the larger the non-polar surface area, the more of the green
water patches are required as contact partners and the higher the
"hydrophobic" costs. And since the vdW-radius of hydrogen is ~ 1.1
Angstrom, and that of Chlorine is ~ 1.7, the exposed non-polar surface
area of chlorine is much larger than that of hydrogen.
Best regards
Andreas
Am 23.01.2013 15:36, schrieb Mannan K malie_03(0)yahoo.co.in:
> Sent to CCL by: "Mannan K" [malie_03|*|yahoo.co.in]
> Hi CCLers,
>
> Chlorine/Fluorine atoms are commonly used to influence the hydrophobic contact in small molecule design.
> But how the hydrophobicity is being measured for halogen atoms with reference to Hydrogen atom?
> How Molar refractivity and steric paramemters are connected to hydrophobicity of an atom?
>
> Thanks in Advance,
> Mannan>
>
>
--
Prof. Dr. Andreas Klamt
CEO / Gesch�ftsf�hrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany
phone +49-2171-731681
fax +49-2171-731689
e-mail klamt:-:cosmologic.de
web www.cosmologic.de
[University address: Inst. of Physical and
Theoretical Chemistry, University of Regensburg]
HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
From owner-chemistry@ccl.net Thu Jan 24 05:12:00 2013
From: "Georg Lefkidis lefkidis###physik.uni-kl.de" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL:G: AW: G: AW: G: 6D, 5D and complex numbers
Message-Id: <-48122-130124051029-11786-MxLSiwNFRbfdn+O/mYfVwA*|*server.ccl.net>
X-Original-From: "Georg Lefkidis" <lefkidis:+:physik.uni-kl.de>
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Date: Thu, 24 Jan 2013 11:10:17 +0100
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Sent to CCL by: "Georg Lefkidis" [lefkidis~~physik.uni-kl.de]
Dear Susi,
Probably I spent too much time in a physics department and I forgot to look up the difference between Y_{lm} and Y_{l}^{m}. This is also consistent with Molden format now.
Thank you.
George
-----Ursprüngliche Nachricht-----
Von: owner-chemistry+lefkidis==physik.uni-kl.de|-|ccl.net [mailto:owner-chemistry+lefkidis==physik.uni-kl.de|-|ccl.net] Im Auftrag von Susi Lehtola susi.lehtola[A]alumni.helsinki.fi
Gesendet: Dienstag, 22. Januar 2013 18:14
An: Lefkidis, Georg
Betreff: CCL:G: AW: G: 6D, 5D and complex numbers
Sent to CCL by: Susi Lehtola [susi.lehtola[a]alumni.helsinki.fi]
On Tue, 22 Jan 2013 16:58:50 +0100
"Georg Lefkidis lefkidis:-:physik.uni-kl.de" <owner-chemistry\a/ccl.net>
wrote:
> Sent to CCL by: "Georg Lefkidis" [lefkidis]~[physik.uni-kl.de] Dear
> Susi,
>
> thank you for your reply, however, it does not really completely
> answer my question. If the coefficients refer to the spherical
> harmonics (which I also tend consider as the most probable) then the
> integrals between the atomic orbitals (which for instance Gaussian can
> print through IOP commands) should be complex as well. And this is not
> the case which is why I am perplexed...
No. Spherical harmonics in the real form are real functions, so the integrals over them are also real. And as I said in the previous mail, you don't lose anything when you go to the real form, since you still have the same amount of degrees of freedom within the spherical harmonics.
--
--------------------------------------------------------
Mr. Susi Lehtola, M. Sc. Doctoral Student
susi.lehtola\a/alumni.helsinki.fi Department of Physics
http://www.helsinki.fi/~jzlehtol University of Helsinki
Office phone: +358 9 191 50 632 Finland
--------------------------------------------------------
Susi Lehtola, FM Tohtorikoulutettava
susi.lehtola\a/alumni.helsinki.fi Fysiikan laitos
http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto
Ty puhelin: (0)9 191 50 632
--------------------------------------------------------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 Thu Jan 24 06:52:00 2013
From: "Rajeev Gangal rajeev.gangal|-|gmail.com" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: r-groups, energy contributins , SAR
Message-Id: <-48123-130124063449-13167-1Y4f+70cj8GKpcOsowGMHw[*]server.ccl.net>
X-Original-From: Rajeev Gangal <rajeev.gangal**gmail.com>
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Date: Thu, 24 Jan 2013 17:04:43 +0530
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Sent to CCL by: Rajeev Gangal [rajeev.gangal^gmail.com]
--089e0102ee227cd52804d407325a
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Is it possible to compute energy terms [hbond, electrostatic etc] for
R-groups of a ligand?
This can then be related to the biological data for analogs. So Increase in
hbond donor /acceptor strength for e.g at R1 may be correlated with binding
..
--089e0102ee227cd52804d407325a
Content-Type: text/html; charset=ISO-8859-1
<div dir="ltr">Is it possible to compute energy terms [hbond, electrostatic etc] for R-groups of a ligand?<br><br>This
can then be related to the biological data for analogs. So Increase in
hbond donor /acceptor strength for e.g at R1 may be correlated with
binding ..</div>
--089e0102ee227cd52804d407325a--
From owner-chemistry@ccl.net Thu Jan 24 08:30:00 2013
From: "Alex Allardyce aallardyce * chemaxon.com" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: =?utf-8?Q?ChemAxon=E2=80=99s_chemicalize.org_extends_PubChem_dat?= =?utf-8?Q?abase_with_crowd-sourced_chemistry_from_the_Web?=
Message-Id: <-48124-130123070103-19463-H6EdebuzLA16BOgi+aSimw!^!server.ccl.net>
X-Original-From: Alex Allardyce <aallardyce,,chemaxon.com>
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Sent to CCL by: Alex Allardyce [aallardyce||chemaxon.com]
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Excuse cross postings=20
ChemAxon=E2=80=99s chemicalize.org extends PubChem database with crowd-sour=
ced chemistry from the Web=20
(Budapest, Hungary & Cambridge, MA =E2=80=93 January 23, 2013) - ChemAxon, =
a leader in providing chemistry software solutions and consulting services =
for life science research, announces that the crowd-sourced chemical struct=
ures gathered via its public website, chemicalize.org, have been deposited =
to the Pubchem repository, with approximately one third of the submission b=
eing novel. The provision also includes links to valuable structure-based d=
ata for each of the submitted structures.=20
chemicalize.org is a public website which extracts and displays chemical st=
ructures from users browsing of web pages and submitting other documents to=
the site. The service builds a database of all identified structures, whic=
h enables structure (and other) searching of gathered content.=20
Since chemicalize.org was started in spring 2009 we have gathered ~300,000 =
unique structures and inline with the aims of the service, to make chemistr=
y more useful, we deposited the collection into PubChem, the world's larges=
t free public chemistry database. From these ~300,000 structures ~100,000 s=
tructures were novel.=20
Continued growth and new users are essential to have a crowd-sourced databa=
se that is up-to-date and follows current interests. chemicalize.org has be=
en growing well in recent months with 15,000 unique visitors/month in Decem=
ber, up 60% in the last 6 months.=20
We will continue to deposit updates to ensure the utility of the service to=
the community and to include a link back to chemicalize.org data pages whe=
re various structure-based calculated properties are presented.=20
The deposition is discussed in more detail at the ChemAxon blog ; http://ww=
w.chemaxon.com/blog/chemicalize-orgs-crowdsourced-database/=20
About chemicalize.org=20
chemicalize.org is a public website created by ChemAxon for adding chemical=
resolution to web browsing, chemical names and structure files. The servic=
e is free and will be useful to anyone wishing to add chemical structures a=
nd predicted data to their web browsing experience or extract chemical stru=
ctures from web pages and other documents.=20
About ChemAxon=20
ChemAxon is a leader in providing cheminformatics software platforms and de=
sktop applications for the biotechnology, pharmaceutical and agrochemical i=
ndustries. With core capabilities for structure visualization, search and m=
anagement, property prediction, virtual synthesis, screening and drug desig=
n, ChemAxon focuses upon active interaction with users and software portabi=
lity to create powerful, cost effective cross platform solutions that power=
modern cheminformatics and chemical communication. The company is privatel=
y owned with European headquarters in Budapest, US East Coast headquarters =
in Cambridge, MA, and sales and support offices in Europe, Japan and across=
North America.=20
Alex Allardyce=20
Marketing Dir.=20
ChemAxon Ltd=20
Z=C3=A1hony u. 7. Building HX, Budapest, 1031 Hungary=20
http://www.chemaxon.com=20
Tel: + 361 453 0435=20
Fax: + 361 4532659=20
mailto:aa*|*chemaxon.com=20
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<html><head><style type=3D'text/css'>p { margin: 0; }</style></head><body><=
div style=3D'font-family: arial,helvetica,sans-serif; font-size: 12pt; colo=
r: #000000'><div><font face=3D"arial, helvetica, sans-serif">Excuse cross p=
ostings</font></div><div><font face=3D"arial, helvetica, sans-serif"><br></=
font></div><div><font face=3D"arial, helvetica, sans-serif">ChemAxon=E2=80=
=99s chemicalize.org extends PubChem database with crowd-sourced chemistry =
> from the Web</font></div><div><font face=3D"arial, helvetica, sans-serif"><=
br></font></div><div><font face=3D"arial, helvetica, sans-serif">(Budapest,=
Hungary & Cambridge, MA =E2=80=93 January 23, 2013) - ChemAxon, a lead=
er in providing chemistry software solutions and consulting services for li=
fe science research, announces that the crowd-sourced chemical structures g=
athered via its public website, chemicalize.org, have been deposited to the=
Pubchem repository, with approximately one third of the submission being n=
ovel. The provision also includes links to valuable structure-based data fo=
r each of the submitted structures. </font></div><div><font face=3D"ar=
ial, helvetica, sans-serif"><br></font></div><div><font face=3D"arial, helv=
etica, sans-serif">chemicalize.org is a public website which extracts and d=
isplays chemical structures from users browsing of web pages and submitting=
other documents to the site. The service builds a database of all identifi=
ed structures, which enables structure (and other) searching of gathered co=
ntent. </font></div><div><font face=3D"arial, helvetica, sans-serif"><=
br></font></div><div><font face=3D"arial, helvetica, sans-serif">Since chem=
icalize.org was started in spring 2009 we have gathered ~300,000 unique str=
uctures and inline with the aims of the service, to make chemistry more use=
ful, we deposited the collection into PubChem, the world's largest free pub=
lic chemistry database. From these ~300,000 structures ~100,000 structures =
were novel. </font></div><div><font face=3D"arial, helvetica, sans-ser=
if"><br></font></div><div><font face=3D"arial, helvetica, sans-serif">Conti=
nued growth and new users are essential to have a crowd-sourced database th=
at is up-to-date and follows current interests. chemicalize.org has been gr=
owing well in recent months with 15,000 unique visitors/month in December, =
up 60% in the last 6 months.</font></div><div><font face=3D"arial, helvetic=
a, sans-serif"><br></font></div><div><font face=3D"arial, helvetica, sans-s=
erif">We will continue to deposit updates to ensure the utility of the serv=
ice to the community and to include a link back to chemicalize.org data pag=
es where various structure-based calculated properties are presented.</font=
></div><div><font face=3D"arial, helvetica, sans-serif"><br></font></div><d=
iv><font face=3D"arial, helvetica, sans-serif">The deposition is discussed =
in more detail at the ChemAxon blog ; http://www.chemaxon.com/blog/chemical=
ize-orgs-crowdsourced-database/</font></div><div><font face=3D"arial, helve=
tica, sans-serif"><br></font></div><div><font face=3D"arial, helvetica, san=
s-serif">About chemicalize.org </font></div><div><font face=3D"arial, =
helvetica, sans-serif">chemicalize.org is a public website created by ChemA=
xon for adding chemical resolution to web browsing, chemical names and stru=
cture files. The service is free and will be useful to anyone wishing to ad=
d chemical structures and predicted data to their web browsing experience o=
r extract chemical structures from web pages and other documents.</font></d=
iv><div><font face=3D"arial, helvetica, sans-serif"><br></font></div><div><=
font face=3D"arial, helvetica, sans-serif">About ChemAxon</font></div><div>=
<font face=3D"arial, helvetica, sans-serif">ChemAxon is a leader in providi=
ng cheminformatics software platforms and desktop applications for the biot=
echnology, pharmaceutical and agrochemical industries. With core capa=
bilities for structure visualization, search and management, property predi=
ction, virtual synthesis, screening and drug design, ChemAxon focuses upon =
active interaction with users and software portability to create powerful, =
cost effective cross platform solutions that power modern cheminformatics a=
nd chemical communication. The company is privately owned with Europe=
an headquarters in Budapest, US East Coast headquarters in Cambridge, MA, a=
nd sales and support offices in Europe, Japan and across North America.</fo=
nt></div><br><div style=3D"color: rgb(0, 0, 0); font-family: arial, helveti=
ca, sans-serif; font-size: 12pt;"><span name=3D"x"></span>Alex <span id=3D"=
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t">Allardyce</span></span><br><font style=3D"color: rgb(102, 102, 102);" si=
ze=3D"1">Marketing Dir.</font><br><font style=3D"color: rgb(153, 102, 51);"=
size=3D"2">ChemAxon Ltd</font><br><font size=3D"2"><font style=3D"color: r=
gb(102, 102, 102);" size=3D"1">Z=C3=A1hony u. 7. Building HX, Budapest, 103=
1 Hungary</font><br><span class=3D"Object" id=3D"OBJ_PREFIX_DWT244_com_zimb=
ra_url"><span class=3D"Object" id=3D"OBJ_PREFIX_DWT245_com_zimbra_url"><a t=
arget=3D"_blank" href=3D"http://www.chemaxon.com/">http://www.chemaxon.com<=
/a></span></span></font><br><font style=3D"color: rgb(102, 102, 102);" size=
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hone"><a href=3D"callto:361%20453%200435">361 453 0435</a></span><br>Fax: +=
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From owner-chemistry@ccl.net Thu Jan 24 10:29:00 2013
From: "Robert.L.Waterland,+,dupont.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Why Chlorine atom is more hydrophobic than Hydrogen
Message-Id: <-48125-130124091041-15642-HRt02wi6rU1oYmJTjOJirw:server.ccl.net>
X-Original-From: <Robert.L.Waterland _ dupont.com>
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Date: Thu, 24 Jan 2013 14:10:06 +0000
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Sent to CCL by: [Robert.L.Waterland _ dupont.com]
This is an interesting explanation but I wonder if there is something more to the story. Fluorine is even more hydrophobic than chlorine - many of the best surfactants are heavily fluorinated and a terminal CF3 group often results in strong water repellency - but the vdW-radius of fluorine (~1.47 Angstrom) lies between that of chlorine (~1.75 Angstrom) and hydrogen (~1.20 Angstrom).
Best wishes
Rob
Robert Waterland
DuPont Central R&D
Experimental Station E320/314
Rt 141 and Henry Clay
Wilmington, DE 19880
e-mail: Robert.L.Waterland[-]dupont.com
phone: +1 302-695-1511
fax: +1 302 695-9873
-----Original Message-----
> From: owner-chemistry+robert.l.waterland==usa.dupont.com[-]ccl.net [mailto:owner-chemistry+robert.l.waterland==usa.dupont.com[-]ccl.net] On Behalf Of Andreas Klamt klamt]![cosmologic.de
Sent: Wednesday, January 23, 2013 11:31 PM
To: WATERLAND, ROBERT L
Subject: CCL: Why Chlorine atom is more hydrophobic than Hydrogen
Sent to CCL by: Andreas Klamt [klamt%%cosmologic.de] Hi Mannan,
this can be quite nicely explained within COSMO-RS theory. Basically the interactions in liquids are surface contacts. Hydrophobicity is sloppy expression for the fact that water does not like to make contayts to non- or slightly polar surface area. By the way, this is an entropic effect, because the really polar parts of water essentially will make no contacts to slightly polar surfaces, and the free high free energy of contact results from the entropy loss which goes along with placing the few "green" (in COMSO-RS the non-polar surface is colored in green) surface pieces of water on the non-polar solute surface area.
Anyway, the larger the non-polar surface area, the more of the green water patches are required as contact partners and the higher the "hydrophobic" costs. And since the vdW-radius of hydrogen is ~ 1.1 Angstrom, and that of Chlorine is ~ 1.7, the exposed non-polar surface area of chlorine is much larger than that of hydrogen.
Best regards
Andreas
Am 23.01.2013 15:36, schrieb Mannan K malie_03(0)yahoo.co.in:
> Sent to CCL by: "Mannan K" [malie_03|*|yahoo.co.in] Hi CCLers,
>
> Chlorine/Fluorine atoms are commonly used to influence the hydrophobic contact in small molecule design.
> But how the hydrophobicity is being measured for halogen atoms with reference to Hydrogen atom?
> How Molar refractivity and steric paramemters are connected to hydrophobicity of an atom?
>
> Thanks in Advance,
> Mannan>
>
>
--
Prof. Dr. Andreas Klamt
CEO / Gesch�ftsf�hrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany
phone +49-2171-731681
fax +49-2171-731689
e-mail klamt:-:cosmologic.de
web www.cosmologic.de
[University address: Inst. of Physical and
Theoretical Chemistry, University of Regensburg]
HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis communication is for use by the intended recipient and contains
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From owner-chemistry@ccl.net Thu Jan 24 11:06:00 2013
From: "Pierre Archirel pierre.archirel|-|u-psud.fr" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL:G: weakly bound electrons
Message-Id: <-48126-130124110441-8875-rgdtRW78hppdn7FkVAd1QQ]![server.ccl.net>
X-Original-From: Pierre Archirel <pierre.archirel]^[u-psud.fr>
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Date: Thu, 24 Jan 2013 17:04:35 +0100
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Sent to CCL by: Pierre Archirel [pierre.archirel:-:u-psud.fr]
Dear colleagues,
What is the best method for calculating the small electron affinitiy
(say 0.01 - 0.10 eV) of a rather large system with many equivalent sites.
For my smallest system the valence CAS would require
37 electrons in 36 orbitals, which is not feasible.
What about MP2, MP4 ?
Is CCSD(T) usable when the electron is not bound at the HF level?
I have gaussian 09 and Molpro available.
Thanks in advance.
Pierre Archirel
LCP, Universite Paris-Sud,
Orsay, France
pierre.archirel!!u-psud.fr
______________________________________________________________
Pierre Archirel
Groupe Th�osim: Th�orie et Simulation
Laboratoire de Chimie Physique Tel: 01 69 15 63 86
B�t 349 Fax: 01 69 15 61 88
91405 Orsay C�dex
France pierre.archirel[]u-psud.fr
______________________________________________________________
From owner-chemistry@ccl.net Thu Jan 24 12:33:00 2013
From: "Rinderspacher, Berend C CIV (US) berend.c.rinderspacher.civ{}mail.mil" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: Why Chlorine atom is more hydrophobic than Hydrogen (UNCLASSIFIED)
Message-Id: <-48127-130124113834-3263-nG3Pwo15+Uxzf8UEA5/YBA/./server.ccl.net>
X-Original-From: "Rinderspacher, Berend C CIV (US)" <berend.c.rinderspacher.civ/./mail.mil>
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Date: Thu, 24 Jan 2013 16:38:19 +0000
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Sent to CCL by: "Rinderspacher, Berend C CIV (US)" [berend.c.rinderspacher.civ^_^mail.mil]
Classification: UNCLASSIFIED
Caveats: NONE
My two cents:
Fluorine is a very hard atom and not particularly polarizable compared to hydrogen or chlorine. Since vdW forces are lead by induced dipole interactions, fluorine screens these interactions. Given flat surfaces of hydrogenated, perfluorinated and perchlorinated hydrocarbons, the accessible surface area should be approximately the same in all cases, but I'd expect the fluorinated species to be the least wettable.
-----Original Message-----
> From: owner-chemistry+berend.rinderspacher==us.army.mil**ccl.net [mailto:owner-chemistry+berend.rinderspacher==us.army.mil**ccl.net] On Behalf Of Robert.L.Waterland,+,dupont.com
Sent: Thursday, January 24, 2013 9:10 AM
To: Rinderspacher, Berend C CIV (US)
Subject: CCL: Why Chlorine atom is more hydrophobic than Hydrogen
Sent to CCL by: [Robert.L.Waterland _ dupont.com] This is an interesting explanation but I wonder if there is something more to the story. Fluorine is even more hydrophobic than chlorine - many of the best surfactants are heavily fluorinated and a terminal CF3 group often results in strong water repellency - but the vdW-radius of fluorine (~1.47 Angstrom) lies between that of chlorine (~1.75 Angstrom) and hydrogen (~1.20 Angstrom).
Best wishes
Rob
Robert Waterland
DuPont Central R&D
Experimental Station E320/314
Rt 141 and Henry Clay
Wilmington, DE 19880
e-mail: Robert.L.Waterland_._dupont.com
phone: +1 302-695-1511
fax: +1 302 695-9873
-----Original Message-----
> From: owner-chemistry+robert.l.waterland==usa.dupont.com_._ccl.net
> [mailto:owner-chemistry+robert.l.waterland==usa.dupont.com_._ccl.net]
> On Behalf Of Andreas Klamt klamt]![cosmologic.de
Sent: Wednesday, January 23, 2013 11:31 PM
To: WATERLAND, ROBERT L
Subject: CCL: Why Chlorine atom is more hydrophobic than Hydrogen
Sent to CCL by: Andreas Klamt [klamt%%cosmologic.de] Hi Mannan,
this can be quite nicely explained within COSMO-RS theory. Basically the interactions in liquids are surface contacts. Hydrophobicity is sloppy expression for the fact that water does not like to make contayts to non- or slightly polar surface area. By the way, this is an entropic effect, because the really polar parts of water essentially will make no contacts to slightly polar surfaces, and the free high free energy of contact results from the entropy loss which goes along with placing the few "green" (in COMSO-RS the non-polar surface is colored in green) surface pieces of water on the non-polar solute surface area.
Anyway, the larger the non-polar surface area, the more of the green water patches are required as contact partners and the higher the "hydrophobic" costs. And since the vdW-radius of hydrogen is ~ 1.1 Angstrom, and that of Chlorine is ~ 1.7, the exposed non-polar surface area of chlorine is much larger than that of hydrogen.
Best regards
Andreas
Am 23.01.2013 15:36, schrieb Mannan K malie_03(0)yahoo.co.in:
> Sent to CCL by: "Mannan K" [malie_03|*|yahoo.co.in] Hi CCLers,
>
> Chlorine/Fluorine atoms are commonly used to influence the hydrophobic contact in small molecule design.
> But how the hydrophobicity is being measured for halogen atoms with reference to Hydrogen atom?
> How Molar refractivity and steric paramemters are connected to hydrophobicity of an atom?
>
> Thanks in Advance,
> Mannan>
>
>
--
Prof. Dr. Andreas Klamt
CEO / Gesch�ftsf�hrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany
phone +49-2171-731681
fax +49-2171-731689
e-mail klamt:-:cosmologic.de
web www.cosmologic.de
[University address: Inst. of Physical and
Theoretical Chemistry, University of Regensburg]
HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties.
Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean
http://www.DuPont.com/corp/email_disclaimer.htmlhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtClassification: UNCLASSIFIED
Caveats: NONE
From owner-chemistry@ccl.net Thu Jan 24 14:15:00 2013
From: "Marcelo Puiatti marcelo.puiatti]^[gmail.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL:G: weakly bound electrons
Message-Id: <-48128-130124141136-17157-yp320a2WOGSuUhiCtcU13A]*[server.ccl.net>
X-Original-From: Marcelo Puiatti <marcelo.puiatti]_[gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Thu, 24 Jan 2013 16:11:30 -0300
MIME-Version: 1.0
Sent to CCL by: Marcelo Puiatti [marcelo.puiatti|gmail.com]
Dear Pierre:
I suggest you to read the following article:
M. Puiatti, D. M. A. Vera, A. B. Pierini, Phys. Chem. Chem. Phys.,
2009, 19, 8957-64.
You could find 2 or 3 methods based on DFT for computing the EA of your system.
Dr. Marcelo Puiatti
INFIQC. Instituto de Investigaciones en F�sico-Qu�mica de C�rdoba.
Facultad de Ciencias Qu�micas,
Universidad Nacional de C�rdoba,
Argentina
On 24 January 2013 14:04, Pierre Archirel pierre.archirel|-|u-psud.fr
<owner-chemistry{=}ccl.net> wrote:
>
> Sent to CCL by: Pierre Archirel [pierre.archirel:-:u-psud.fr]
> Dear colleagues,
> What is the best method for calculating the small electron affinitiy
> (say 0.01 - 0.10 eV) of a rather large system with many equivalent sites.
> For my smallest system the valence CAS would require
> 37 electrons in 36 orbitals, which is not feasible.
> What about MP2, MP4 ?
> Is CCSD(T) usable when the electron is not bound at the HF level?
> I have gaussian 09 and Molpro available.
> Thanks in advance.
>
> Pierre Archirel
> LCP, Universite Paris-Sud,
> Orsay, France
> pierre.archirel!!u-psud.fr
>
>
> ______________________________________________________________
>
> Pierre Archirel
> Groupe Th�osim: Th�orie et Simulation
> Laboratoire de Chimie Physique Tel: 01 69 15 63 86
> B�t 349 Fax: 01 69 15 61 88
> 91405 Orsay C�dex
> France pierre.archirel(-)u-psud.fr
> ______________________________________________________________http://www.ccl.net/chemistry/sub_unsub.shtmlConferences:
> http://server.ccl.net/chemistry/announcements/conferences/>
>
From owner-chemistry@ccl.net Thu Jan 24 16:59:00 2013
From: "Andreas Klamt klamt(-)cosmologic.de" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL: Why Chlorine atom is more hydrophobic than Hydrogen (UNCLASSIFIED)
Message-Id: <-48129-130124155931-19416-4PzlZAuaHsQwQECSAKDaxA*|*server.ccl.net>
X-Original-From: Andreas Klamt <klamt:cosmologic.de>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1; format=flowed
Date: Thu, 24 Jan 2013 21:59:20 +0100
MIME-Version: 1.0
Sent to CCL by: Andreas Klamt [klamt_-_cosmologic.de]
You are right that pefluorinated compounds are ultrahydrophobic, but
please note that perfluorinated alkanes do even phase-separate from
alkanes. This clearly indicates that there are two different modes of
repulsive interactions: One is the normal hydrophobic effect, as
explained before, and the other one results from the excess-vdW (or
dispersive) interactions of fluorine (due to its hardness).
Am 24.01.2013 17:38, schrieb Rinderspacher, Berend C CIV (US)
berend.c.rinderspacher.civ{}mail.mil:
> Sent to CCL by: "Rinderspacher, Berend C CIV (US)" [berend.c.rinderspacher.civ^_^mail.mil]
> Classification: UNCLASSIFIED
> Caveats: NONE
>
> My two cents:
>
> Fluorine is a very hard atom and not particularly polarizable compared to hydrogen or chlorine. Since vdW forces are lead by induced dipole interactions, fluorine screens these interactions. Given flat surfaces of hydrogenated, perfluorinated and perchlorinated hydrocarbons, the accessible surface area should be approximately the same in all cases, but I'd expect the fluorinated species to be the least wettable.
>
> -----Original Message-----
>> From: owner-chemistry+berend.rinderspacher==us.army.mil*|*ccl.net [mailto:owner-chemistry+berend.rinderspacher==us.army.mil*|*ccl.net] On Behalf Of Robert.L.Waterland,+,dupont.com
> Sent: Thursday, January 24, 2013 9:10 AM
> To: Rinderspacher, Berend C CIV (US)
> Subject: CCL: Why Chlorine atom is more hydrophobic than Hydrogen
>
>
> Sent to CCL by: [Robert.L.Waterland _ dupont.com] This is an interesting explanation but I wonder if there is something more to the story. Fluorine is even more hydrophobic than chlorine - many of the best surfactants are heavily fluorinated and a terminal CF3 group often results in strong water repellency - but the vdW-radius of fluorine (~1.47 Angstrom) lies between that of chlorine (~1.75 Angstrom) and hydrogen (~1.20 Angstrom).
>
> Best wishes
>
> Rob
>
> Robert Waterland
> DuPont Central R&D
> Experimental Station E320/314
> Rt 141 and Henry Clay
> Wilmington, DE 19880
> e-mail: Robert.L.Waterland_._dupont.com
> phone: +1 302-695-1511
> fax: +1 302 695-9873
>
> -----Original Message-----
>> From: owner-chemistry+robert.l.waterland==usa.dupont.com_._ccl.net
>> [mailto:owner-chemistry+robert.l.waterland==usa.dupont.com_._ccl.net]
>> On Behalf Of Andreas Klamt klamt]![cosmologic.de
> Sent: Wednesday, January 23, 2013 11:31 PM
> To: WATERLAND, ROBERT L
> Subject: CCL: Why Chlorine atom is more hydrophobic than Hydrogen
>
>
> Sent to CCL by: Andreas Klamt [klamt%%cosmologic.de] Hi Mannan,
>
> this can be quite nicely explained within COSMO-RS theory. Basically the interactions in liquids are surface contacts. Hydrophobicity is sloppy expression for the fact that water does not like to make contayts to non- or slightly polar surface area. By the way, this is an entropic effect, because the really polar parts of water essentially will make no contacts to slightly polar surfaces, and the free high free energy of contact results from the entropy loss which goes along with placing the few "green" (in COMSO-RS the non-polar surface is colored in green) surface pieces of water on the non-polar solute surface area.
>
> Anyway, the larger the non-polar surface area, the more of the green water patches are required as contact partners and the higher the "hydrophobic" costs. And since the vdW-radius of hydrogen is ~ 1.1 Angstrom, and that of Chlorine is ~ 1.7, the exposed non-polar surface area of chlorine is much larger than that of hydrogen.
>
> Best regards
>
> Andreas
>
> Am 23.01.2013 15:36, schrieb Mannan K malie_03(0)yahoo.co.in:
>> Sent to CCL by: "Mannan K" [malie_03|*|yahoo.co.in] Hi CCLers,
>>
>> Chlorine/Fluorine atoms are commonly used to influence the hydrophobic contact in small molecule design.
>> But how the hydrophobicity is being measured for halogen atoms with reference to Hydrogen atom?
>> How Molar refractivity and steric paramemters are connected to hydrophobicity of an atom?
>>
>> Thanks in Advance,
>> Mannan>
>>
>>
>
> --
> Prof. Dr. Andreas Klamt
> CEO / Gesch�ftsf�hrer
> COSMOlogic GmbH & Co. KG
> Burscheider Strasse 515
> D-51381 Leverkusen, Germany
>
> phone +49-2171-731681
> fax +49-2171-731689
> e-mail klamt:-:cosmologic.de
> web www.cosmologic.de
>
> [University address: Inst. of Physical and
> Theoretical Chemistry, University of Regensburg]
>
> HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
> Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties.
>
> Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean
>
> http://www.DuPont.com/corp/email_disclaimer.htmlhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtClassification: UNCLASSIFIED
> Caveats: NONE>
>
>
--
Prof. Dr. Andreas Klamt
CEO / Gesch�ftsf�hrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany
phone +49-2171-731681
fax +49-2171-731689
e-mail klamt-x-cosmologic.de
web www.cosmologic.de
[University address: Inst. of Physical and
Theoretical Chemistry, University of Regensburg]
HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
From owner-chemistry@ccl.net Thu Jan 24 20:50:00 2013
From: "Angela Walker alwalker_+_scripps.edu" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL: GPCR Dock 2013 Assessment
Message-Id: <-48130-130124195526-28775-Jfy4fiweqo+jfho+dqgbsw[-]server.ccl.net>
X-Original-From: "Angela Walker" <alwalker^^^scripps.edu>
Date: Thu, 24 Jan 2013 19:55:25 -0500
Sent to CCL by: "Angela Walker" [alwalker~~scripps.edu]
Dear GPCR modeling and docking researcher,
We are writing to announce the 3rd round of the GPCR Docking and Modeling
Assessment, GPCR Dock 2013, and to invite you to submit your predictions of
GPCR-ligand structures for comparison prior to publication of the results.
The first two GPCR Dock assessments were conducted in 2008 and 2010 and were
based on the structures of A2A adenosine receptor (GPCR Dock 2008; NRDD
2009), dopamine D3 receptor and chemokine receptor CXCR4 (GPCR Dock 2010;
Structure 2011). As before, the results from GPCR Dock 2013 will be
published once an analysis is complete.
We encourage all industry and academic groups to participate and so please
pass word of this assessment onto your colleagues who may have not directly
been contacted.
The present round of the assessment will be focused on four target
complexes. Participants can choose to predict any one, two, three, or all
four targets. Predicting all four targets is strongly encouraged. Registered
participants will receive receptor and ligand information at midnight
(Pacific standard time) on Feb 1st, and will have until midnight (PST) March
3rd (30 days) to deposit models. Further information about the assessment
and registration forms to participate can be found at
http://gpcr.scripps.edu/GPCRDock2013
If you have any questions, please email (gpcrdock_+_scripps.edu) we will try
to get back to you quickly and will also post any general comments to all
registered participants.
GPCR Network
Ray Stevens
Ruben Abagyan
Irina Kufareva
Angela Walker
Seva Katritch