From owner-chemistry@ccl.net Thu Oct 20 03:54:00 2016
From: "Marcel Swart marcel.swart : icrea.cat" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: DFT-Poll
Message-Id: <-52439-161020034944-15584-s0kGHJ+EP7T8BWxHKdgXlQ{}server.ccl.net>
X-Original-From: "Marcel  Swart" <marcel.swart|-|icrea.cat>
Date: Thu, 20 Oct 2016 03:49:40 -0400


Sent to CCL by: "Marcel  Swart" [marcel.swart**icrea.cat]
Dear all,

the DFT-Poll is set up to be small. Already with the 40-50 functionals in it, people are complaining there's 
too many included (and I tend to agree with them). Having 400-500 is simply out of the question, and will 
be counterproductive. The rules are quite simple about this:
http://www.marcelswart.eu/dft-poll/rules.html

There will be a Primera Divisi with the 20 most popular functionals. At the end of each year, the 5 least 
popular of the Primera Divisi will relegate to the Segona Divisi.
Each year, only the 20 most popular functionals of the Segona Divisi will be kept. The five most popular 
ones of the Segona will be promoted to the Primera, while the 15 next will form the Segona for the next 
year together with the 5 relegated from the Primera.
The other functionals will not take part in the poll for the year after (unless suggested again). There is a 
maximum of 10 additional suggestions for each year, which are added chronologically (after being 
suggested by mail to M. Swart, marcel.swart|,|udg.edu).

If no one proposes new functionals, no new functionals will get in. It is as simple as that. Every year I try 
to add some new ones, such as MVS and SCAN this year, MN12L in 2014, or PWPB95-D3 and wB97X-D in 
2011. Some break through to top 5 in Primera Divisi, others don't.

Therefore, please propose new functionals to be included in next year's edition (maximum of 10 slots 
available).

Marcel


From owner-chemistry@ccl.net Thu Oct 20 06:25:00 2016
From: "Jeya Vimalan jeyavimalan2k||gmail.com" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: Formation Energy
Message-Id: <-52440-161020060725-7767-8mRsMP6oYXw0SzvGhUECgA---server.ccl.net>
X-Original-From: Jeya Vimalan <jeyavimalan2k###gmail.com>
Content-Type: multipart/alternative; boundary=001a113f9a1043028c053f4917a1
Date: Thu, 20 Oct 2016 15:37:18 +0530
MIME-Version: 1.0


Sent to CCL by: Jeya Vimalan [jeyavimalan2k:-:gmail.com]
--001a113f9a1043028c053f4917a1
Content-Type: text/plain; charset=UTF-8

Dear All,

I have three composition.

A1-B3-C4
A2-B4-C5
A4-B3-C7

I would like to understand
which structures are stable and hence
decided to calculate formation (or Cohesive) energy.

Lets take the first two cases and
calculate Formation energy by the below formulae.


Formation Energy of 1 (E1) = Total energy of A1-B3-C4 -(Energy of 1*A +
Energy of 3*B + Energy of 4*C).
Formation Energy of 1 (E2) = Total energy of A2-B4-C5 -(Energy of 2*A +
Energy of 4*B + Energy of 5*C).


Does the direct comparison (E1, E2) makes sense?
Can i conclude if E1>E2, then composition 1 is more stable.

I feel, i am missing something.
Your help would be appreciable.

Best regards,
Vimal

--001a113f9a1043028c053f4917a1
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr"><div>Dear All,</div><div><br></div><div>I have three compo=
sition.</div><div><br></div><div>A1-B3-C4</div><div>A2-B4-C5</div><div>A4-B=
3-C7</div><div><br></div><div>I would like to understand</div><div>which st=
ructures are stable and hence</div><div>decided to calculate formation (or =
Cohesive) energy.</div><div><br></div><div>Lets take the first two cases an=
d=C2=A0</div><div>calculate Formation energy by the below formulae.</div><d=
iv><br></div><div><br></div><div>Formation Energy of 1 (E1) =3D Total energ=
y of A1-B3-C4 -(Energy of 1*A + Energy of 3*B + Energy of 4*C).</div><div>F=
ormation Energy of 1 (E2) =3D Total energy of A2-B4-C5 -(Energy of 2*A + En=
ergy of 4*B + Energy of 5*C).</div><div><br></div><div><br></div><div>Does =
the direct comparison (E1, E2) makes sense?</div><div>Can i conclude if E1&=
gt;E2, then composition 1 is more stable.</div><div><br></div><div>I feel, =
i am missing something.</div><div>Your help would be appreciable.</div><div=
><br></div><div>Best regards,</div><div>Vimal</div><div><br></div></div>

--001a113f9a1043028c053f4917a1--


From owner-chemistry@ccl.net Thu Oct 20 08:02:01 2016
From: "Susi Lehtola susi.lehtola_-_alumni.helsinki.fi" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL:G: CCL #DFT16poll results are out
Message-Id: <-52441-161019202936-18761-tPDj5LZWr6E8W82acl1BUw]![server.ccl.net>
X-Original-From: Susi Lehtola <susi.lehtola=-=alumni.helsinki.fi>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=windows-1252; format=flowed
Date: Wed, 19 Oct 2016 17:29:12 -0700
MIME-Version: 1.0


Sent to CCL by: Susi Lehtola [susi.lehtola]*[alumni.helsinki.fi]
On 10/19/2016 08:28 AM, Jim Kress jimkress35 : gmail.com wrote:
>
> Sent to CCL by: "Jim Kress" [jimkress35,+,gmail.com]
> " ready to use in real calculations"
>
> Please show me where these functionals are available in Orca, Gamess,
> Firefly, Jaguar, Gaussian, NWChem or the other mainstream QC codes.

... but by the same standard you have completely invalidated the DFT 
poll you have so strongheartedly been defending. Many functionals that 
made the present poll aren't supported by those codes.

Besides, if you have access to those programs, then nothing prevents you 
> from modifying them to link to libxc. This is far easier than 
reimplementing 250+ functionals yourself. [Out of the list, only NWChem 
is open source. But even the closed-source programs could use libxc if 
they wanted to.]
-- 
-----------------------------------------------------------------------
Mr. Susi Lehtola, PhD             Chemist Postdoctoral Fellow
susi.lehtola%alumni.helsinki.fi   Lawrence Berkeley National Laboratory
http://www.helsinki.fi/~jzlehtol  USA
-----------------------------------------------------------------------


From owner-chemistry@ccl.net Thu Oct 20 08:36:00 2016
From: "Marcel Swart marcel.swart .. icrea.cat" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: Formation Energy
Message-Id: <-52442-161020081840-21315-dWTTvNmCVsFNdr8SMR68KQ- -server.ccl.net>
X-Original-From: Marcel Swart <marcel.swart-#-icrea.cat>
Content-Type: multipart/alternative; boundary="Apple-Mail=_0F32FE5C-08D8-45BC-9775-D905ED42B3F2"
Date: Thu, 20 Oct 2016 14:18:32 +0200
Mime-Version: 1.0 (Mac OS X Mail 9.3 \(3124\))


Sent to CCL by: Marcel Swart [marcel.swart.:.icrea.cat]

--Apple-Mail=_0F32FE5C-08D8-45BC-9775-D905ED42B3F2
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset=utf-8

Dear Vimal,

I would say that your approach is valid, under the condition that the A, =
B, and C and
sensible moieties. It reminds a bit of atomization energies.

However, I would say that if E1 > E2 (e.g.  +2  vs. -10) that 2 is more =
stable, not 1.

Marcel

> On 20 Oct 2016, at 12:07 , Jeya Vimalan jeyavimalan2k||gmail.com =
<owner-chemistry|,|ccl.net> wrote:
>=20
> Dear All,
>=20
> I have three composition.
>=20
> A1-B3-C4
> A2-B4-C5
> A4-B3-C7
>=20
> I would like to understand
> which structures are stable and hence
> decided to calculate formation (or Cohesive) energy.
>=20
> Lets take the first two cases and=20
> calculate Formation energy by the below formulae.
>=20
>=20
> Formation Energy of 1 (E1) =3D Total energy of A1-B3-C4 -(Energy of =
1*A + Energy of 3*B + Energy of 4*C).
> Formation Energy of 1 (E2) =3D Total energy of A2-B4-C5 -(Energy of =
2*A + Energy of 4*B + Energy of 5*C).
>=20
>=20
> Does the direct comparison (E1, E2) makes sense?
> Can i conclude if E1>E2, then composition 1 is more stable.
>=20
> I feel, i am missing something.
> Your help would be appreciable.
>=20
> Best regards,
> Vimal
>=20


_____________________________________
Prof Dr Marcel Swart, FRSC

ICREA Research Professor at
Institut de Qu=C3=ADmica Computacional i Cat=C3=A0lisi (IQCC)
Univ. Girona (Spain)

COST Action CM1305 (ECOSTBio) chair
Girona Seminar 2016 organizer
IQCC director
Young Academy of Europe (Board) member

Web
http://www.marcelswart.eu
vCard
addressbook://www.marcelswart.eu/MSwart.vcf


--Apple-Mail=_0F32FE5C-08D8-45BC-9775-D905ED42B3F2
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html;
	charset=utf-8

<html><head><meta http-equiv=3D"Content-Type" content=3D"text/html =
charset=3Dutf-8"></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" =
class=3D"">Dear Vimal,<div class=3D""><br class=3D""></div><div =
class=3D"">I would say that your approach is valid, under the condition =
that the A, B, and C and</div><div class=3D"">sensible moieties. It =
reminds a bit of atomization energies.</div><div class=3D""><br =
class=3D""></div><div class=3D"">However, I would say that if E1 &gt; E2 =
(e.g. &nbsp;+2 &nbsp;vs. -10) that 2 is more stable, not 1.</div><div =
class=3D""><br class=3D""></div><div class=3D"">Marcel</div><div =
class=3D""><br class=3D""><div><blockquote type=3D"cite" class=3D""><div =
class=3D"">On 20 Oct 2016, at 12:07 , Jeya Vimalan jeyavimalan2k||<a =
href=3D"http://gmail.com" class=3D"">gmail.com</a> &lt;<a =
href=3D"mailto:owner-chemistry|,|ccl.net" =
class=3D"">owner-chemistry|,|ccl.net</a>&gt; wrote:</div><br =
class=3D"Apple-interchange-newline"><div class=3D""><div dir=3D"ltr" =
class=3D""><div class=3D"">Dear All,</div><div class=3D""><br =
class=3D""></div><div class=3D"">I have three composition.</div><div =
class=3D""><br class=3D""></div><div class=3D"">A1-B3-C4</div><div =
class=3D"">A2-B4-C5</div><div class=3D"">A4-B3-C7</div><div class=3D""><br=
 class=3D""></div><div class=3D"">I would like to understand</div><div =
class=3D"">which structures are stable and hence</div><div =
class=3D"">decided to calculate formation (or Cohesive) =
energy.</div><div class=3D""><br class=3D""></div><div class=3D"">Lets =
take the first two cases and&nbsp;</div><div class=3D"">calculate =
Formation energy by the below formulae.</div><div class=3D""><br =
class=3D""></div><div class=3D""><br class=3D""></div><div =
class=3D"">Formation Energy of 1 (E1) =3D Total energy of A1-B3-C4 =
-(Energy of 1*A + Energy of 3*B + Energy of 4*C).</div><div =
class=3D"">Formation Energy of 1 (E2) =3D Total energy of A2-B4-C5 =
-(Energy of 2*A + Energy of 4*B + Energy of 5*C).</div><div class=3D""><br=
 class=3D""></div><div class=3D""><br class=3D""></div><div =
class=3D"">Does the direct comparison (E1, E2) makes sense?</div><div =
class=3D"">Can i conclude if E1&gt;E2, then composition 1 is more =
stable.</div><div class=3D""><br class=3D""></div><div class=3D"">I =
feel, i am missing something.</div><div class=3D"">Your help would be =
appreciable.</div><div class=3D""><br class=3D""></div><div =
class=3D"">Best regards,</div><div class=3D"">Vimal</div><div =
class=3D""><br class=3D""></div></div>
</div></blockquote></div><br class=3D""><div class=3D"">
<div style=3D"color: rgb(0, 0, 0); font-family: Geneva; font-size: 12px; =
font-style: normal; font-variant-ligatures: normal; =
font-variant-position: normal; font-variant-caps: normal; =
font-variant-numeric: normal; font-variant-alternates: normal; =
font-variant-east-asian: normal; font-weight: normal; letter-spacing: =
normal; orphans: auto; text-align: start; text-indent: 0px; =
text-transform: none; white-space: normal; widows: auto; word-spacing: =
0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" =
class=3D""><br =
class=3D"Apple-interchange-newline">_____________________________________<=
br class=3D"">Prof Dr Marcel Swart, FRSC<br class=3D""><br =
class=3D"">ICREA Research Professor at<br class=3D"">Institut de =
Qu=C3=ADmica Computacional i Cat=C3=A0lisi (IQCC)<br class=3D"">Univ. =
Girona (Spain)<br class=3D""><br class=3D"">COST Action CM1305 =
(ECOSTBio) chair<br class=3D"">Girona Seminar 2016 organizer<br =
class=3D"">IQCC director<br class=3D"">Young Academy of Europe (Board) =
member<br class=3D""><br class=3D""></div><div style=3D"color: rgb(0, 0, =
0); font-family: Geneva; font-size: 12px; font-style: normal; =
font-variant-ligatures: normal; font-variant-position: normal; =
font-variant-caps: normal; font-variant-numeric: normal; =
font-variant-alternates: normal; font-variant-east-asian: normal; =
font-weight: normal; letter-spacing: normal; orphans: auto; text-align: =
start; text-indent: 0px; text-transform: none; white-space: normal; =
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; =
word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: =
after-white-space;" class=3D"">Web<br class=3D""><a =
href=3D"http://www.marcelswart.eu" =
class=3D"">http://www.marcelswart.eu</a><br class=3D"">vCard<br =
class=3D"">addressbook://www.marcelswart.eu/MSwart.vcf<br =
class=3D""></div>
</div>
<br class=3D""></div></body></html>=

--Apple-Mail=_0F32FE5C-08D8-45BC-9775-D905ED42B3F2--


From owner-chemistry@ccl.net Thu Oct 20 09:11:00 2016
From: "Cina Foroutan-Nejad canyslopus/./yahoo.co.uk" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: Formation Energy
Message-Id: <-52443-161020084030-19139-XnubaoaTxnNRidBXLo12LA^server.ccl.net>
X-Original-From: Cina Foroutan-Nejad <canyslopus^_^yahoo.co.uk>
Content-Type: multipart/alternative; 
	boundary="----=_Part_752408_919648662.1476967221352"
Date: Thu, 20 Oct 2016 12:40:21 +0000 (UTC)
MIME-Version: 1.0


Sent to CCL by: Cina Foroutan-Nejad [canyslopus]^[yahoo.co.uk]
------=_Part_752408_919648662.1476967221352
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

Dear Vimal:
Unfortunately, the concept of stability is not that straightforward. Thermo=
dynamics does not provide the final answer. The stability of a molecule not=
 only depends on its formation energy, but it depends also on the relative =
energies of its neighboring local minima on its potential energy surface an=
d the energy barrier between the minimum and its immediate neighboring mini=
ma (kinetic stability). To begin, I would rather check the depth of minimum=
 energy well by looking at frequencies. In the next step ab initio/MC/DFT- =
MD simulations can provide more insight toward the kinetic stability. Then =
of course we can define stability with respect to a particular reaction. Is=
 your molecule stable when it is in the presence of air/water/light/etc.You=
 must be more precise about stability.=C2=A0
I hope my general answer can help you to solve your problem.
Good luck,Cina


--------------------------------------------------------------Cina Foroutan=
-Nejad, PhDCEITEC-Central European Institute of TechnologyKamenice 5/A4, Ma=
saryk University, Brno, Czech Republichttps://muni.academia.edu/CinaForouta=
nNejad
=20

    On Thursday, 20 October 2016, 14:18, Jeya Vimalan jeyavimalan2k||gmail.=
com <owner-chemistry],[ccl.net> wrote:
=20

 Dear All,
I have three composition.
A1-B3-C4A2-B4-C5A4-B3-C7
I would like to understandwhich structures are stable and hencedecided to c=
alculate formation (or Cohesive) energy.
Lets take the first two cases and=C2=A0calculate Formation energy by the be=
low formulae.

Formation Energy of 1 (E1) =3D Total energy of A1-B3-C4 -(Energy of 1*A + E=
nergy of 3*B + Energy of 4*C).Formation Energy of 1 (E2) =3D Total energy o=
f A2-B4-C5 -(Energy of 2*A + Energy of 4*B + Energy of 5*C).

Does the direct comparison (E1, E2) makes sense?Can i conclude if E1>E2, th=
en composition 1 is more stable.
I feel, i am missing something.Your help would be appreciable.
Best regards,Vimal


  =20
------=_Part_752408_919648662.1476967221352
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<html><head></head><body><div style=3D"color:#000; background-color:#fff; f=
ont-family:bookman old style, new york, times, serif;font-size:16px"><div i=
d=3D"yui_3_16_0_ym19_1_1476951389691_117996"><span id=3D"yui_3_16_0_ym19_1_=
1476951389691_118251">Dear Vimal:</span></div><div id=3D"yui_3_16_0_ym19_1_=
1476951389691_117996"><span><br></span></div><div id=3D"yui_3_16_0_ym19_1_1=
476951389691_117996"><span id=3D"yui_3_16_0_ym19_1_1476951389691_117995">Un=
fortunately, the concept of stability is not that straightforward. Thermody=
namics does not provide the final answer. The stability of a molecule not o=
nly depends on its formation energy, but it depends also on the relative en=
ergies of its neighboring local minima on its potential energy surface and =
the energy barrier between the minimum and its immediate neighboring minima=
 (kinetic stability). To begin, I would rather check the depth of minimum e=
nergy well by looking at frequencies. In the next step ab initio/MC/DFT- MD=
 simulations can provide more insight toward the kinetic stability. Then of=
 course we can define stability with respect to a particular reaction. Is y=
our molecule stable when it is in the presence of air/water/light/etc.</spa=
n></div><div id=3D"yui_3_16_0_ym19_1_1476951389691_117996"><span id=3D"yui_=
3_16_0_ym19_1_1476951389691_118688">You must be more precise about stabilit=
y.&nbsp;</span></div><div id=3D"yui_3_16_0_ym19_1_1476951389691_117996"><sp=
an><br></span></div><div id=3D"yui_3_16_0_ym19_1_1476951389691_117996"><spa=
n id=3D"yui_3_16_0_ym19_1_1476951389691_118659">I hope my general answer ca=
n help you to solve your problem.</span></div><div id=3D"yui_3_16_0_ym19_1_=
1476951389691_117996"><span><br></span></div><div id=3D"yui_3_16_0_ym19_1_1=
476951389691_117996"><span>Good luck,</span></div><div id=3D"yui_3_16_0_ym1=
9_1_1476951389691_117996"><span>Cina</span></div><div id=3D"yui_3_16_0_ym19=
_1_1476951389691_117996"><span><br></span></div><div id=3D"yui_3_16_0_ym19_=
1_1476951389691_117996"><span><br></span></div><div id=3D"yui_3_16_0_ym19_1=
_1476951389691_117996"><span><br></span></div><div id=3D"yui_3_16_0_ym19_1_=
1476951389691_117996">-----------------------------------------------------=
---------</div><div id=3D"yui_3_16_0_ym19_1_1476951389691_117996">Cina Foro=
utan-Nejad, PhD</div><div id=3D"yui_3_16_0_ym19_1_1476951389691_117996" dir=
=3D"ltr">CEITEC-Central European Institute of Technology</div><div id=3D"yu=
i_3_16_0_ym19_1_1476951389691_117996" dir=3D"ltr">Kamenice 5/A4, Masaryk Un=
iversity, Brno, Czech Republic</div><div id=3D"yui_3_16_0_ym19_1_1476951389=
691_117996" dir=3D"ltr"><a href=3D"https://muni.academia.edu/CinaForoutanNe=
jad" id=3D"yui_3_16_0_ym19_1_1476951389691_118689">https://muni.academia.ed=
u/CinaForoutanNejad</a><br></div> <div class=3D"qtdSeparateBR"><br><br></di=
v><div class=3D"yahoo_quoted" style=3D"display: block;"> <div style=3D"font=
-family: bookman old style, new york, times, serif; font-size: 16px;"> <div=
 style=3D"font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Luc=
ida Grande, Sans-Serif; font-size: 16px;"> <div dir=3D"ltr"><font size=3D"2=
" face=3D"Arial"> On Thursday, 20 October 2016, 14:18, Jeya Vimalan jeyavim=
alan2k||gmail.com &lt;owner-chemistry],[ccl.net&gt; wrote:<br></font></div>  =
<br><br> <div class=3D"y_msg_container"><div id=3D"yiv6361109446"><div dir=
=3D"ltr"><div>Dear All,</div><div><br></div><div>I have three composition.<=
/div><div><br></div><div>A1-B3-C4</div><div>A2-B4-C5</div><div>A4-B3-C7</di=
v><div><br></div><div>I would like to understand</div><div>which structures=
 are stable and hence</div><div>decided to calculate formation (or Cohesive=
) energy.</div><div><br></div><div>Lets take the first two cases and&nbsp;<=
/div><div>calculate Formation energy by the below formulae.</div><div><br><=
/div><div><br></div><div>Formation Energy of 1 (E1) =3D Total energy of A1-=
B3-C4 -(Energy of 1*A + Energy of 3*B + Energy of 4*C).</div><div>Formation=
 Energy of 1 (E2) =3D Total energy of A2-B4-C5 -(Energy of 2*A + Energy of =
4*B + Energy of 5*C).</div><div><br></div><div><br></div><div>Does the dire=
ct comparison (E1, E2) makes sense?</div><div>Can i conclude if E1&gt;E2, t=
hen composition 1 is more stable.</div><div><br></div><div>I feel, i am mis=
sing something.</div><div>Your help would be appreciable.</div><div><br></d=
iv><div>Best regards,</div><div>Vimal</div><div><br></div></div></div><br><=
br></div>  </div> </div>  </div></div></body></html>
------=_Part_752408_919648662.1476967221352--


From owner-chemistry@ccl.net Thu Oct 20 10:15:00 2016
From: "Abrash, Samuel sabrash..richmond.edu" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL:G: CCL #DFT16poll results are out
Message-Id: <-52444-161020101238-11674-ReCmgWKlqEyDZ/hkqF3D2Q=server.ccl.net>
X-Original-From: "Abrash, Samuel" <sabrash(-)richmond.edu>
Content-Language: en-US
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset="iso-8859-7"
Date: Thu, 20 Oct 2016 14:12:29 +0000
MIME-Version: 1.0


Sent to CCL by: "Abrash, Samuel" [sabrash|-|richmond.edu]
PLEASE.  It is time for this thread to end.  The discussion has continued far beyond the point where it is valuable for the readers of this list, and frankly for the disputants. It's time to put it to rest.  

Samuel A. Abrash
Associate Professor, Department of Chemistry
University of Richmond
sabrash-.-richmond.edu
Cell: (804) 363-2597
www.richmond.edu/~sabrash
"Let no one be discouraged by the belief there is nothing one person can do against the enormous array of the world's ills, misery, ignorance, and violence. Few will have the greatness to bend history, but each of us can work to change a small portion of events. And in the total of all those acts will be written the history of a generation." ¯ Robert F. Kennedy



-----Original Message-----
> From: owner-chemistry+sabrash==richmond.edu-.-ccl.net [mailto:owner-chemistry+sabrash==richmond.edu-.-ccl.net] On Behalf Of Susi Lehtola susi.lehtola_-_alumni.helsinki.fi
Sent: Wednesday, October 19, 2016 8:29 PM
To: Abrash, Samuel <sabrash-.-richmond.edu>
Subject: CCL:G: CCL #DFT16poll results are out


Sent to CCL by: Susi Lehtola [susi.lehtola]*[alumni.helsinki.fi]
On 10/19/2016 08:28 AM, Jim Kress jimkress35 : gmail.com wrote:
>
> Sent to CCL by: "Jim Kress" [jimkress35,+,gmail.com] " ready to use in 
> real calculations"
>
> Please show me where these functionals are available in Orca, Gamess, 
> Firefly, Jaguar, Gaussian, NWChem or the other mainstream QC codes.

... but by the same standard you have completely invalidated the DFT poll you have so strongheartedly been defending. Many functionals that made the present poll aren't supported by those codes.

Besides, if you have access to those programs, then nothing prevents you 
> from modifying them to link to libxc. This is far easier than
reimplementing 250+ functionals yourself. [Out of the list, only NWChem is open source. But even the closed-source programs could use libxc if they wanted to.]
--
-----------------------------------------------------------------------
Mr. Susi Lehtola, PhD             Chemist Postdoctoral Fellow
susi.lehtola(a)alumni.helsinki.fi   Lawrence Berkeley National Laboratory
http://www.helsinki.fi/~jzlehtol  USA
-----------------------------------------------------------------------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 Oct 20 10:49:00 2016
From: "Jim Kress jimkress35++gmail.com" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL:G: CCL #DFT16poll results are out
Message-Id: <-52445-161020101458-12847-WDDRBac+2owD1JKRRtyKCw]=[server.ccl.net>
X-Original-From: "Jim Kress" <jimkress35**gmail.com>
Content-Language: en-us
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
	charset="us-ascii"
Date: Thu, 20 Oct 2016 10:11:06 -0400
MIME-Version: 1.0


Sent to CCL by: "Jim Kress" [jimkress35]-[gmail.com]
> Besides, if you have access to those programs, then nothing prevents you 
> from modifying them to link to libxc. This is far easier than
> reimplementing 250+ functionals yourself. [Out of the list, only NWChem is
open source. 
> But even the closed-source programs could use libxc if they wanted to.]

Your last statement invalidates the rest of your post.  There is no point to
continuing this discussion.  I have already agreed that it is pointless
since the "poll antagonists" refuse to admit they might be incorrect and
still offer no solutions.  Modifying commercial code is not possible.
Modifying and validating NWChem and other available source codes is a time
consuming and laborious task.

If you want to waste your time doing that, fine.  I have better things to do
with the time and money I need to spend on doing actual research.

There will be no more responses from me on you posts.  I have used the CCL
filter function to eliminate you from any CCL messages sent to me.

Have a nice day.  

-----Original Message-----
> From: owner-chemistry+jimkress35==gmail.com!=!ccl.net
[mailto:owner-chemistry+jimkress35==gmail.com!=!ccl.net] On Behalf Of Susi
Lehtola susi.lehtola_-_alumni.helsinki.fi
Sent: Wednesday, October 19, 2016 8:29 PM
To: Kress, Jim  <jimkress35!=!gmail.com>
Subject: CCL:G: CCL #DFT16poll results are out


Sent to CCL by: Susi Lehtola [susi.lehtola]*[alumni.helsinki.fi]
On 10/19/2016 08:28 AM, Jim Kress jimkress35 : gmail.com wrote:
>
> Sent to CCL by: "Jim Kress" [jimkress35,+,gmail.com] " ready to use in 
> real calculations"
>
> Please show me where these functionals are available in Orca, Gamess, 
> Firefly, Jaguar, Gaussian, NWChem or the other mainstream QC codes.

... but by the same standard you have completely invalidated the DFT poll
you have so strongheartedly been defending. Many functionals that made the
present poll aren't supported by those codes.

Besides, if you have access to those programs, then nothing prevents you 
> from modifying them to link to libxc. This is far easier than
reimplementing 250+ functionals yourself. [Out of the list, only NWChem is
open source. But even the closed-source programs could use libxc if they
wanted to.]
--
-----------------------------------------------------------------------
Mr. Susi Lehtola, PhD             Chemist Postdoctoral Fellow
susi.lehtola(a)alumni.helsinki.fi   Lawrence Berkeley National Laboratory
http://www.helsinki.fi/~jzlehtol  USA
-----------------------------------------------------------------------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 Oct 20 12:50:00 2016
From: "Raul Alvarez ralvarez=chemcomp.com" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: CCG releases MOE 2016.08 with MOEsaic
Message-Id: <-52446-161020113347-14379-ZsxcWKXTt4YFD/so/1XTvA{:}server.ccl.net>
X-Original-From: "Raul  Alvarez" <ralvarez#chemcomp.com>
Date: Thu, 20 Oct 2016 11:33:36 -0400


Sent to CCL by: "Raul  Alvarez" [ralvarez..chemcomp.com]
We are pleased to announce the 2016 release of the Molecular Operating 
Environment (MOE). The 2016.08 version of MOE contains a unified web-
based framework for ligand analytics as well as enhanced spectral 
analysis tools for structure determination. Additional features in MOE 
2016.08 include 2D Protein Patch maps, Protein Patch Descriptors for QSPR 
modeling and updates to the Protein-Protein Docking and Protein Design 
applications.
 
To request a free trial of MOE 2016.08 or for additional information, 
please contact: Raul Alvarez, Senior Manager, Marketing Strategy, 
ralvarez() chemcomp.com 

===============================================================
NEW & ENHANCED FEATURES IN MOE 2016.08
===============================================================
* MOEsaic: Web-Application for Ligand Analytics 
* Spectral Analysis for Structure Determination
* Enhanced Protein Patch Analyzer 
* Integrated Antibody Project Database and Antibody Homology Modeler
* Small Footprint MOE to Facilitate Large Scale Deployments
* Physical and Virtual Rendering of Structures
===============================================================

Key application areas in MOE: http://www.chemcomp.com/index.htm
Structure-Based Design - Fragment-Based Design - Pharmacophore Discovery 
- Medicinal Chemistry Applications - Biologics Applications - Protein and 
Antibody Modeling - Molecular Modeling and Simulations - Cheminformatics 
& QSAR  Methods Development and Deployment


Raul Alvarez
Senior Manager, Marketing Strategy
Chemical Computing Group
T. + 1 (514) 393-1055 | F. +1 (514) 874-9538
ralvarez() chemcomp.com | www.chemcomp.com


From owner-chemistry@ccl.net Thu Oct 20 14:00:00 2016
From: "Marcel Swart marcel.swart _ icrea.cat" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: DFT-Poll: Reviews and Perspectives
Message-Id: <-52447-161020135834-31929-vw/gNbuF+bUOGeik9S1bsw%x%server.ccl.net>
X-Original-From: "Marcel  Swart" <marcel.swart::icrea.cat>
Date: Thu, 20 Oct 2016 13:58:31 -0400


Sent to CCL by: "Marcel  Swart" [marcel.swart{}icrea.cat]
Several people have put forward the idea of adding reviews about and perspectives on DFT into the 
news-item. Instead I think it is much more useful to have them on the website, so here is the initial 
batch:
http://www.marcelswart.eu/dft-poll/reviews.html

It will be updated in the coming days, if you have suggestions to be included, please send me privately 
a mail with the DOI (or citation).

Marcel

_____________________________________
Prof Dr Marcel Swart, FRSC

ICREA Research Professor at
Institut de Qumica Computacional i Catlisi (IQCC)
Univ. Girona (Spain)

COST Action CM1305 (ECOSTBio) chair
Girona Seminar 2016 organizer
IQCC director
Young Academy of Europe (Board) member

Web
http://www.marcelswart.eu
vCard
addressbook://www.marcelswart.eu/MSwart.vcf


From owner-chemistry@ccl.net Thu Oct 20 14:34:00 2016
From: "Kathrin Helen Hopmann kathrin.hopmann{}uit.no" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL:G: SV: CCL:G: CCL #DFT16poll results are out
Message-Id: <-52448-161020124905-19045-bl1Q1rLOCUIqiVPyAoncow:_:server.ccl.net>
X-Original-From: Kathrin Helen Hopmann <kathrin.hopmann .. uit.no>
Content-Language: nb-NO
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset="iso-8859-1"
Date: Thu, 20 Oct 2016 16:48:54 +0000
MIME-Version: 1.0


Sent to CCL by: Kathrin Helen Hopmann [kathrin.hopmann+/-uit.no]
>There will be no more responses from me on you posts.  I have used the CCL
>filter function to eliminate you from any CCL messages sent to me.

I cannot see that Mr. Lehtola has said anything that deserves this violent attack.  
On this list, there should be room for a scientific discussion without getting personal. 

Kathrin 
________________________________________
Fra: owner-chemistry+kathrin.hopmann==uit.no[-]ccl.net <owner-chemistry+kathrin.hopmann==uit.no[-]ccl.net> på vegne av Jim Kress jimkress35++gmail.com <owner-chemistry[-]ccl.net>
Sendt: 20. oktober 2016 16:11
Til: Kathrin Helen Hopmann
Emne: CCL:G: CCL #DFT16poll results are out

Sent to CCL by: "Jim Kress" [jimkress35]-[gmail.com]
> Besides, if you have access to those programs, then nothing prevents you
> from modifying them to link to libxc. This is far easier than
> reimplementing 250+ functionals yourself. [Out of the list, only NWChem is
open source.
> But even the closed-source programs could use libxc if they wanted to.]

Your last statement invalidates the rest of your post.  There is no point to
continuing this discussion.  I have already agreed that it is pointless
since the "poll antagonists" refuse to admit they might be incorrect and
still offer no solutions.  Modifying commercial code is not possible.
Modifying and validating NWChem and other available source codes is a time
consuming and laborious task.

If you want to waste your time doing that, fine.  I have better things to do
with the time and money I need to spend on doing actual research.

There will be no more responses from me on you posts.  I have used the CCL
filter function to eliminate you from any CCL messages sent to me.

Have a nice day.

-----Original Message-----
> From: owner-chemistry+jimkress35==gmail.com!^!ccl.net
[mailto:owner-chemistry+jimkress35==gmail.com!^!ccl.net] On Behalf Of Susi
Lehtola susi.lehtola_-_alumni.helsinki.fi
Sent: Wednesday, October 19, 2016 8:29 PM
To: Kress, Jim  <jimkress35!^!gmail.com>
Subject: CCL:G: CCL #DFT16poll results are out


Sent to CCL by: Susi Lehtola [susi.lehtola]*[alumni.helsinki.fi]
On 10/19/2016 08:28 AM, Jim Kress jimkress35 : gmail.com wrote:
>
> Sent to CCL by: "Jim Kress" [jimkress35,+,gmail.com] " ready to use in
> real calculations"
>
> Please show me where these functionals are available in Orca, Gamess,
> Firefly, Jaguar, Gaussian, NWChem or the other mainstream QC codes.

... but by the same standard you have completely invalidated the DFT poll
you have so strongheartedly been defending. Many functionals that made the
present poll aren't supported by those codes.

Besides, if you have access to those programs, then nothing prevents you
> from modifying them to link to libxc. This is far easier than
reimplementing 250+ functionals yourself. [Out of the list, only NWChem is
open source. But even the closed-source programs could use libxc if they
wanted to.]
--
-----------------------------------------------------------------------
Mr. Susi Lehtola, PhD             Chemist Postdoctoral Fellow
susi.lehtola(a)alumni.helsinki.fi   Lawrence Berkeley National Laboratory
http://www.helsinki.fi/~jzlehtol  USA
-----------------------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://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 Oct 20 17:23:01 2016
From: "Jim Kress jimkress35*gmail.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: DFT-Poll: Reviews and Perspectives
Message-Id: <-52449-161020170617-22360-98CTpUEdMzEXUEqITZh1sQ]_[server.ccl.net>
X-Original-From: "Jim Kress" <jimkress35,+,gmail.com>
Content-Language: en-us
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
	charset="us-ascii"
Date: Thu, 20 Oct 2016 17:05:55 -0400
MIME-Version: 1.0


Sent to CCL by: "Jim Kress" [jimkress35:_:gmail.com]
Marcel,

Excellent!  Thanks.

Jim

-----Original Message-----
> From: owner-chemistry+jimkress35==gmail.com**ccl.net
[mailto:owner-chemistry+jimkress35==gmail.com**ccl.net] On Behalf Of Marcel
Swart marcel.swart _ icrea.cat
Sent: Thursday, October 20, 2016 1:59 PM
To: Kress, Jim  <jimkress35**gmail.com>
Subject: CCL: DFT-Poll: Reviews and Perspectives


Sent to CCL by: "Marcel  Swart" [marcel.swart{}icrea.cat] Several people
have put forward the idea of adding reviews about and perspectives on DFT
into the news-item. Instead I think it is much more useful to have them on
the website, so here is the initial
batch:
http://www.marcelswart.eu/dft-poll/reviews.html

It will be updated in the coming days, if you have suggestions to be
included, please send me privately a mail with the DOI (or citation).

Marcel

_____________________________________
Prof Dr Marcel Swart, FRSC

ICREA Research Professor at
Institut de Qumica Computacional i Catlisi (IQCC) Univ. Girona (Spain)

COST Action CM1305 (ECOSTBio) chair
Girona Seminar 2016 organizer
IQCC director
Young Academy of Europe (Board) member

Web
http://www.marcelswart.eu
vCard
addressbook://www.marcelswart.eu/MSwart.vcfhttp://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 Oct 20 18:11:00 2016
From: "brupalf brupalf|umich.edu" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL: IR chemiluminescence?
Message-Id: <-52450-161020142246-14057-WDkPbahUhko+qyysdXN49g|,|server.ccl.net>
X-Original-From: brupalf <brupalf-#-umich.edu>
Content-Type: multipart/alternative; boundary="Apple-Mail=_56C767C1-7035-46AC-B56C-91606751451F"
Date: Thu, 20 Oct 2016 14:22:30 -0400
Mime-Version: 1.0 (Mac OS X Mail 9.3 \(3124\))


Sent to CCL by: brupalf [brupalf[-]umich.edu]

--Apple-Mail=_56C767C1-7035-46AC-B56C-91606751451F
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset=utf-8

A general, likely naive, question from an experimentalist:  If one were =
to simulate a gas-phase reaction by QM/MM, the transition structure =
could transform into a vibrationally excited product, depending, I =
guess, on the reaction and the state of the reactants. I mean, that =
energy has to be somewhere when things roll down the hill. =
Experimentally, that energy is sometimes emitted from the product and =
detected as IR radiation. Can that emission arise as a matter of course =
in =E2=80=9Cstandard" QM/MM simulations, or would such IR emission =
require separate/additional calculations?=20

ciao,
Bruce

Bruce A. Palfey
Associate Professor of Biological Chemistry &
Associate Director, Program in Chemical Biology
Department of Biological Chemistry
University of Michigan Medical School
5220E MSRB III
1150 W. Medical Center Drive
Ann Arbor, MI 48109-0606
(734) 615-2452
brupalf**umich.edu <mailto:brupalf**umich.edu>

http://www.biochem.med.umich.edu/?q=3Dpalfey =
<http://www.biochem.med.umich.edu/?q=3Dpalfey>
http://www.chembio.umich.edu/people/palfey.html =
<http://www.chembio.umich.edu/people/palfey.html>
http://tinyurl.com/webzyme


--Apple-Mail=_56C767C1-7035-46AC-B56C-91606751451F
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html;
	charset=utf-8

<html><head><meta http-equiv=3D"Content-Type" content=3D"text/html =
charset=3Dutf-8"></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" =
class=3D"">A general, likely naive, question from an experimentalist: =
&nbsp;If one were to simulate a gas-phase reaction by QM/MM, the =
transition structure could transform into a vibrationally excited =
product, depending, I guess, on the reaction and the state of the =
reactants. I mean, that energy has to be somewhere when things roll down =
the hill. Experimentally, that energy is sometimes emitted from the =
product and detected as IR radiation. Can that emission arise as a =
matter of course in =E2=80=9Cstandard" QM/MM simulations, or would such =
IR emission require separate/additional calculations?&nbsp;<br =
class=3D""><div class=3D"">
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-size: =
12px; font-style: normal; font-variant: normal; font-weight: normal; =
letter-spacing: normal; line-height: normal; orphans: 2; text-align: =
-webkit-auto; text-indent: 0px; text-transform: none; white-space: =
normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; =
-webkit-text-stroke-width: 0px; " class=3D""><br =
class=3D"Apple-interchange-newline">ciao,</div><div style=3D"color: =
rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: =
normal; font-variant: normal; font-weight: normal; letter-spacing: =
normal; line-height: normal; orphans: 2; text-align: -webkit-auto; =
text-indent: 0px; text-transform: none; white-space: normal; widows: 2; =
word-spacing: 0px; -webkit-text-size-adjust: auto; =
-webkit-text-stroke-width: 0px; " class=3D"">Bruce</div><div =
style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; =
font-style: normal; font-variant: normal; font-weight: normal; =
letter-spacing: normal; line-height: normal; orphans: 2; text-align: =
-webkit-auto; text-indent: 0px; text-transform: none; white-space: =
normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; =
-webkit-text-stroke-width: 0px; " class=3D""><br class=3D""></div><div =
style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; =
font-style: normal; font-variant: normal; font-weight: normal; =
letter-spacing: normal; line-height: normal; orphans: 2; text-align: =
-webkit-auto; text-indent: 0px; text-transform: none; white-space: =
normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; =
-webkit-text-stroke-width: 0px; " class=3D"">Bruce A. Palfey<br =
class=3D"">Associate Professor&nbsp;of Biological =
Chemistry&nbsp;&amp;</div><div style=3D"color: rgb(0, 0, 0); =
font-family: Helvetica; font-size: 12px; font-style: normal; =
font-variant: normal; font-weight: normal; letter-spacing: normal; =
line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: =
0px; text-transform: none; white-space: normal; widows: 2; word-spacing: =
0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; " =
class=3D"">Associate Director, Program in Chemical Biology<br =
class=3D"">Department of Biological Chemistry<br class=3D"">University =
of Michigan Medical School<br class=3D"">5220E MSRB III<br class=3D"">1150=
 W. Medical Center Drive<br class=3D"">Ann Arbor, MI 48109-0606<br =
class=3D"">(734) 615-2452<br class=3D""><a =
href=3D"mailto:brupalf**umich.edu" class=3D"">brupalf**umich.edu</a><br =
class=3D""><br class=3D""><a =
href=3D"http://www.biochem.med.umich.edu/?q=3Dpalfey" =
class=3D"">http://www.biochem.med.umich.edu/?q=3Dpalfey</a><br =
class=3D""><a href=3D"http://www.chembio.umich.edu/people/palfey.html" =
class=3D"">http://www.chembio.umich.edu/people/palfey.html</a><br =
class=3D""></div><div style=3D"color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: 12px; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: =
none; white-space: normal; widows: 2; word-spacing: 0px; =
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; " =
class=3D""><a href=3D"http://tinyurl.com/webzyme" =
class=3D"">http://tinyurl.com/webzyme</a></div>
</div>

<br class=3D""></body></html>=

--Apple-Mail=_56C767C1-7035-46AC-B56C-91606751451F--


From owner-chemistry@ccl.net Thu Oct 20 18:46:00 2016
From: "Susi Lehtola susi.lehtola||alumni.helsinki.fi" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: DFT-Poll: Reviews and Perspectives
Message-Id: <-52451-161020162118-12467-yBTSOfup0n4XbwKEL+jdVQ|a|server.ccl.net>
X-Original-From: Susi Lehtola <susi.lehtola/./alumni.helsinki.fi>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=windows-1252; format=flowed
Date: Thu, 20 Oct 2016 13:21:00 -0700
MIME-Version: 1.0


Sent to CCL by: Susi Lehtola [susi.lehtola[]alumni.helsinki.fi]
On 10/20/2016 10:58 AM, Marcel Swart marcel.swart _ icrea.cat wrote:
>
> Sent to CCL by: "Marcel  Swart" [marcel.swart{}icrea.cat]
> Several people have put forward the idea of adding reviews about and perspectives on DFT into the
> news-item. Instead I think it is much more useful to have them on the website, so here is the initial
> batch:
> http://www.marcelswart.eu/dft-poll/reviews.html
>
> It will be updated in the coming days, if you have suggestions to be included, please send me privately
> a mail with the DOI (or citation).

This is indeed an excellent addition. I would propose further that in 
addition to links to general reviews on DFT, it would be very useful to 
have property-specific lists of specialized reviews and benchmark papers.

However, when discussing functionals the basis set is also important. 
Namely, functional errors may fortuitously cancel with basis set 
incompleteness error, such as in the extremely successful B3LYP/6-31G* 
model (see e.g. doi 10.1021/jo302156p). Thus, it'd be good to include 
guidelines on the basis set in that listing as well, which should be 
available from the benchmark papers.
-- 
-----------------------------------------------------------------------
Mr. Susi Lehtola, PhD             Chemist Postdoctoral Fellow
susi.lehtola : alumni.helsinki.fi   Lawrence Berkeley National Laboratory
http://www.helsinki.fi/~jzlehtol  USA
-----------------------------------------------------------------------


From owner-chemistry@ccl.net Thu Oct 20 20:10:00 2016
From: "Yingduo Gao yingduo * yahoo.com" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL: Free program/software for calculating logD?
Message-Id: <-52452-161020192726-11945-lyOdRv+PibBw1RSj0IhxJw###server.ccl.net>
X-Original-From: Yingduo Gao <yingduo++yahoo.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_850567_236841069.1477006029700"
Date: Thu, 20 Oct 2016 23:27:09 +0000 (UTC)
MIME-Version: 1.0


Sent to CCL by: Yingduo Gao [yingduo ~ yahoo.com]
------=_Part_850567_236841069.1477006029700
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

Hi,=C2=A0
A medicinal chemistry friend in academia is looking for=C2=A0a freeprogram/=
software to calculate logD? Any info or suggestion will be really appreciat=
ed.

=C2=A0Thanks,

=C2=A0Ying


------=_Part_850567_236841069.1477006029700
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: 7bit

<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yui_3_16_0_ym19_1_1477005886488_3288" dir="ltr"><span style="color:#1F497D" id="yui_3_16_0_ym19_1_1477005886488_3289">Hi,&nbsp;</span></div><div id="yui_3_16_0_ym19_1_1477005886488_3288" dir="ltr"><span style="color:#1F497D"><br></span></div><div id="yui_3_16_0_ym19_1_1477005886488_3288" dir="ltr"><span style="color:#1F497D" id="yui_3_16_0_ym19_1_1477005886488_3312">A medicinal chemistry friend in academia is looking for&nbsp;a free
program/software to calculate logD? Any info or suggestion will be really appreciated.<o:p id="yui_3_16_0_ym19_1_1477005886488_3290"></o:p></span></div><div id="yui_3_16_0_ym19_1_1477005886488_3291"><span style="color:#1F497D" id="yui_3_16_0_ym19_1_1477005886488_3292">&nbsp;</span></div><div id="yui_3_16_0_ym19_1_1477005886488_3293"><span style="color:#1F497D" id="yui_3_16_0_ym19_1_1477005886488_3294">Thanks,<o:p id="yui_3_16_0_ym19_1_1477005886488_3295"></o:p></span></div><div id="yui_3_16_0_ym19_1_1477005886488_3296"><span style="color:#1F497D" id="yui_3_16_0_ym19_1_1477005886488_3297">&nbsp;</span></div><div id="yui_3_16_0_ym19_1_1477005886488_3085">







</div><div dir="ltr" id="yui_3_16_0_ym19_1_1477005886488_3298"><span style="color:#1F497D" id="yui_3_16_0_ym19_1_1477005886488_3299">Ying<o:p id="yui_3_16_0_ym19_1_1477005886488_3300"></o:p></span></div></div></body></html>
------=_Part_850567_236841069.1477006029700--


From owner-chemistry@ccl.net Thu Oct 20 22:22:00 2016
From: "Brian Skinn bskinn*alum.mit.edu" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: IR chemiluminescence?
Message-Id: <-52453-161020204042-16665-uohzEWuFj72l/wF/S18Cjw|-|server.ccl.net>
X-Original-From: Brian Skinn <bskinn:_:alum.mit.edu>
Content-Type: multipart/alternative; boundary=001a1144023653c7ca053f554a41
Date: Thu, 20 Oct 2016 20:40:14 -0400
MIME-Version: 1.0


Sent to CCL by: Brian Skinn [bskinn[A]alum.mit.edu]
--001a1144023653c7ca053f554a41
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

Bruce,

No, those data would not fall out of 'standard' QM/MM simulation, or even
fully quantum MD simulations.

Both types routinely use the Born-Oppenheimer approximation, where nuclear
and electronic motions are taken to be independent. The Further
approximation of classical (non-quantum mechanical) motion of the nuclei is
also typically introduced. This classical treatment of nuclear motion
eliminates any notion of vibrational quantization that would be necessary
for the simulations to naturally 'spin out' IR emission information.

Additional processing of the MD simulation results would be required to
obtain such information, if it is even possible to do so.

-Brian

On Thu, Oct 20, 2016 at 2:22 PM, brupalf brupalf|umich.edu <
owner-chemistry_-_ccl.net> wrote:

> A general, likely naive, question from an experimentalist:  If one were t=
o
> simulate a gas-phase reaction by QM/MM, the transition structure could
> transform into a vibrationally excited product, depending, I guess, on th=
e
> reaction and the state of the reactants. I mean, that energy has to be
> somewhere when things roll down the hill. Experimentally, that energy is
> sometimes emitted from the product and detected as IR radiation. Can that
> emission arise as a matter of course in =E2=80=9Cstandard" QM/MM simulati=
ons, or
> would such IR emission require separate/additional calculations?
>
> ciao,
> Bruce
>
> Bruce A. Palfey
> Associate Professor of Biological Chemistry &
> Associate Director, Program in Chemical Biology
> Department of Biological Chemistry
> University of Michigan Medical School
> 5220E MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor, MI 48109-0606
> (734) 615-2452
> brupalf{}umich.edu
>
> http://www.biochem.med.umich.edu/?q=3Dpalfey
> http://www.chembio.umich.edu/people/palfey.html
> http://tinyurl.com/webzyme
>
>

--001a1144023653c7ca053f554a41
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr">Bruce,<div><br></div><div>No, those data would not fall ou=
t of &#39;standard&#39; QM/MM simulation, or even fully quantum MD simulati=
ons.</div><div><br></div><div>Both types routinely use the Born-Oppenheimer=
 approximation, where nuclear and electronic motions are taken to be indepe=
ndent. The Further approximation of classical (non-quantum mechanical) moti=
on of the nuclei is also typically introduced. This classical treatment of =
nuclear motion eliminates any notion of vibrational quantization that would=
 be necessary for the simulations to naturally &#39;spin out&#39; IR emissi=
on information.</div><div><br></div><div>Additional processing of the MD si=
mulation results would be required to obtain such information, if it is eve=
n possible to do so.</div><div><br></div><div>-Brian</div></div><div class=
=3D"gmail_extra"><br><div class=3D"gmail_quote">On Thu, Oct 20, 2016 at 2:2=
2 PM, brupalf brupalf|<a href=3D"http://umich.edu">umich.edu</a> <span dir=
=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry_-_ccl.net" target=3D"_blank">o=
wner-chemistry_-_ccl.net</a>&gt;</span> wrote:<br><blockquote class=3D"gmail_=
quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1=
ex"><div style=3D"word-wrap:break-word">A general, likely naive, question f=
rom an experimentalist: =C2=A0If one were to simulate a gas-phase reaction =
by QM/MM, the transition structure could transform into a vibrationally exc=
ited product, depending, I guess, on the reaction and the state of the reac=
tants. I mean, that energy has to be somewhere when things roll down the hi=
ll. Experimentally, that energy is sometimes emitted from the product and d=
etected as IR radiation. Can that emission arise as a matter of course in =
=E2=80=9Cstandard&quot; QM/MM simulations, or would such IR emission requir=
e separate/additional calculations?=C2=A0<br><div>
<div style=3D"color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-st=
yle:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;lin=
e-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none=
;white-space:normal;word-spacing:0px"><br class=3D"m_8250174149552602876App=
le-interchange-newline">ciao,</div><div style=3D"color:rgb(0,0,0);font-fami=
ly:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weig=
ht:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;=
text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Br=
uce</div><div style=3D"color:rgb(0,0,0);font-family:Helvetica;font-size:12p=
x;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:n=
ormal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-trans=
form:none;white-space:normal;word-spacing:0px"><br></div><div style=3D"colo=
r:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-va=
riant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;te=
xt-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:norma=
l;word-spacing:0px">Bruce A. Palfey<br>Associate Professor=C2=A0of Biologic=
al Chemistry=C2=A0&amp;</div><div style=3D"color:rgb(0,0,0);font-family:Hel=
vetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:nor=
mal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-i=
ndent:0px;text-transform:none;white-space:normal;word-spacing:0px">Associat=
e Director, Program in Chemical Biology<br>Department of Biological Chemist=
ry<br>University of Michigan Medical School<br>5220E MSRB III<br>1150 W. Me=
dical Center Drive<br>Ann Arbor, MI 48109-0606<br><a href=3D"tel:%28734%29%=
20615-2452" value=3D"+17346152452" target=3D"_blank">(734) 615-2452</a><br>=
<a href=3D"mailto:brupalf%7B%7Dumich.edu" target=3D"_blank">brupalf{}umich.=
edu</a><br><br><a href=3D"http://www.biochem.med.umich.edu/?q=3Dpalfey" tar=
get=3D"_blank">http://www.biochem.med.umich.<wbr>edu/?q=3Dpalfey</a><br><a =
href=3D"http://www.chembio.umich.edu/people/palfey.html" target=3D"_blank">=
http://www.chembio.umich.edu/<wbr>people/palfey.html</a><br></div><div styl=
e=3D"color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:norma=
l;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:=
normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-sp=
ace:normal;word-spacing:0px"><a href=3D"http://tinyurl.com/webzyme" target=
=3D"_blank">http://tinyurl.com/webzyme</a></div>
</div>

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

--001a1144023653c7ca053f554a41--


From owner-chemistry@ccl.net Thu Oct 20 22:57:00 2016
From: "rjensen-#-ualberta.ca" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: Free program/software for calculating logD?
Message-Id: <-52454-161020215306-13726-SeJ9tFt3NUkDlIwi70iy1Q+/-server.ccl.net>
X-Original-From: rjensen*ualberta.ca
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Thu, 20 Oct 2016 19:52:56 -0600
MIME-Version: 1.0


Sent to CCL by: rjensen^ualberta.ca
Have your friend contact me. I am not sure what you mean by 'calculate
logD'. I know what logD is, but now what you want to calculate.

Thanks,
 Dr. Roy Jensen
(==========)-----------------------------------------€
 Lecturer, Chemistry
 W5-19, University of Alberta
 780.248.1808



On Thu, 20 Oct 2016 23:27:09 +0000 (UTC), you wrote:

>Hi, 
>A medicinal chemistry friend in academia is looking for a freeprogram/software to calculate logD? Any info or suggestion will be really appreciated.
>
> Thanks,
>
> Ying