From owner-chemistry@ccl.net Tue Aug 28 10:09:01 2012
From: "G. Gopakumar gopakumar.gopinadhan]^[gmail.com" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: Dihedral angle: DFT vs Crystal structure
Message-Id: <-47488-120828100717-3022-gtvYJwapujSrFo5NB0D/7w[a]server.ccl.net>
X-Original-From: "G. Gopakumar" <gopakumar.gopinadhan()gmail.com>
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Date: Tue, 28 Aug 2012 16:06:26 +0200
MIME-Version: 1.0


Sent to CCL by: "G. Gopakumar" [gopakumar.gopinadhan]*[gmail.com]
--f46d044481d71c951704c853f5a1
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Dear CCL members,

     I was calculating a molecule (71 atoms) for which the crystal
structure is
known. However, according to my calculation, one of the dihedral angles
shows
large mismatch (deviation of 12 degrees). I repeated the calculation with
both
B3LYP and BP86 functional and the values are given below:

B3LYP/def2-TZVP   ~ 21.2
BP86/def2-TZVP     ~ 20
Experimental          ~ 8.1

I would not worry too much if it was 2-3 degree deviation, but 12 is
something
that I should be careful with.

I was wondering, whether there is a chance for an experimental error? Or is
it
just that DFT overestimates the dihedral angle? Does any body know any
references
where people encountered similar problem.

I would be thankful for your comments

with kind regards

Gopakumar

--f46d044481d71c951704c853f5a1
Content-Type: text/html; charset=ISO-8859-1
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Dear CCL members,<br><br>=A0=A0=A0=A0 I was calculating a molecule (71 atom=
s) for which the crystal structure is<br>known. However, according to my ca=
lculation, one of the dihedral angles shows<br>large mismatch (deviation of=
 12 degrees). I repeated the calculation with both<br>

B3LYP and BP86 functional and the values are given below:<br><br>B3LYP/def2=
-TZVP=A0=A0 ~ 21.2 <br>BP86/def2-TZVP=A0=A0=A0=A0 ~ 20<br>Experimental=A0=
=A0=A0=A0=A0=A0=A0=A0=A0 ~ 8.1<br><br>I would not worry too much if it was =
2-3 degree deviation, but 12 is something<br>

that I should be careful with.<br><br>I was wondering, whether there is a c=
hance for an experimental error? Or is it<br>just that DFT overestimates th=
e dihedral angle? Does any body know any references<br>where people encount=
ered similar problem.<br>

<br>I would be thankful for your comments<br><br>with kind regards<br><br>G=
opakumar<br clear=3D"all"><br><br>

--f46d044481d71c951704c853f5a1--


From owner-chemistry@ccl.net Tue Aug 28 10:54:00 2012
From: "Cina Foroutan-Nejad canyslopus,+,yahoo.co.uk" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: Dihedral angle: DFT vs Crystal structure
Message-Id: <-47489-120828104532-18905-Mnthp+TvdBmDsvvzrnyGOQ||server.ccl.net>
X-Original-From: Cina Foroutan-Nejad <canyslopus-*-yahoo.co.uk>
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Date: Tue, 28 Aug 2012 15:45:20 +0100 (BST)
MIME-Version: 1.0


Sent to CCL by: Cina Foroutan-Nejad [canyslopus_+_yahoo.co.uk]
--1507048413-54790685-1346165120=:23824
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Dear Gopakumar,=0A=0AYou did not mention but I guess you have studied your =
molecule in gas phase by DFT (if not please provide some details). You shou=
ld not expect to see the solid phase geometry in gas phase! In solid phase =
several effects particularly influence of other molecules in the crystal pa=
cking affect the geometry. A famous example in this case is biphenyl. You m=
ay know that in the gas phase the dihedral anglebetween two phenyl rings is=
 ~44 degrees but in solid phase the angle reduces to 0! If you compute geom=
etry of biphenyl at any DFT or any other computational level you will see t=
hat the solid state geometry is a first order saddle point, i.e. TS.=0ABe c=
areful in interpretation of gas phase computations and comparing them with =
X-ray crystallography data...=0A=0A=0AGood luck,=0ACina=0A=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=0ACina Foroutan-Nejad, Ph.D.=0Ahttp://independent.academia.=
edu/CinaForoutanNejad=0A=0A=0A=0A________________________________=0A From: =
G. Gopakumar gopakumar.gopinadhan]^[gmail.com <owner-chemistry() ccl.net>=0AT=
o: "Foroutan-Nejad, Cina " <canyslopus() yahoo.co.uk> =0ASent: Tuesda=
y, 28 August 2012, 17:36=0ASubject: CCL: Dihedral angle: DFT vs Crystal str=
ucture=0A =0A=0ADear CCL members,=0A=0A=A0=A0=A0=A0 I was calculating a mol=
ecule (71 atoms) for which the crystal structure is=0Aknown. However, accor=
ding to my calculation, one of the dihedral angles shows=0Alarge mismatch (=
deviation of 12 degrees). I repeated the calculation with both=0AB3LYP and =
BP86 functional and the values are given below:=0A=0AB3LYP/def2-TZVP=A0=A0 =
~ 21.2 =0ABP86/def2-TZVP=A0=A0=A0=A0 ~ 20=0AExperimental=A0=A0=A0=A0=A0=A0=
=A0=A0=A0 ~ 8.1=0A=0AI would not worry too much if it was 2-3 degree deviat=
ion, but 12 is something=0Athat I should be careful with.=0A=0AI was wonder=
ing, whether there is a chance for an experimental error? Or is it=0Ajust t=
hat DFT overestimates the dihedral angle? Does any body know any references=
=0Awhere people encountered similar problem.=0A=0AI would be thankful for y=
our comments=0A=0Awith kind regards=0A=0AGopakumar
--1507048413-54790685-1346165120=:23824
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<html><body><div style=3D"color:#000; background-color:#fff; font-family:bo=
okman old style, new york, times, serif;font-size:12pt"><div><span>Dear Gop=
akumar,</span></div><div style=3D"color: rgb(0, 0, 0); font-size: 16px; fon=
t-family: bookman old style,new york,times,serif; background-color: transpa=
rent; font-style: normal;"><br><span></span></div><div style=3D"color: rgb(=
0, 0, 0); font-size: 16px; font-family: bookman old style,new york,times,se=
rif; background-color: transparent; font-style: normal;"><span>You did not =
mention but I guess you have studied your molecule in gas phase by DFT (if =
not please provide some details). You should not expect to see the solid ph=
ase geometry in gas phase! In solid phase several effects particularly infl=
uence of other molecules in the crystal packing affect the geometry. A famo=
us example in this case is biphenyl. You may know that in the gas phase the=
 dihedral angl</span><span>e</span><span> between two phenyl rings is ~44
 degrees but in solid phase the angle reduces to 0! If you compute geometry=
 of biphenyl at any DFT or any other computational level you will see that =
the solid state geometry is a first order saddle point, i.e. TS.</span></di=
v><div style=3D"color: rgb(0, 0, 0); font-size: 16px; font-family: bookman =
old style,new york,times,serif; background-color: transparent; font-style: =
normal;"><span>Be careful in interpretation of gas phase computations and c=
omparing them with X-ray crystallography data...</span></div><div style=3D"=
color: rgb(0, 0, 0); font-size: 16px; font-family: bookman old style,new yo=
rk,times,serif; background-color: transparent; font-style: normal;"><br><sp=
an></span></div><div style=3D"color: rgb(0, 0, 0); font-size: 16px; font-fa=
mily: bookman old style,new york,times,serif; background-color: transparent=
; font-style: normal;"><br><span></span></div><div style=3D"color: rgb(0, 0=
, 0); font-size: 16px; font-family: bookman old style,new york,times,serif;
 background-color: transparent; font-style: normal;"><span>Good luck,</span=
></div><div style=3D"color: rgb(0, 0, 0); font-size: 16px; font-family: boo=
kman old style,new york,times,serif; background-color: transparent; font-st=
yle: normal;"><span>Cina</span></div><div style=3D"color: rgb(0, 0, 0); fon=
t-size: 16px; font-family: bookman old style,new york,times,serif; backgrou=
nd-color: transparent; font-style: normal;"><span>=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D</span></div><div style=3D"color: rgb(0, 0, 0); font-size: 16px; font=
-family: bookman old style,new york,times,serif; background-color: transpar=
ent; font-style: normal;"><span>Cina Foroutan-Nejad, Ph.D.</span></div><div=
 style=3D"color: rgb(0, 0, 0); font-size: 16px; font-family: bookman old st=
yle,new york,times,serif; background-color: transparent; font-style: normal=
;"><span>http://independent.academia.edu/CinaForoutanNejad</span></div><div=
><br></div>  <div style=3D"font-family: bookman
 old style, new york, times, serif; font-size: 12pt;"> <div style=3D"font-f=
amily: times new roman, new york, times, serif; font-size: 12pt;"> <div dir=
=3D"ltr"> <font face=3D"Arial" size=3D"2"> <hr size=3D"1">  <b><span style=
=3D"font-weight:bold;">From:</span></b> G. Gopakumar gopakumar.gopinadhan]^=
[gmail.com &lt;owner-chemistry() ccl.net&gt;<br> <b><span style=3D"font-weigh=
t: bold;">To:</span></b> "Foroutan-Nejad, Cina " &lt;canyslopus() yah=
oo.co.uk&gt; <br> <b><span style=3D"font-weight: bold;">Sent:</span></b> Tu=
esday, 28 August 2012, 17:36<br> <b><span style=3D"font-weight: bold;">Subj=
ect:</span></b> CCL: Dihedral angle: DFT vs Crystal structure<br> </font> <=
/div> <br><div id=3D"yiv398633065">Dear CCL members,<br><br>&nbsp;&nbsp;&nb=
sp;&nbsp; I was calculating a molecule (71 atoms) for which the crystal str=
ucture is<br>known. However, according to my calculation, one of the dihedr=
al angles shows<br>large mismatch (deviation of 12 degrees). I repeated the=
 calculation
 with both<br>=0A=0AB3LYP and BP86 functional and the values are given belo=
w:<br><br>B3LYP/def2-TZVP&nbsp;&nbsp; ~ 21.2 <br>BP86/def2-TZVP&nbsp;&nbsp;=
&nbsp;&nbsp; ~ 20<br>Experimental&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp; ~ 8.1<br><br>I would not worry too much if it was 2-3 degree d=
eviation, but 12 is something<br>=0A=0Athat I should be careful with.<br><b=
r>I was wondering, whether there is a chance for an experimental error? Or =
is it<br>just that DFT overestimates the dihedral angle? Does any body know=
 any references<br>where people encountered similar problem.<br>=0A=0A<br>I=
 would be thankful for your comments<br><br>with kind regards<br><br>Gopaku=
mar<br clear=3D"all"><br><br>=0A</div><br><br> </div> </div>  </div></body>=
</html>
--1507048413-54790685-1346165120=:23824--


From owner-chemistry@ccl.net Tue Aug 28 11:37:00 2012
From: "Eike Huebner ccl*eike-huebner.de" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL: Dihedral angle: DFT vs Crystal structure
Message-Id: <-47490-120828112912-15405-NNFvjE6GETFAMxTNgTQGPA-$-server.ccl.net>
X-Original-From: "Eike Huebner" <ccl,+,eike-huebner.de>
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Date: Tue, 28 Aug 2012 17:29:09 +0200
Mime-Version: 1.0


Sent to CCL by: "Eike Huebner" [ccl*eike-huebner.de]

Usually, in these cases the energy difference of the structures at the given dihedral angles is very small. If you are interested a bit more in detail, you could calculate the rotational barrier (at fixed dihedral angles, in steps from something around 5 ° beginning at the energy minimum for example) around your dihedral angle. In most of these cases, you will find the energy difference between the nimimum and the crystal structure to be in the range of some kJ/mol, which is easily compensated by crystal packing effects, pi-stacking, hydrogen bonding and so on.

*********** REPLY SEPARATOR  ***********

________________________________
 From: G. Gopakumar gopakumar.gopinadhan]^[gmail.com <owner-chemistry]|[ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus]|[yahoo.co.uk> 
Sent: Tuesday, 28 August 2012, 17:36
Subject: CCL: Dihedral angle: DFT vs Crystal structure
 

Dear CCL members,

     I was calculating a molecule (71 atoms) for which the crystal structure is
known. However, according to my calculation, one of the dihedral angles shows
large mismatch (deviation of 12 degrees). I repeated the calculation with both
B3LYP and BP86 functional and the values are given below:

B3LYP/def2-TZVP   ~ 21.2 
BP86/def2-TZVP     ~ 20
Experimental          ~ 8.1

I would not worry too much if it was 2-3 degree deviation, but 12 is something
that I should be careful with.

I was wondering, whether there is a chance for an experimental error? Or is it
just that DFT overestimates the dihedral angle? Does any body know any references
where people encountered similar problem.

I would be thankful for your comments

with kind regards

Gopakumar

From owner-chemistry@ccl.net Tue Aug 28 13:59:00 2012
From: "haya kornweitz hayak]|[ariel.ac.il" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: What is the scaling parameter in VASP
Message-Id: <-47491-120828135707-4000-iMsFkmoTzocQYFvDluq9eA^server.ccl.net>
X-Original-From: "haya  kornweitz" <hayak-#-ariel.ac.il>
Date: Tue, 28 Aug 2012 13:57:06 -0400


Sent to CCL by: "haya  kornweitz" [hayak*|*ariel.ac.il]
Can someone explain what is the scaling parameter in POSCAR file in VASP?
How can it be calculated?
I'll be grateful for any information
Haya


From owner-chemistry@ccl.net Tue Aug 28 14:34:00 2012
From: "Alexander Kos software[#]akosgmbh.de" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL:G: Free version of CWM Global Search - the Internet Search Engine for Chemists and Biologists
Message-Id: <-47492-120828094253-1630-oC/fxK4Jbgk5mR8xDh+GWw_._server.ccl.net>
X-Original-From: "Alexander Kos" <software^akosgmbh.de>
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Sent to CCL by: "Alexander Kos" [software^akosgmbh.de]
This is a multipart message in MIME format.

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------=_NextPart_000_012F_01CD8533.FCEDED90--


From owner-chemistry@ccl.net Tue Aug 28 15:09:00 2012
From: "M. Nicklaus mn1 : helix.nih.gov" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL: Dihedral angle: DFT vs Crystal structure
Message-Id: <-47493-120828132115-2141-ivxrZrvIj0IcXD8xJkGTaw]![server.ccl.net>
X-Original-From: "M. Nicklaus" <mn1+/-helix.nih.gov>
Content-Type: multipart/mixed; boundary="13144343-29567-1346174444=:2364"
Date: Tue, 28 Aug 2012 13:20:44 -0400
MIME-Version: 1.0


Sent to CCL by: "M. Nicklaus" [mn1]*[helix.nih.gov]
--13144343-29567-1346174444=:2364
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
Content-Transfer-Encoding: 8BIT

I fully agree with Cina.

We recently published a study of several hundred instances of small molecules 
bound to protein structures in the PDB (Sitzmann et al., PDB Ligand 
Conformational Energies Calculated Quantum-Mechanically, J. Chem. Inf. Model., 
52(3), 739-756, 2012).  In this context, we also looked at a number of 
small-molecule crystal structures in the CSD.

The upshot was that significant changes both in geometry and energy vs. the 
vacuum (or gas phase) structure are possible in any crystal environment.

Marc

------------------------------------------------------------------------
  Marc C. Nicklaus, Ph.D.                 Frederick National Lab
  E-mail: mn1-.-helix.nih.gov               Bldg 376, Rm 207
  Phone:  (301) 846-5903                  376 Boyles Street
  Fax:    (301) 846-6033                  FREDERICK, MD 21702      USA
             Head, Computer-Aided Drug Design (CADD) Group
        Chemical Biology Laboratory, Center for Cancer Research,
        National Cancer Institute, National Institutes of Health
            Frederick National Laboratory for Cancer Research
          http://ccr.cancer.gov/Staff/Staff.asp?profileid=6282
            CADD Group Web Server: http://cactus.nci.nih.gov
------------------------------------------------------------------------



On Tue, 28 Aug 2012, Cina Foroutan-Nejad canyslopus,+,yahoo.co.uk wrote:

Dear Gopakumar,

You did not mention but I guess you have studied your molecule in gas phase by DFT (if not please provide some details). You should not expect to see the solid phase geometry in gas phase! In solid phase several effects particularly influence of other molecules in the crystal packing affect the geometry. A famous example in this case is biphenyl. You may know that in the gas phase the dihedral anglebetween two phenyl rings is ~44 degrees but in solid phase the angle reduces to 0! If you compute geometry of biphenyl at any DFT or any other computational level you will see that the solid state geometry is a first order saddle point, i.e. TS.
Be careful in interpretation of gas phase computations and comparing them with X-ray crystallography data...


Good luck,
Cina
============================================================
Cina Foroutan-Nejad, Ph.D.
http://independent.academia.edu/CinaForoutanNejad



________________________________
  From: G. Gopakumar gopakumar.gopinadhan]^[gmail.com <owner-chemistry]|[ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus]|[yahoo.co.uk> 
Sent: Tuesday, 28 August 2012, 17:36
Subject: CCL: Dihedral angle: DFT vs Crystal structure


Dear CCL members,

     I was calculating a molecule (71 atoms) for which the crystal structure is
known. However, according to my calculation, one of the dihedral angles shows
large mismatch (deviation of 12 degrees). I repeated the calculation with both
B3LYP and BP86 functional and the values are given below:

B3LYP/def2-TZVP   ~ 21.2 
BP86/def2-TZVP     ~ 20
Experimental          ~ 8.1

I would not worry too much if it was 2-3 degree deviation, but 12 is something
that I should be careful with.

I was wondering, whether there is a chance for an experimental error? Or is it
just that DFT overestimates the dihedral angle? Does any body know any references
where people encountered similar problem.

I would be thankful for your comments

with kind regards

Gopakumar
--13144343-29567-1346174444=:2364--


From owner-chemistry@ccl.net Tue Aug 28 16:35:00 2012
From: "Mark Zottola mzottola*o*gmail.com" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: Dihedral angle: DFT vs Crystal structure
Message-Id: <-47494-120828161333-1867-zxcczLYp0krpCIk8gIodMg=-=server.ccl.net>
X-Original-From: Mark Zottola <mzottola^gmail.com>
Content-Type: multipart/alternative; boundary=20cf302d4d6202b24804c859131a
Date: Tue, 28 Aug 2012 16:13:23 -0400
MIME-Version: 1.0


Sent to CCL by: Mark Zottola [mzottola,,gmail.com]
--20cf302d4d6202b24804c859131a
Content-Type: text/plain; charset=ISO-8859-1

While in the main I can agree that molecules in a crystal structure can
have different geometries than those in the gas phase, there is usually a
reason why the difference exists.  However, just using the idea of solid
state effects as a nebulous rationalization for those differences is not
justified nor intellectually honest.

TO be clear, I fully agree with with Dr. Nicklaus' statement that
"significant changes both in geometry and energy vs. the vacuum (or gas
phase) structure are possible in any crystal environment".  However, in
relation to the original poster, just because differences can occur is not
sufficient rationalization for a difference.

On Tue, Aug 28, 2012 at 1:20 PM, M. Nicklaus mn1 : helix.nih.gov <
owner-chemistry{}ccl.net> wrote:

> I fully agree with Cina.
>
> We recently published a study of several hundred instances of small
> molecules bound to protein structures in the PDB (Sitzmann et al., PDB
> Ligand Conformational Energies Calculated Quantum-Mechanically, J. Chem.
> Inf. Model., 52(3), 739-756, 2012).  In this context, we also looked at a
> number of small-molecule crystal structures in the CSD.
>
> The upshot was that significant changes both in geometry and energy vs.
> the vacuum (or gas phase) structure are possible in any crystal environment.
>
> Marc
>
> ------------------------------**------------------------------**
> ------------
>  Marc C. Nicklaus, Ph.D.                 Frederick National Lab
>  E-mail: mn1!^!helix.nih.gov               Bldg 376, Rm 207
>  Phone:  (301) 846-5903                  376 Boyles Street
>  Fax:    (301) 846-6033                  FREDERICK, MD 21702      USA
>             Head, Computer-Aided Drug Design (CADD) Group
>        Chemical Biology Laboratory, Center for Cancer Research,
>        National Cancer Institute, National Institutes of Health
>            Frederick National Laboratory for Cancer Research
>          http://ccr.cancer.gov/Staff/**Staff.asp?profileid=6282<http://ccr.cancer.gov/Staff/Staff.asp?profileid=6282>
>            CADD Group Web Server: http://cactus.nci.nih.gov
> ------------------------------**------------------------------**
> ------------
>
>
>
>
> On Tue, 28 Aug 2012, Cina Foroutan-Nejad canyslopus,+,yahoo.co.uk wrote:
>
> Dear Gopakumar,
>
> You did not mention but I guess you have studied your molecule in gas
> phase by DFT (if not please provide some details). You should not expect to
> see the solid phase geometry in gas phase! In solid phase several effects
> particularly influence of other molecules in the crystal packing affect the
> geometry. A famous example in this case is biphenyl. You may know that in
> the gas phase the dihedral anglebetween two phenyl rings is ~44 degrees but
> in solid phase the angle reduces to 0! If you compute geometry of biphenyl
> at any DFT or any other computational level you will see that the solid
> state geometry is a first order saddle point, i.e. TS.
>
> Be careful in interpretation of gas phase computations and comparing them
> with X-ray crystallography data...
>
>
> Good luck,
> Cina
> ==============================**==============================
> Cina Foroutan-Nejad, Ph.D.
> http://independent.academia.**edu/CinaForoutanNejad<http://independent.academia.edu/CinaForoutanNejad>
>
>
>
> ______________________________**__
>  From: G. Gopakumar gopakumar.gopinadhan]^[gmail.**com <http://gmail.com><owner-chemistry]|[
> ccl.net>
> To: "Foroutan-Nejad, Cina " <canyslopus]|[yahoo.co.uk> Sent: Tuesday, 28
> August 2012, 17:36
> Subject: CCL: Dihedral angle: DFT vs Crystal structure
>
>
> Dear CCL members,
>
>      I was calculating a molecule (71 atoms) for which the crystal
> structure is
> known. However, according to my calculation, one of the dihedral angles
> shows
> large mismatch (deviation of 12 degrees). I repeated the calculation with
> both
> B3LYP and BP86 functional and the values are given below:
>
> B3LYP/def2-TZVP   ~ 21.2 BP86/def2-TZVP     ~ 20
> Experimental          ~ 8.1
>
> I would not worry too much if it was 2-3 degree deviation, but 12 is
> something
> that I should be careful with.
>
> I was wondering, whether there is a chance for an experimental error? Or
> is it
> just that DFT overestimates the dihedral angle? Does any body know any
> references
> where people encountered similar problem.
>
> I would be thankful for your comments
>
> with kind regards
>
> Gopakumar
>

--20cf302d4d6202b24804c859131a
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

While in the main I can agree that molecules in a crystal structure can hav=
e different geometries than those in the gas phase, there is usually a reas=
on why the difference exists. =A0However, just using the idea of solid stat=
e effects as a nebulous rationalization for those differences is not justif=
ied nor intellectually honest. =A0<div>
<br></div><div>TO be clear, I fully agree with with Dr. Nicklaus&#39; state=
ment that &quot;significant changes both in geometry and energy vs. the vac=
uum (or gas phase) structure are possible in any crystal environment&quot;.=
 =A0However, in relation to the original poster, just because differences c=
an occur is not sufficient rationalization for a difference. =A0<br>
<div><br><div class=3D"gmail_quote">On Tue, Aug 28, 2012 at 1:20 PM, M. Nic=
klaus mn1 : <a href=3D"http://helix.nih.gov">helix.nih.gov</a> <span dir=3D=
"ltr">&lt;<a href=3D"mailto:owner-chemistry{}ccl.net" target=3D"_blank">owne=
r-chemistry{}ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">I fully agree with Cina.<br>
<br>
We recently published a study of several hundred instances of small molecul=
es bound to protein structures in the PDB (Sitzmann et al., PDB Ligand Conf=
ormational Energies Calculated Quantum-Mechanically, J. Chem. Inf. Model., =
52(3), 739-756, 2012). =A0In this context, we also looked at a number of sm=
all-molecule crystal structures in the CSD.<br>

<br>
The upshot was that significant changes both in geometry and energy vs. the=
 vacuum (or gas phase) structure are possible in any crystal environment.<b=
r>
<br>
Marc<br>
<br>
------------------------------<u></u>------------------------------<u></u>-=
-----------<br>
=A0Marc C. Nicklaus, Ph.D. =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Frederick Nation=
al Lab<br>
=A0E-mail: mn1!^!<a href=3D"http://helix.nih.gov" target=3D"_blank">helix.n=
ih.gov</a> =A0 =A0 =A0 =A0 =A0 =A0 =A0 Bldg 376, Rm 207<br>
=A0Phone: =A0<a href=3D"tel:%28301%29%20846-5903" value=3D"+13018465903" ta=
rget=3D"_blank">(301) 846-5903</a> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0376 B=
oyles Street<br>
=A0Fax: =A0 =A0<a href=3D"tel:%28301%29%20846-6033" value=3D"+13018466033" =
target=3D"_blank">(301) 846-6033</a> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0FRE=
DERICK, MD 21702 =A0 =A0 =A0USA<br>
=A0 =A0 =A0 =A0 =A0 =A0 Head, Computer-Aided Drug Design (CADD) Group<br>
=A0 =A0 =A0 =A0Chemical Biology Laboratory, Center for Cancer Research,<br>
=A0 =A0 =A0 =A0National Cancer Institute, National Institutes of Health<br>
=A0 =A0 =A0 =A0 =A0 =A0Frederick National Laboratory for Cancer Research<br=
>
=A0 =A0 =A0 =A0 =A0<a href=3D"http://ccr.cancer.gov/Staff/Staff.asp?profile=
id=3D6282" target=3D"_blank">http://ccr.cancer.gov/Staff/<u></u>Staff.asp?p=
rofileid=3D6282</a><br>
=A0 =A0 =A0 =A0 =A0 =A0CADD Group Web Server: <a href=3D"http://cactus.nci.=
nih.gov" target=3D"_blank">http://cactus.nci.nih.gov</a><br>
------------------------------<u></u>------------------------------<u></u>-=
-----------<div class=3D"im"><br>
<br>
<br>
<br>
On Tue, 28 Aug 2012, Cina Foroutan-Nejad canyslopus,+,<a href=3D"http://yah=
oo.co.uk" target=3D"_blank">yahoo.co.uk</a> wrote:<br>
<br>
Dear Gopakumar,<br>
<br></div>
You did not mention but I guess you have studied your molecule in gas phase=
 by DFT (if not please provide some details). You should not expect to see =
the solid phase geometry in gas phase! In solid phase several effects parti=
cularly influence of other molecules in the crystal packing affect the geom=
etry. A famous example in this case is biphenyl. You may know that in the g=
as phase the dihedral anglebetween two phenyl rings is ~44 degrees but in s=
olid phase the angle reduces to 0! If you compute geometry of biphenyl at a=
ny DFT or any other computational level you will see that the solid state g=
eometry is a first order saddle point, i.e. TS.<div class=3D"im HOEnZb">
<br>
Be careful in interpretation of gas phase computations and comparing them w=
ith X-ray crystallography data...<br>
<br>
<br>
Good luck,<br>
Cina<br>
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D<u></u>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<br>
Cina Foroutan-Nejad, Ph.D.<br>
<a href=3D"http://independent.academia.edu/CinaForoutanNejad" target=3D"_bl=
ank">http://independent.academia.<u></u>edu/CinaForoutanNejad</a><br>
<br>
<br>
<br></div><div class=3D"HOEnZb"><div class=3D"h5">
______________________________<u></u>__<br>
=A0From: G. Gopakumar gopakumar.gopinadhan]^[<a href=3D"http://gmail.com" t=
arget=3D"_blank">gmail.<u></u>com</a> &lt;owner-chemistry]|[<a href=3D"http=
://ccl.net" target=3D"_blank">ccl.net</a>&gt;<br>
To: &quot;Foroutan-Nejad, Cina &quot; &lt;canyslopus]|[<a href=3D"http://ya=
hoo.co.uk" target=3D"_blank">yahoo.co.uk</a>&gt; Sent: Tuesday, 28 August 2=
012, 17:36<br>
Subject: CCL: Dihedral angle: DFT vs Crystal structure<br>
<br>
<br>
Dear CCL members,<br>
<br>
=A0=A0=A0=A0 I was calculating a molecule (71 atoms) for which the crystal =
structure is<br>
known. However, according to my calculation, one of the dihedral angles sho=
ws<br>
large mismatch (deviation of 12 degrees). I repeated the calculation with b=
oth<br>
B3LYP and BP86 functional and the values are given below:<br>
<br>
B3LYP/def2-TZVP=A0=A0 ~ 21.2 BP86/def2-TZVP=A0=A0=A0=A0 ~ 20<br>
Experimental=A0=A0=A0=A0=A0=A0=A0=A0=A0 ~ 8.1<br>
<br>
I would not worry too much if it was 2-3 degree deviation, but 12 is someth=
ing<br>
that I should be careful with.<br>
<br>
I was wondering, whether there is a chance for an experimental error? Or is=
 it<br>
just that DFT overestimates the dihedral angle? Does any body know any refe=
rences<br>
where people encountered similar problem.<br>
<br>
I would be thankful for your comments<br>
<br>
with kind regards<br>
<br>
Gopakumar</div></div></blockquote></div><br></div></div>

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