From owner-chemistry@ccl.net Fri Nov 29 08:06:01 2013
From: "Sergio Manzetti sergio.manzetti%x%gmx.com" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL:G: Earth metal oxides in Gaussian
Message-Id: <-49383-131129041624-5269-4WezsA1tG/jCk9oyTNWsyg###server.ccl.net>
X-Original-From: "Sergio Manzetti" <sergio.manzetti(-)gmx.com>
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Sent to CCL by: "Sergio Manzetti" [sergio.manzetti]|[gmx.com]
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How does one distingusih from a calculation of:

1. One Table salt molecule.

2. One Sodium atom and one Chloride atom next to each other, spaced by 1.2 Å.



Sergio
----- Original Message -----
> From: Laurence Cuffe cuffe(~)mac.com
Sent: 11/28/13 10:29 PM
To: Manzetti, Sergio 
Subject: CCL:G: Earth metal oxides in Gaussian

Sent from QCloud
On Nov 28, 2013, at 05:03 AM, "Sergio Manzetti sergio.manzetti:gmx.com" <owner-chemistry]^[ccl.net> wrote:

Sent to CCL by: "Sergio Manzetti" [sergio.manzetti(a)gmx.com]
Dear all, as earth metal oxides, such as ZnO are particles, how can these be represented correctly as single molecules for calculations? Considering their charge, for instance, Mg2+ and O2-, their bonding should be ionic, however this is not clearly represented in the gaussian outputs when running simple MgO calculations and Mg can assimilate multiple bonds to other neighbouring atoms.

How can this be correctly defined? Should open shell calculations be used?

Thanks
There is a bit of a culture and language issue here. We are taught all sorts of models of bonding and electron behavior in our chemical education, and it is sometimes dificult to realise that an electronic structure model, as implemented by an ab initio program such as the one you mentioned, is a deeper model where the language of interation which we inherit from the simpler descriptions, may no longer be the most acurate way of describing what is happening. By all means try open shell calculations, but be prepared for the eventuality that they may not clarify the picture in terms of a simpler understanding.
All the best
Laurence Cuffethe strange characters on the top line to the ]^[ sign. You can alsoE-mail to subscribers:  CHEMISTRY%5D%5E%5Bccl.net  or use:E-mail to administrators:  CHEMISTRY-REQUEST%5D%5E%5Bccl.net  or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--========GMXBoundary208791385716574266531
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<span style=3D'font-family:Verdana'><span style=3D'font-size:12px'>How does=
 one distingusih from a calculation of:<br /><br />1. One Table salt molecu=
le.<br /><br />2. One Sodium atom and one Chloride atom next to each other,=
 spaced by 1.2 =C3=85.<br /><br /><br /><br />Sergio<p style=3D"margin:0px;=
 padding:0px;" >=C2=A0</p><blockquote style=3D"border-left: 1px solid #CCC;=
 padding-left: 5px; margin-left: 5px; margin-bottom: 0px; margin-top: 0px; =
margin-right: 0px;" type=3D"cite"><p style=3D"margin:0px; padding:0px;" ><s=
pan style=3D"font-family:Verdana"><span style=3D"font-size:12px">----- Orig=
inal Message -----</span></span></p><p style=3D"margin:0px; padding:0px;" >=
<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">From: La=
urence Cuffe cuffe(~)mac.com</span></span></p><p style=3D"margin:0px; paddi=
ng:0px;" ><span style=3D"font-family:Verdana"><span style=3D"font-size:12px=
">Sent: 11/28/13 10:29 PM</span></span></p><p style=3D"margin:0px; padding:=
0px;" ><span style=3D"font-family:Verdana"><span style=3D"font-size:12px">T=
o: Manzetti, Sergio </span></span></p><p style=3D"margin:0px; paddi=
ng:0px;" ><span style=3D"font-family:Verdana"><span style=3D"font-size:12px=
">Subject: CCL:G: Earth metal oxides in Gaussian</span></span></p>=C2=A0<di=
v><div>=C2=A0</div><div><pre style=3D"white-space: pre-wrap; word-wrap: bre=
ak-word; font-size:11;font-family: 'Helvetica Neue', Helvetica, sans-serif;=
 font-size: 15px; white-space: pre-wrap">Sent from QCloud</pre></div><div><=
br />On Nov 28, 2013, at 05:03 AM, "Sergio Manzetti sergio.manzetti:gmx.com=
" &lt;owner-chemistry]^[ccl.net&gt; wrote:<br />=C2=A0<div><blockquote type=
=3D"cite"><div class=3D"msg-quote"><div class=3D"_stretch"><br />Sent to CC=
L by: "Sergio Manzetti" [sergio.manzetti(a)gmx.com]<br />Dear all, as earth=
 metal oxides, such as ZnO are particles, how can these be represented corr=
ectly as single molecules for calculations? Considering their charge, for i=
nstance, Mg2+ and O2-, their bonding should be ionic, however this is not c=
learly represented in the gaussian outputs when running simple MgO calculat=
ions and Mg can assimilate multiple bonds to other neighbouring atoms.<br /=
><br />How can this be correctly defined? Should open shell calculations be=
 used?<br /><br />Thanks</div></div></blockquote><span>&nbsp;</span><br />T=
here is a bit of a culture and language issue here. We are taught all sorts=
 of models of bonding and electron behavior in our chemical education, and =
it is sometimes dificult to realise that an electronic structure model, as =
implemented by an ab initio program such as the one you mentioned, is a dee=
per model where the language of interation which we inherit from the simple=
r descriptions, may no longer be the most acurate way of describing what is=
 happening. By all means try open shell calculations, but be prepared for t=
he eventuality that they may not clarify the picture in terms of a simpler =
understanding.<br />All the best<br />Laurence Cuffe<br /><br />=C2=A0<bloc=
kquote type=3D"cite"><div class=3D"msg-quote"><div class=3D"_stretch"><br /=
><br /><br />-=3D This is automatically added to each message by the mailin=
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padding:0px;" >=C2=A0</p></span></span>

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From owner-chemistry@ccl.net Fri Nov 29 09:53:00 2013
From: "Herbert Fruchtl herbert.fruchtl!A!st-andrews.ac.uk" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL:G: Earth metal oxides in Gaussian
Message-Id: <-49384-131129081715-19241-FWHsQgjQQQredKzFaQQKUQ#,#server.ccl.net>
X-Original-From: Herbert Fruchtl <herbert.fruchtl.:.st-andrews.ac.uk>
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Date: Fri, 29 Nov 2013 13:16:39 +0000
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Sent to CCL by: Herbert Fruchtl [herbert.fruchtl|-|st-andrews.ac.uk]
There are two questions here: How do you treat mineral particles theoretically, 
and how do you find out things like ionicity and bond order from quantum 
mechanical calculations?

For the first question: A molecule of MgO in the gas phase (if that exists) is 
different from the solid. You don't say how large the particles are that you 
want to treat, but if you are using the cluster approach with a program like 
Gaussian, you are limited to a few tens of atoms. There is debate as to when the 
properties of a cluster of atoms or molecules become bulk-like. Some people take 
the opposite approach of treating solids as infinite crystals, and surfaces as 
periodic thin slabs of a few layers of atoms, which is of course also an 
approximation that may or may not be good if you look at nanoparticles or rough 
surfaces. You need to know what you want to describe, which properties you want 
to determine, and what approximations are acceptable.

To the second question: ab initio or DFT calculations give you a wavefunction or 
charge density of a number of electrons in the field of nuclei or cores. Bonds, 
atoms, ions, etc. are interpretations of this. There are theories that give you 
numbers, and holy wars are being fought between the adherents of different 
theories. If you use Gaussian, NBO is a reasonable first approximation. Mulliken 
isn't, particularly if you use diffuse basis functions. QTAIM (for which you 
need a different program) is the most intuitive for atomic charges, but not 
everybody will agree with this statement.

Good luck,

   Herbert

On 28/11/13 13:03, Sergio Manzetti sergio.manzetti:gmx.com wrote:
>
> Sent to CCL by: "Sergio  Manzetti" [sergio.manzetti(a)gmx.com]
> Dear all, as earth metal oxides, such as ZnO are particles, how can these be represented correctly as single molecules for calculations? Considering their charge, for instance, Mg2+ and O2-, their bonding should be ionic, however this is not clearly represented in the gaussian outputs when running simple MgO calculations and Mg can assimilate multiple bonds to other neighbouring atoms.
>
> How can this be correctly defined? Should open shell calculations be used?
>
> Thanks>
>

-- 
Herbert Fruchtl
Senior Scientific Computing Officer
School of Chemistry, School of Mathematics and Statistics
University of St Andrews
--
The University of St Andrews is a charity registered in Scotland:
No SC013532


From owner-chemistry@ccl.net Fri Nov 29 10:28:00 2013
From: "Brian Skinn brian.skinn---gmail.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL:G: Earth metal oxides in Gaussian
Message-Id: <-49385-131129091544-14173-IZZTrfdXdzik9QKOVthUZQ]_[server.ccl.net>
X-Original-From: Brian Skinn <brian.skinn * gmail.com>
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Date: Fri, 29 Nov 2013 09:15:13 -0500
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Sent to CCL by: Brian Skinn [brian.skinn,,gmail.com]
--f46d043c7e769ebdcb04ec5176dc
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Or:

3) One Na atom next to a Cl atom in a three-dimensional matrix of Na and Cl
atoms.

Gas phase simulations of crystal unit cells do not, in general, represent a
good model for the extended phase properties of that crystal.  If I'm
understanding what you're seeking to investigate, you should probably
consider something more like CPMD or CASINO (quantum Monte Carlo), using an
infinitely repeating simulation box.  These should allow more ready
examination of the extended system of, e.g., your MgO particle or the
surface of that particle, and also of the various geometrical
configurations/microstates accessible to that system at your temperature of
interest.

-Brian



On Fri, Nov 29, 2013 at 4:16 AM, Sergio Manzetti sergio.manzetti%x%gmx.com =
<
owner-chemistry^^ccl.net> wrote:

> How does one distingusih from a calculation of:
>
> 1. One Table salt molecule.
>
> 2. One Sodium atom and one Chloride atom next to each other, spaced by 1.=
2
> =C5.
>
>
>
> Sergio
> ----- Original Message -----
> > From: Laurence Cuffe cuffe(~)mac.com
> Sent: 11/28/13 10:29 PM
> To: Manzetti, Sergio
> Subject: CCL:G: Earth metal oxides in Gaussian
>
> Sent from QCloud
> On Nov 28, 2013, at 05:03 AM, "Sergio Manzetti sergio.manzetti:gmx.com"
> <owner-chemistry]^[ccl.net> wrote:
>
> Sent to CCL by: "Sergio Manzetti" [sergio.manzetti(a)gmx.com]
> Dear all, as earth metal oxides, such as ZnO are particles, how can these
> be represented correctly as single molecules for calculations? Considerin=
g
> their charge, for instance, Mg2+ and O2-, their bonding should be ionic,
> however this is not clearly represented in the gaussian outputs when
> running simple MgO calculations and Mg can assimilate multiple bonds to
> other neighbouring atoms.
>
> How can this be correctly defined? Should open shell calculations be used=
?
>
> Thanks
> There is a bit of a culture and language issue here. We are taught all
> sorts of models of bonding and electron behavior in our chemical educatio=
n,
> and it is sometimes dificult to realise that an electronic structure mode=
l,
> as implemented by an ab initio program such as the one you mentioned, is =
a
> deeper model where the language of interation which we inherit from the
> simpler descriptions, may no longer be the most acurate way of describing
> what is happening. By all means try open shell calculations, but be
> prepared for the eventuality that they may not clarify the picture in ter=
ms
> of a simpler understanding.
> All the best
> Laurence Cuffethe strange characters on the top line to the ]^[ sign. You
> can alsoE-mail to subscribers:  CHEMISTRY%5D%5E%5Bccl.net  or use:E-mail =
to
> administrators:  CHEMISTRY-REQUEST%5D%5E%5Bccl.net  or usehttp://
> www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=3D=
=3D=3D=3D=3D=3D=3D=3DGMXBoundary208791385716574266531
> Content-Type: text/html; charset=3D"utf-8"
> Content-Transfer-Encoding: quoted-printable
>
> <span style=3D3D'font-family:Verdana'><span style=3D3D'font-size:12px'>Ho=
w
> does=3D
>  one distingusih from a calculation of:<br /><br />1. One Table salt
> molecu=3D
> le.<br /><br />2. One Sodium atom and one Chloride atom next to each
> other,=3D
>  spaced by 1.2 =3DC3=3D85.<br /><br /><br /><br />Sergio<p
> style=3D3D"margin:0px;=3D
>  padding:0px;" >=3DC2=3DA0</p><blockquote style=3D3D"border-left: 1px sol=
id
> #CCC;=3D
>  padding-left: 5px; margin-left: 5px; margin-bottom: 0px; margin-top: 0px=
;
> =3D
> margin-right: 0px;" type=3D3D"cite"><p style=3D3D"margin:0px; padding:0px=
;"
> ><s=3D
> pan style=3D3D"font-family:Verdana"><span style=3D3D"font-size:12px">----=
-
> Orig=3D
> inal Message -----</span></span></p><p style=3D3D"margin:0px; padding:0px=
;"
> >=3D
> <span style=3D3D"font-family:Verdana"><span style=3D3D"font-size:12px">Fr=
om:
> La=3D
> urence Cuffe cuffe(~)mac.com</span></span></p><p style=3D3D"margin:0px;
> paddi=3D
> ng:0px;" ><span style=3D3D"font-family:Verdana"><span
> style=3D3D"font-size:12px=3D
> ">Sent: 11/28/13 10:29 PM</span></span></p><p style=3D3D"margin:0px;
> padding:=3D
> 0px;" ><span style=3D3D"font-family:Verdana"><span
> style=3D3D"font-size:12px">T=3D
> o: Manzetti, Sergio </span></span></p><p style=3D3D"margin:0px; paddi=3D
> ng:0px;" ><span style=3D3D"font-family:Verdana"><span
> style=3D3D"font-size:12px=3D
> ">Subject: CCL:G: Earth metal oxides in
> Gaussian</span></span></p>=3DC2=3DA0<di=3D
> v><div>=3DC2=3DA0</div><div><pre style=3D3D"white-space: pre-wrap; word-w=
rap:
> bre=3D
> ak-word; font-size:11;font-family: 'Helvetica Neue', Helvetica,
> sans-serif;=3D
>  font-size: 15px; white-space: pre-wrap">Sent from
> QCloud</pre></div><div><=3D
> br />On Nov 28, 2013, at 05:03 AM, "Sergio Manzetti sergio.manzetti:
> gmx.com=3D
> " &lt;owner-chemistry]^[ccl.net&gt; wrote:<br />=3DC2=3DA0<div><blockquot=
e
> type=3D
> =3D3D"cite"><div class=3D3D"msg-quote"><div class=3D3D"_stretch"><br />Se=
nt to
> CC=3D
> L by: "Sergio Manzetti" [sergio.manzetti(a)gmx.com]<br />Dear all, as
> earth=3D
>  metal oxides, such as ZnO are particles, how can these be represented
> corr=3D
> ectly as single molecules for calculations? Considering their charge, for
> i=3D
> nstance, Mg2+ and O2-, their bonding should be ionic, however this is not
> c=3D
> learly represented in the gaussian outputs when running simple MgO
> calculat=3D
> ions and Mg can assimilate multiple bonds to other neighbouring atoms.<br
> /=3D
> ><br />How can this be correctly defined? Should open shell calculations
> be=3D
>  used?<br /><br />Thanks</div></div></blockquote><span>&nbsp;</span><br
> />T=3D
> here is a bit of a culture and language issue here. We are taught all
> sorts=3D
>  of models of bonding and electron behavior in our chemical education, an=
d
> =3D
> it is sometimes dificult to realise that an electronic structure model, a=
s
> =3D
> implemented by an ab initio program such as the one you mentioned, is a
> dee=3D
> per model where the language of interation which we inherit from the
> simple=3D
> r descriptions, may no longer be the most acurate way of describing what
> is=3D
>  happening. By all means try open shell calculations, but be prepared for
> t=3D
> he eventuality that they may not clarify the picture in terms of a simple=
r
> =3D
> understanding.<br />All the best<br />Laurence Cuffe<br /><br
> />=3DC2=3DA0<bloc=3D
> kquote type=3D3D"cite"><div class=3D3D"msg-quote"><div class=3D3D"_stretc=
h"><br
> /=3D
> ><br /><br />-=3D3D This is automatically added to each message by the
> mailin=3D
> g script =3D3D-<br />To recover the email address of the author of the
> messag=3D
> e, please change<br />the strange characters on the top line to the ]^[
> sig=3D
> n. You can also<br /<=3D
> br /><br />E-mail to subscribers: <a href=3D3D"mailto:
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> et">CHEMISTRY]^[ccl.net</a> or use:<br /><a href=3D3D"
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> padding:0px;" >=3DC2=3DA0</p></span></span>
>

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<div dir=3D"ltr"><div><div>Or:<br><br></div>3) One Na atom next to a Cl ato=
m in a three-dimensional matrix of Na and Cl atoms.<br><br></div>Gas phase =
simulations of crystal unit cells do not, in general, represent a good mode=
l for the extended phase properties of that crystal.=A0 If I&#39;m understa=
nding what you&#39;re seeking to investigate, you should probably consider =
something more like CPMD or CASINO (quantum Monte Carlo), using an infinite=
ly repeating simulation box.=A0 These should allow more ready examination o=
f the extended system of, e.g., your MgO particle or the surface of that pa=
rticle, and also of the various geometrical configurations/microstates acce=
ssible to that system at your temperature of interest.<br>

<br>-Brian<br><br></div><div class=3D"gmail_extra"><br><br><div class=3D"gm=
ail_quote">On Fri, Nov 29, 2013 at 4:16 AM, Sergio Manzetti sergio.manzetti=
%x%<a href=3D"http://gmx.com">gmx.com</a> <span dir=3D"ltr">&lt;<a href=3D"=
mailto:owner-chemistry^^ccl.net" target=3D"_blank">owner-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">How does one distingusih from a calculation =
of:<br>
<br>
1. One Table salt molecule.<br>
<br>
2. One Sodium atom and one Chloride atom next to each other, spaced by 1.2 =
=C5.<br>
<br>
<br>
<br>
Sergio<br>
<div class=3D"im">----- Original Message -----<br>
&gt; From: Laurence Cuffe cuffe(~)<a href=3D"http://mac.com" target=3D"_bla=
nk">mac.com</a><br>
Sent: 11/28/13 10:29 PM<br>
To: Manzetti, Sergio<br>
Subject: CCL:G: Earth metal oxides in Gaussian<br>
<br>
Sent from QCloud<br>
On Nov 28, 2013, at 05:03 AM, &quot;Sergio Manzetti sergio.manzetti:<a href=
=3D"http://gmx.com" target=3D"_blank">gmx.com</a>&quot; &lt;owner-chemistry=
]^[<a href=3D"http://ccl.net" target=3D"_blank">ccl.net</a>&gt; wrote:<br>
<br>
Sent to CCL by: &quot;Sergio Manzetti&quot; [sergio.manzetti(a)<a href=3D"h=
ttp://gmx.com" target=3D"_blank">gmx.com</a>]<br>
Dear all, as earth metal oxides, such as ZnO are particles, how can these b=
e represented correctly as single molecules for calculations? Considering t=
heir charge, for instance, Mg2+ and O2-, their bonding should be ionic, how=
ever this is not clearly represented in the gaussian outputs when running s=
imple MgO calculations and Mg can assimilate multiple bonds to other neighb=
ouring atoms.<br>


<br>
How can this be correctly defined? Should open shell calculations be used?<=
br>
<br>
Thanks<br>
There is a bit of a culture and language issue here. We are taught all sort=
s of models of bonding and electron behavior in our chemical education, and=
 it is sometimes dificult to realise that an electronic structure model, as=
 implemented by an ab initio program such as the one you mentioned, is a de=
eper model where the language of interation which we inherit from the simpl=
er descriptions, may no longer be the most acurate way of describing what i=
s happening. By all means try open shell calculations, but be prepared for =
the eventuality that they may not clarify the picture in terms of a simpler=
 understanding.<br>


All the best<br>
</div>Laurence Cuffethe strange characters on the top line to the ]^[ sign.=
 You can alsoE-mail to subscribers: =A0CHEMISTRY%5D%5E%5Bccl.net =A0or use:=
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<br>
&lt;span style=3D3D&#39;font-family:Verdana&#39;&gt;&lt;span style=3D3D&#39=
;font-size:12px&#39;&gt;How does=3D<br>
=A0one distingusih from a calculation of:&lt;br /&gt;&lt;br /&gt;1. One Tab=
le salt molecu=3D<br>
le.&lt;br /&gt;&lt;br /&gt;2. One Sodium atom and one Chloride atom next to=
 each other,=3D<br>
=A0spaced by 1.2 =3DC3=3D85.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt=
;Sergio&lt;p style=3D3D&quot;margin:0px;=3D<br>
=A0padding:0px;&quot; &gt;=3DC2=3DA0&lt;/p&gt;&lt;blockquote style=3D3D&quo=
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=A0padding-left: 5px; margin-left: 5px; margin-bottom: 0px; margin-top: 0px=
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pan style=3D3D&quot;font-family:Verdana&quot;&gt;&lt;span style=3D3D&quot;f=
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inal Message -----&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p style=3D3D&quot=
;margin:0px; padding:0px;&quot; &gt;=3D<br>
&lt;span style=3D3D&quot;font-family:Verdana&quot;&gt;&lt;span style=3D3D&q=
uot;font-size:12px&quot;&gt;From: La=3D<br>
urence Cuffe cuffe(~)<a href=3D"http://mac.com" target=3D"_blank">mac.com</=
a>&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p style=3D3D&quot;margin:0px; pad=
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;span style=3D3D&quot;font-size:12px=3D<br>
&quot;&gt;Sent: 11/28/13 10:29 PM&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p =
style=3D3D&quot;margin:0px; padding:=3D<br>
0px;&quot; &gt;&lt;span style=3D3D&quot;font-family:Verdana&quot;&gt;&lt;sp=
an style=3D3D&quot;font-size:12px&quot;&gt;T=3D<br>
o: Manzetti, Sergio &lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p style=3D3D&qu=
ot;margin:0px; paddi=3D<br>
ng:0px;&quot; &gt;&lt;span style=3D3D&quot;font-family:Verdana&quot;&gt;&lt=
;span style=3D3D&quot;font-size:12px=3D<br>
&quot;&gt;Subject: CCL:G: Earth metal oxides in Gaussian&lt;/span&gt;&lt;/s=
pan&gt;&lt;/p&gt;=3DC2=3DA0&lt;di=3D<br>
v&gt;&lt;div&gt;=3DC2=3DA0&lt;/div&gt;&lt;div&gt;&lt;pre style=3D3D&quot;wh=
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=A0font-size: 15px; white-space: pre-wrap&quot;&gt;Sent from QCloud&lt;/pre=
&gt;&lt;/div&gt;&lt;div&gt;&lt;=3D<br>
br /&gt;On Nov 28, 2013, at 05:03 AM, &quot;Sergio Manzetti sergio.manzetti=
:<a href=3D"http://gmx.com" target=3D"_blank">gmx.com</a>=3D<br>
&quot; &amp;lt;owner-chemistry]^[<a href=3D"http://ccl.net" target=3D"_blan=
k">ccl.net</a>&amp;gt; wrote:&lt;br /&gt;=3DC2=3DA0&lt;div&gt;&lt;blockquot=
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=3D3D&quot;cite&quot;&gt;&lt;div class=3D3D&quot;msg-quote&quot;&gt;&lt;div=
 class=3D3D&quot;_stretch&quot;&gt;&lt;br /&gt;Sent to CC=3D<br>
L by: &quot;Sergio Manzetti&quot; [sergio.manzetti(a)<a href=3D"http://gmx.=
com" target=3D"_blank">gmx.com</a>]&lt;br /&gt;Dear all, as earth=3D<br>
=A0metal oxides, such as ZnO are particles, how can these be represented co=
rr=3D<br>
ectly as single molecules for calculations? Considering their charge, for i=
=3D<br>
nstance, Mg2+ and O2-, their bonding should be ionic, however this is not c=
=3D<br>
learly represented in the gaussian outputs when running simple MgO calculat=
=3D<br>
ions and Mg can assimilate multiple bonds to other neighbouring atoms.&lt;b=
r /=3D<br>
&gt;&lt;br /&gt;How can this be correctly defined? Should open shell calcul=
ations be=3D<br>
=A0used?&lt;br /&gt;&lt;br /&gt;Thanks&lt;/div&gt;&lt;/div&gt;&lt;/blockquo=
te&gt;&lt;span&gt;&amp;nbsp;&lt;/span&gt;&lt;br /&gt;T=3D<br>
here is a bit of a culture and language issue here. We are taught all sorts=
=3D<br>
=A0of models of bonding and electron behavior in our chemical education, an=
d =3D<br>
it is sometimes dificult to realise that an electronic structure model, as =
=3D<br>
implemented by an ab initio program such as the one you mentioned, is a dee=
=3D<br>
per model where the language of interation which we inherit from the simple=
=3D<br>
r descriptions, may no longer be the most acurate way of describing what is=
=3D<br>
=A0happening. By all means try open shell calculations, but be prepared for=
 t=3D<br>
he eventuality that they may not clarify the picture in terms of a simpler =
=3D<br>
understanding.&lt;br /&gt;All the best&lt;br /&gt;Laurence Cuffe&lt;br /&gt=
;&lt;br /&gt;=3DC2=3DA0&lt;bloc=3D<br>
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--f46d043c7e769ebdcb04ec5176dc--


From owner-chemistry@ccl.net Fri Nov 29 11:03:01 2013
From: "Susi Lehtola susi.lehtola- -alumni.helsinki.fi" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL:G: Earth metal oxides in Gaussian
Message-Id: <-49386-131129102840-618-mU96Uo3v6dzg7oBImRNlTw a server.ccl.net>
X-Original-From: Susi Lehtola <susi.lehtola__alumni.helsinki.fi>
Content-Transfer-Encoding: 8bit
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Date: Fri, 29 Nov 2013 17:28:31 +0200
Mime-Version: 1.0


Sent to CCL by: Susi Lehtola [susi.lehtola() alumni.helsinki.fi]
On Fri, 29 Nov 2013 13:16:39 +0000
"Herbert Fruchtl herbert.fruchtl!A!st-andrews.ac.uk"
<owner-chemistry**ccl.net> wrote:
> To the second question: ab initio or DFT calculations give you a wavefunction or 
> charge density of a number of electrons in the field of nuclei or cores. Bonds, 
> atoms, ions, etc. are interpretations of this. There are theories that give you 
> numbers, and holy wars are being fought between the adherents of different 
> theories. If you use Gaussian, NBO is a reasonable first approximation. Mulliken 
> isn't, particularly if you use diffuse basis functions. QTAIM (for which you 
> need a different program) is the most intuitive for atomic charges, but not 
> everybody will agree with this statement.

QTAIM is not without problems, e.g. H2O and HCN are ionic according to
it.

I'm not quite sure why people bash Mulliken, in my experience it's
usually not hopelessly unstable wrt diffuse basis sets. Löwdin, on the
other hand, is very, very bad... and for some reason, lots of people
proclaim Löwdin to be better in this respect than Mulliken!
-- 
---------------------------------------------------------------
Mr. Susi Lehtola, PhD             Research Associate
susi.lehtola**alumni.helsinki.fi   Department of Applied Physics
http://www.helsinki.fi/~jzlehtol  Aalto University
                                  Finland
---------------------------------------------------------------
Susi Lehtola, FT                  Tutkijatohtori
susi.lehtola**alumni.helsinki.fi   Fysiikan laitos
http://www.helsinki.fi/~jzlehtol  Aalto-yliopisto
---------------------------------------------------------------


From owner-chemistry@ccl.net Fri Nov 29 12:06:00 2013
From: "Sergio Manzetti sergio.manzetti[#]gmx.com" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL:G: Earth metal oxides in Gaussian
Message-Id: <-49387-131129103550-6198-Xiri0SwgHEcuDv0LyT3mPA a server.ccl.net>
X-Original-From: "Sergio Manzetti" <sergio.manzetti * gmx.com>
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Date: Fri, 29 Nov 2013 16:35:36 +0100
MIME-Version: 1.0


Sent to CCL by: "Sergio Manzetti" [sergio.manzetti!^!gmx.com]
--========GMXBoundary131991385739336985609
Content-Type: text/plain; charset="utf-8"
Content-Transfer-Encoding: 8bit

Thanks Herbert! This was very clear.

My approach is in treating a solid state of MgO where one MgO molecule on the surface participates in a reactions. Thus; One MgO molecule as a reagent part of a MgO ensemble with additional reactants on the surface.

I suspect I should consult mineral lattice resources here, and then extrapolate a suitable model of the MgO molecule as a reactant , and becoming converted to MgCl2 during this postulated E1 reaction.

I am not sure,

Sergio
----- Original Message -----
> From: Herbert Fruchtl herbert.fruchtl!A!st-andrews.ac.uk
Sent: 11/29/13 02:16 PM
To: Manzetti, Sergio 
Subject: CCL:G: Earth metal oxides in Gaussian

Sent to CCL by: Herbert Fruchtl [herbert.fruchtl|-|st-andrews.ac.uk] There are two questions here: How do you treat mineral particles theoretically, and how do you find out things like ionicity and bond order from quantum mechanical calculations? For the first question: A molecule of MgO in the gas phase (if that exists) is different from the solid. You don't say how large the particles are that you want to treat, but if you are using the cluster approach with a program like Gaussian, you are limited to a few tens of atoms. There is debate as to when the properties of a cluster of atoms or molecules become bulk-like. Some people take the opposite approach of treating solids as infinite crystals, and surfaces as periodic thin slabs of a few layers of atoms, which is of course also an approximation that may or may not be good if you look at nanoparticles or rough surfaces. You need to know what you want to describe, which properties you want to determine, and what approximations are acceptable. To the second question: ab initio or DFT calculations give you a wavefunction or charge density of a number of electrons in the field of nuclei or cores. Bonds, atoms, ions, etc. are interpretations of this. There are theories that give you numbers, and holy wars are being fought between the adherents of different theories. If you use Gaussian, NBO is a reasonable first approximation. Mulliken isn't, particularly if you use diffuse basis functions. QTAIM (for which you need a different program) is the most intuitive for atomic charges, but not everybody will agree with this statement. Good luck, Herbert On 28/11/13 13:03, Sergio Manzetti sergio.manzetti:gmx.com wrote: > > Sent to CCL by: "Sergio Manzetti" [sergio.manzetti(a)gmx.com] > Dear all, as earth metal oxides, such as ZnO are particles, how can these be represented correctly as single molecules for calculations? Considering their charge, for instance, Mg2+ and O2-, their bonding should be ionic, however this is not clearly represented in the gaussian outputs when running simple MgO calculations and Mg can assimilate multiple bonds to other neighbouring atoms. > > How can this be correctly defined? Should open shell calculations be used? > > Thanks> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--========GMXBoundary131991385739336985609
Content-Type: text/html; charset="utf-8"
Content-Transfer-Encoding: quoted-printable

<span style=3D'font-family:Verdana'><span style=3D'font-size:12px'>Thanks H=
erbert! This was very&nbsp; clear.<br /><br />My approach is in treating a =
solid state of MgO where one MgO molecule on the surface participates in a =
reactions. Thus; One MgO molecule as a reagent part of a MgO ensemble with =
additional reactants on the surface.<br /><br />I suspect I should consult =
mineral lattice resources here, and then extrapolate a suitable model of th=
e MgO molecule as a reactant , and becoming converted to MgCl2 during this =
postulated E1 reaction.<br /><br />I am not sure,<br /><br />Sergio<p style=
=3D"margin:0px; padding:0px;" >=C2=A0</p><blockquote style=3D"border-left: =
1px solid #CCC; padding-left: 5px; margin-left: 5px; margin-bottom: 0px; ma=
rgin-top: 0px; margin-right: 0px;" type=3D"cite"><p style=3D"margin:0px; pa=
dding:0px;" ><span style=3D"font-family:Verdana"><span style=3D"font-size:1=
2px">----- Original Message -----</span></span></p><p style=3D"margin:0px; =
padding:0px;" ><span style=3D"font-family:Verdana"><span style=3D"font-size=
:12px">From: Herbert Fruchtl herbert.fruchtl!A!st-andrews.ac.uk</span></spa=
n></p><p style=3D"margin:0px; padding:0px;" ><span style=3D"font-family:Ver=
dana"><span style=3D"font-size:12px">Sent: 11/29/13 02:16 PM</span></span><=
/p><p style=3D"margin:0px; padding:0px;" ><span style=3D"font-family:Verdan=
a"><span style=3D"font-size:12px">To: Manzetti, Sergio </span></spa=
n></p><p style=3D"margin:0px; padding:0px;" ><span style=3D"font-family:Ver=
dana"><span style=3D"font-size:12px">Subject: CCL:G: Earth metal oxides in =
Gaussian</span></span></p>=C2=A0<div><div><pre style=3D"white-space: pre-wr=
ap; word-wrap: break-word; font-size:11;pre">Sent to CCL by: Herbert Frucht=
l [herbert.fruchtl|-|st-andrews.ac.uk]=20
There are two questions here: How do you treat mineral particles theoretica=
lly,=20
and how do you find out things like ionicity and bond order from quantum=20
mechanical calculations?=20

For the first question: A molecule of MgO in the gas phase (if that exists)=
 is=20
different from the solid. You don't say how large the particles are that yo=
u=20
want to treat, but if you are using the cluster approach with a program lik=
e=20
Gaussian, you are limited to a few tens of atoms. There is debate as to whe=
n the=20
properties of a cluster of atoms or molecules become bulk-like. Some people=
 take=20
the opposite approach of treating solids as infinite crystals, and surfaces=
 as=20
periodic thin slabs of a few layers of atoms, which is of course also an=20
approximation that may or may not be good if you look at nanoparticles or r=
ough=20
surfaces. You need to know what you want to describe, which properties you =
want=20
to determine, and what approximations are acceptable.=20

To the second question: ab initio or DFT calculations give you a wavefuncti=
on or=20
charge density of a number of electrons in the field of nuclei or cores. Bo=
nds,=20
atoms, ions, etc. are interpretations of this. There are theories that give=
 you=20
numbers, and holy wars are being fought between the adherents of different=
=20
theories. If you use Gaussian, NBO is a reasonable first approximation. Mul=
liken=20
isn't, particularly if you use diffuse basis functions. QTAIM (for which yo=
u=20
need a different program) is the most intuitive for atomic charges, but not=
=20
everybody will agree with this statement.=20

Good luck,=20

   Herbert=20

On 28/11/13 13:03, Sergio Manzetti sergio.manzetti:gmx.com wrote:=20
&gt;=20
&gt; Sent to CCL by: "Sergio  Manzetti" [sergio.manzetti(a)gmx.com]=20
&gt; Dear all, as earth metal oxides, such as ZnO are particles, how can th=
ese be represented correctly as single molecules for calculations? Consider=
ing their charge, for instance, Mg2+ and O2-, their bonding should be ionic=
, however this is not clearly represented in the gaussian outputs when runn=
ing simple MgO calculations and Mg can assimilate multiple bonds to other n=
eighbouring atoms.=20
&gt;=20
&gt; How can this be correctly defined? Should open shell calculations be u=
sed?=20
&gt;=20
&gt; Thanks&gt;=20
&gt;=20

--=20
Herbert Fruchtl=20
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--========GMXBoundary131991385739336985609--


From owner-chemistry@ccl.net Fri Nov 29 12:41:00 2013
From: "Sergio Manzetti sergio.manzetti#gmx.com" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL:G: Earth metal oxides in Gaussian
Message-Id: <-49388-131129115603-24166-3eg2w5OpmW+2W2RWnuEeLg::server.ccl.net>
X-Original-From: "Sergio Manzetti" <sergio.manzetti-.-gmx.com>
Content-Type: multipart/alternative;
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Date: Fri, 29 Nov 2013 17:55:52 +0100
MIME-Version: 1.0


Sent to CCL by: "Sergio Manzetti" [sergio.manzetti[#]gmx.com]
--========GMXBoundary260831385744153140214
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Content-Transfer-Encoding: 8bit

The idea is hybrid QM/MM:

MM for the lattice of Earth oxide, and QM for one selected earth oxide molecule is contact with the reactant (QM as well).

----- Original Message -----
> From: Brian Skinn brian.skinn---gmail.com
Sent: 11/29/13 03:15 PM
To: Manzetti, Sergio 
Subject: CCL:G: Earth metal oxides in Gaussian

Or:
3) One Na atom next to a Cl atom in a three-dimensional matrix of Na and Cl atoms.
Gas phase simulations of crystal unit cells do not, in general, represent a good model for the extended phase properties of that crystal. If I'm understanding what you're seeking to investigate, you should probably consider something more like CPMD or CASINO (quantum Monte Carlo), using an infinitely repeating simulation box. These should allow more ready examination of the extended system of, e.g., your MgO particle or the surface of that particle, and also of the various geometrical configurations/microstates accessible to that system at your temperature of interest.

-Brian

On Fri, Nov 29, 2013 at 4:16 AM, Sergio Manzetti sergio.manzetti%x%http://gmx.com < owner-chemistry%C3%8Cl.net > wrote:How does one distingusih from a calculation of:

1. One Table salt molecule.

2. One Sodium atom and one Chloride atom next to each other, spaced by 1.2 Å.



Sergio
----- Original Message -----
> From: Laurence Cuffe cuffe(~)http://mac.com 
Sent: 11/28/13 10:29 PM
To: Manzetti, Sergio
Subject: CCL:G: Earth metal oxides in Gaussian

Sent from QCloud
On Nov 28, 2013, at 05:03 AM, "Sergio Manzetti sergio.manzetti:http://gmx.com " <owner-chemistry]^[http://ccl.net > wrote:

Sent to CCL by: "Sergio Manzetti" [sergio.manzetti(a)http://gmx.com ]
Dear all, as earth metal oxides, such as ZnO are particles, how can these be represented correctly as single molecules for calculations? Considering their charge, for instance, Mg2+ and O2-, their bonding should be ionic, however this is not clearly represented in the gaussian outputs when running simple MgO calculations and Mg can assimilate multiple bonds to other neighbouring atoms.

How can this be correctly defined? Should open shell calculations be used?

Thanks
There is a bit of a culture and language issue here. We are taught all sorts of models of bonding and electron behavior in our chemical education, and it is sometimes dificult to realise that an electronic structure model, as implemented by an ab initio program such as the one you mentioned, is a deeper model where the language of interation which we inherit from the simpler descriptions, may no longer be the most acurate way of describing what is happening. By all means try open shell calculations, but be prepared for the eventuality that they may not clarify the picture in terms of a simpler understanding.
All the bestLaurence Cuffethe strange characters on the top line to the ]^[ sign. You can alsoE-mail to subscribers: CHEMISTRY%5D%5E%5Bccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST%5D%5E%5Bccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--========GMXBoundary208791385716574266531
Content-Typehttp://www.ccl.net/spammers.txt--========GMXBoundary208791385716574266531%0AContent-Type : text/html; charset="utf-8"
Content-Transfer-Encoding: quoted-printable

<span style=3D'font-family:Verdana'><span style=3D'font-size:12px'>How does=
 one distingusih from a calculation of:<br /><br />1. One Table salt molecu=
le.<br /><br />2. One Sodium atom and one Chloride atom next to each other,=
 spaced by 1.2 =C3=85.<br /><br /><br /><br />Sergio<p style=3D"margin:0px;=
 padding:0px;" >=C2=A0</p><blockquote style=3D"border-left: 1px solid #CCC;=
 padding-left: 5px; margin-left: 5px; margin-bottom: 0px; margin-top: 0px; =
margin-right: 0px;" type=3D"cite"><p style=3D"margin:0px; padding:0px;" ><s=
pan style=3D"font-family:Verdana"><span style=3D"font-size:12px">----- Orig=
inal Message -----</span></span></p><p style=3D"margin:0px; padding:0px;" >=
<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">From: La=
urence Cuffe cuffe(~)http://mac.com </span></span></p><p style=3D"margin:0px; paddi=
ng:0px;" ><span style=3D"font-family:Verdana"><span style=3D"font-size:12px=
">Sent: 11/28/13 10:29 PM</span></span></p><p style=3D"margin:0px; padding:=
0px;" ><span style=3D"font-family:Verdana"><span style=3D"font-size:12px">T=
o: Manzetti, Sergio </span></span></p><p style=3D"margin:0px; paddi=
ng:0px;" ><span style=3D"font-family:Verdana"><span style=3D"font-size:12px=
">Subject: CCL:G: Earth metal oxides in Gaussian</span></span></p>=C2=A0<di=
v><div>=C2=A0</div><div><pre style=3D"white-space: pre-wrap; word-wrap: bre=
ak-word; font-size:11;font-family: 'Helvetica Neue', Helvetica, sans-serif;=
 font-size: 15px; white-space: pre-wrap">Sent from QCloud</pre></div><div><=
br />On Nov 28, 2013, at 05:03 AM, "Sergio Manzetti sergio.manzetti:http://gmx.com =
" &lt;owner-chemistry]^[http://ccl.net &gt; wrote:<br />=C2=A0<div><blockquote type=
=3D"cite"><div class=3D"msg-quote"><div class=3D"_stretch"><br />Sent to CC=
L by: "Sergio Manzetti" [sergio.manzetti(a)http://gmx.com ]<br />Dear all, as earth=
 metal oxides, such as ZnO are particles, how can these be represented corr=
ectly as single molecules for calculations? Considering their charge, for i=
nstance, Mg2+ and O2-, their bonding should be ionic, however this is not c=
learly represented in the gaussian outputs when running simple MgO calculat=
ions and Mg can assimilate multiple bonds to other neighbouring atoms.<br /=
><br />How can this be correctly defined? Should open shell calculations be=
 used?<br /><br />Thanks</div></div></blockquote><span>&nbsp;</span><br />T=
here is a bit of a culture and language issue here. We are taught all sorts=
 of models of bonding and electron behavior in our chemical education, and =
it is sometimes dificult to realise that an electronic structure model, as =
implemented by an ab initio program such as the one you mentioned, is a dee=
per model where the language of interation which we inherit from the simple=
r descriptions, may no longer be the most acurate way of describing what is=
 happening. By all means try open shell calculations, but be prepared for t=
he eventuality that they may not clarify the picture in terms of a simpler =
understanding.<br />All the best<br />Laurence Cuffe<br /><br />=C2=A0<bloc=
kquote type=3D"cite"><div class=3D"msg-quote"><div class=3D"_stretch"><br /=
><br /><br />-=3D This is automatically added to each message by the mailin=
g script =3D-<br />To recover the email address of the author of the messag=
e, please change<br />the strange characters on the top line to the ]^[ sig=
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--========GMXBoundary260831385744153140214
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<span style=3D'font-family:Verdana'><span style=3D'font-size:12px'>The idea=
 is hybrid QM/MM:<br /><br />MM for the lattice of Earth oxide, and QM for =
one selected earth oxide molecule is contact with the reactant (QM as well)=
.<br /><br />=C2=A0<p style=3D"margin:0px; padding:0px;" >=C2=A0</p><blockq=
uote style=3D"border-left: 1px solid #CCC; padding-left: 5px; margin-left: =
5px; margin-bottom: 0px; margin-top: 0px; margin-right: 0px;" type=3D"cite"=
><p style=3D"margin:0px; padding:0px;" ><span style=3D"font-family:Verdana"=
><span style=3D"font-size:12px">----- Original Message -----</span></span><=
/p><p style=3D"margin:0px; padding:0px;" ><span style=3D"font-family:Verdan=
a"><span style=3D"font-size:12px">From: Brian Skinn brian.skinn---gmail.com=
</span></span></p><p style=3D"margin:0px; padding:0px;" ><span style=3D"fon=
t-family:Verdana"><span style=3D"font-size:12px">Sent: 11/29/13 03:15 PM</s=
pan></span></p><p style=3D"margin:0px; padding:0px;" ><span style=3D"font-f=
amily:Verdana"><span style=3D"font-size:12px">To: Manzetti, Sergio =
</span></span></p><p style=3D"margin:0px; padding:0px;" ><span style=3D"fon=
t-family:Verdana"><span style=3D"font-size:12px">Subject: CCL:G: Earth meta=
l oxides in Gaussian</span></span></p>=C2=A0<div><div><div><div>Or:<br />=
=C2=A0</div>3) One Na atom next to a Cl atom in a three-dimensional matrix =
of Na and Cl atoms.<br />=C2=A0</div>Gas phase simulations of crystal unit =
cells do not, in general, represent a good model for the extended phase pro=
perties of that crystal.&nbsp; If I'm understanding what you're seeking to =
investigate, you should probably consider something more like CPMD or CASIN=
O (quantum Monte Carlo), using an infinitely repeating simulation box.&nbsp=
; These should allow more ready examination of the extended system of, e.g.=
, your MgO particle or the surface of that particle, and also of the variou=
s geometrical configurations/microstates accessible to that system at your =
temperature of interest.<br /><br />-Brian<br />=C2=A0</div><div class=3D"g=
mail_extra">=C2=A0<div class=3D"gmail_quote">On Fri, Nov 29, 2013 at 4:16 A=
M, Sergio Manzetti sergio.manzetti%x%<a href=3D"http://gmx.com">gmx.com</a>=
 <span>&lt;<a target=3D"_blank" href=3D"mailto:owner-chemistry%C3%8Cl.net">=
owner-chemistry=C3=8Cl.net</a>&gt;</span> wrote:<blockquote class=3D"gmail_=
quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1=
ex">How does one distingusih from a calculation of:<br /><br />1. One Table=
 salt molecule.<br /><br />2. One Sodium atom and one Chloride atom next to=
 each other, spaced by 1.2 =C3=85.<br /><br /><br /><br />Sergio<div class=
=3D"im">----- Original Message -----<br />&gt; From: Laurence Cuffe cuffe(~=
)<a target=3D"_blank" href=3D"http://mac.com">mac.com</a><br />Sent: 11/28/=
13 10:29 PM<br />To: Manzetti, Sergio<br />Subject: CCL:G: Earth metal oxid=
es in Gaussian<br /><br />Sent from QCloud<br />On Nov 28, 2013, at 05:03 A=
M, "Sergio Manzetti sergio.manzetti:<a target=3D"_blank" href=3D"http://gmx=
.com">gmx.com</a>" &lt;owner-chemistry]^[<a target=3D"_blank" href=3D"http:=
//ccl.net">ccl.net</a>&gt; wrote:<br /><br />Sent to CCL by: "Sergio Manzet=
ti" [sergio.manzetti(a)<a target=3D"_blank" href=3D"http://gmx.com">gmx.com=
</a>]<br />Dear all, as earth metal oxides, such as ZnO are particles, how =
can these be represented correctly as single molecules for calculations? Co=
nsidering their charge, for instance, Mg2+ and O2-, their bonding should be=
 ionic, however this is not clearly represented in the gaussian outputs whe=
n running simple MgO calculations and Mg can assimilate multiple bonds to o=
ther neighbouring atoms.<br /><br />How can this be correctly defined? Shou=
ld open shell calculations be used?<br /><br />Thanks<br />There is a bit o=
f a culture and language issue here. We are taught all sorts of models of b=
onding and electron behavior in our chemical education, and it is sometimes=
 dificult to realise that an electronic structure model, as implemented by =
an ab initio program such as the one you mentioned, is a deeper model where=
 the language of interation which we inherit from the simpler descriptions,=
 may no longer be the most acurate way of describing what is happening. By =
all means try open shell calculations, but be prepared for the eventuality =
that they may not clarify the picture in terms of a simpler understanding.<=
br />All the best</div>Laurence Cuffethe strange characters on the top line=
 to the ]^[ sign. You can alsoE-mail to subscribers: &nbsp;CHEMISTRY%5D%5E%=
5Bccl.net &nbsp;or use:E-mail to administrators: &nbsp;CHEMISTRY-REQUEST%5D=
%5E%5Bccl.net &nbsp;or usehttp://<a target=3D"_blank" href=3D"http://www.cc=
l.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=3D=3D=3D=
=3D=3D=3D=3D=3DGMXBoundary208791385716574266531%0AContent-Type">www.ccl.net=
/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=3D=3D=3D=3D=3D=
=3D=3D=3DGMXBoundary208791385716574266531<br />Content-Type</a>: text/html;=
 charset=3D"utf-8"<br />Content-Transfer-Encoding: quoted-printable<br /><b=
r />&lt;span style=3D3D'font-family:Verdana'&gt;&lt;span style=3D3D'font-si=
ze:12px'&gt;How does=3D<br />&nbsp;one distingusih from a calculation of:&l=
t;br /&gt;&lt;br /&gt;1. One Table salt molecu=3D<br />le.&lt;br /&gt;&lt;b=
r /&gt;2. One Sodium atom and one Chloride atom next to each other,=3D<br /=
>&nbsp;spaced by 1.2 =3DC3=3D85.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br =
/&gt;Sergio&lt;p style=3D3D"margin:0px;=3D<br />&nbsp;padding:0px;" &gt;=3D=
C2=3DA0&lt;/p&gt;&lt;blockquote style=3D3D"border-left: 1px solid #CCC;=3D<=
br />&nbsp;padding-left: 5px; margin-left: 5px; margin-bottom: 0px; margin-=
top: 0px; =3D<br />margin-right: 0px;" type=3D3D"cite"&gt;&lt;p style=3D3D"=
margin:0px; padding:0px;" &gt;&lt;s=3D<br />pan style=3D3D"font-family:Verd=
ana"&gt;&lt;span style=3D3D"font-size:12px"&gt;----- Orig=3D<br />inal Mess=
age -----&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p style=3D3D"margin:0px; p=
adding:0px;" &gt;=3D<br />&lt;span style=3D3D"font-family:Verdana"&gt;&lt;s=
pan style=3D3D"font-size:12px"&gt;From: La=3D<br />urence Cuffe cuffe(~)<a =
target=3D"_blank" href=3D"http://mac.com">mac.com</a>&lt;/span&gt;&lt;/span=
&gt;&lt;/p&gt;&lt;p style=3D3D"margin:0px; paddi=3D<br />ng:0px;" &gt;&lt;s=
pan style=3D3D"font-family:Verdana"&gt;&lt;span style=3D3D"font-size:12px=
=3D<br />"&gt;Sent: 11/28/13 10:29 PM&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&l=
t;p style=3D3D"margin:0px; padding:=3D<br />0px;" &gt;&lt;span style=3D3D"f=
ont-family:Verdana"&gt;&lt;span style=3D3D"font-size:12px"&gt;T=3D<br />o: =
Manzetti, Sergio &lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p style=3D3D"margi=
n:0px; paddi=3D<br />ng:0px;" &gt;&lt;span style=3D3D"font-family:Verdana"&=
gt;&lt;span style=3D3D"font-size:12px=3D<br />"&gt;Subject: CCL:G: Earth me=
tal oxides in Gaussian&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;=3DC2=3DA0&lt;di=
=3D<br />v&gt;&lt;div&gt;=3DC2=3DA0&lt;/div&gt;&lt;div&gt;&lt;pre style=3D3=
D"white-space: pre-wrap; word-wrap: bre=3D<br />ak-word; font-size:11;font-=
family: 'Helvetica Neue', Helvetica, sans-serif;=3D<br />&nbsp;font-size: 1=
5px; white-space: pre-wrap"&gt;Sent from QCloud&lt;/pre&gt;&lt;/div&gt;&lt;=
div&gt;&lt;=3D<br />br /&gt;On Nov 28, 2013, at 05:03 AM, "Sergio Manzetti =
sergio.manzetti:<a target=3D"_blank" href=3D"http://gmx.com">gmx.com</a>=3D=
<br />" &amp;lt;owner-chemistry]^[<a target=3D"_blank" href=3D"http://ccl.n=
et">ccl.net</a>&amp;gt; wrote:&lt;br /&gt;=3DC2=3DA0&lt;div&gt;&lt;blockquo=
te type=3D<br />=3D3D"cite"&gt;&lt;div class=3D3D"msg-quote"&gt;&lt;div cla=
ss=3D3D"_stretch"&gt;&lt;br /&gt;Sent to CC=3D<br />L by: "Sergio Manzetti"=
 [sergio.manzetti(a)<a target=3D"_blank" href=3D"http://gmx.com">gmx.com</a=
>]&lt;br /&gt;Dear all, as earth=3D<br />&nbsp;metal oxides, such as ZnO ar=
e particles, how can these be represented corr=3D<br />ectly as single mole=
cules for calculations? Considering their charge, for i=3D<br />nstance, Mg=
2+ and O2-, their bonding should be ionic, however this is not c=3D<br />le=
arly represented in the gaussian outputs when running simple MgO calculat=
=3D<br />ions and Mg can assimilate multiple bonds to other neighbouring at=
oms.&lt;br /=3D<br />&gt;&lt;br /&gt;How can this be correctly defined? Sho=
uld open shell calculations be=3D<br />&nbsp;used?&lt;br /&gt;&lt;br /&gt;T=
hanks&lt;/div&gt;&lt;/div&gt;&lt;/blockquote&gt;&lt;span&gt;&amp;nbsp;&lt;/=
span&gt;&lt;br /&gt;T=3D<br />here is a bit of a culture and language issue=
 here. We are taught all sorts=3D<br />&nbsp;of models of bonding and elect=
ron behavior in our chemical education, and =3D<br />it is sometimes dificu=
lt to realise that an electronic structure model, as =3D<br />implemented b=
y an ab initio program such as the one you mentioned, is a dee=3D<br />per =
model where the language of interation which we inherit from the simple=3D<=
br />r descriptions, may no longer be the most acurate way of describing wh=
at is=3D<br />&nbsp;happening. By all means try open shell calculations, bu=
t be prepared for t=3D<br />he eventuality that they may not clarify the pi=
cture in terms of a simpler =3D<br />understanding.&lt;br /&gt;All the best=
&lt;br /&gt;Laurence Cuffe&lt;br /&gt;&lt;br /&gt;=3DC2=3DA0&lt;bloc=3D<br =
/>kquote type=3D3D"cite"&gt;&lt;div class=3D3D"msg-quote"&gt;&lt;div class=
=3D3D"_stretch"&gt;&lt;br /=3D<br />&gt;&lt;br /&gt;&lt;br /&gt;-=3D3D This=
 is automatically added to each message by the mailin=3D<br />g script =3D3=
D-&lt;br /&gt;To recover the email address of the author of the messag=3D<b=
r />e, please change&lt;br /&gt;the strange characters on the top line to t=
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E-mail to subscribers: &lt;a href=3D3D"mailto:<a href=3D"mailto:CHEMISTRY%2=
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<a target=3D"_blank" href=3D"http://ccl.net">ccl.net</a>&lt;/a&gt; or use:&=
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--========GMXBoundary260831385744153140214--


From owner-chemistry@ccl.net Fri Nov 29 13:16:00 2013
From: "Marcel Swart marcel.swart^icrea.cat" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL:G: Earth metal oxides in Gaussian
Message-Id: <-49389-131129121301-2074-6EcaXVDyVUTrvgKN6rN2Tg+*+server.ccl.net>
X-Original-From: Marcel Swart <marcel.swart||icrea.cat>
Content-Type: multipart/alternative; boundary="Apple-Mail=_88816C54-2A40-418E-920D-C993C2C393EE"
Date: Fri, 29 Nov 2013 18:12:50 +0100
Mime-Version: 1.0 (Mac OS X Mail 7.0 \(1822\))


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

--Apple-Mail=_88816C54-2A40-418E-920D-C993C2C393EE
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset=iso-8859-1

I would say a cluster model of real atoms embedded in the Madelung =
potential
of surrounding crystal environment. This is standard practice with =
people using
MOLCAS such as Coen de Graaf, Ria Broer, Francesc Illas, Carmen Sousa
to name just a few. For MgO, see e.g.
http://prb.aps.org/abstract/PRB/v62/i15/p10013_1

Marcel

On 29 Nov 2013, at 15:15, Brian Skinn brian.skinn---gmail.com =
<owner-chemistry~~ccl.net> wrote:

> Or:
>=20
> 3) One Na atom next to a Cl atom in a three-dimensional matrix of Na =
and Cl atoms.
>=20
> Gas phase simulations of crystal unit cells do not, in general, =
represent a good model for the extended phase properties of that =
crystal.  If I'm understanding what you're seeking to investigate, you =
should probably consider something more like CPMD or CASINO (quantum =
Monte Carlo), using an infinitely repeating simulation box.  These =
should allow more ready examination of the extended system of, e.g., =
your MgO particle or the surface of that particle, and also of the =
various geometrical configurations/microstates accessible to that system =
at your temperature of interest.
>=20
> -Brian
>=20
>=20
>=20
> On Fri, Nov 29, 2013 at 4:16 AM, Sergio Manzetti =
sergio.manzetti%x%gmx.com <owner-chemistry=CCl.net> wrote:
> How does one distingusih from a calculation of:
>=20
> 1. One Table salt molecule.
>=20
> 2. One Sodium atom and one Chloride atom next to each other, spaced by =
1.2 =C5.
>=20
>=20
>=20
> Sergio
> ----- Original Message -----
> > From: Laurence Cuffe cuffe(~)mac.com
> Sent: 11/28/13 10:29 PM
> To: Manzetti, Sergio
> Subject: CCL:G: Earth metal oxides in Gaussian
>=20
> Sent from QCloud
> On Nov 28, 2013, at 05:03 AM, "Sergio Manzetti =
sergio.manzetti:gmx.com" <owner-chemistry]^[ccl.net> wrote:
>=20
> Sent to CCL by: "Sergio Manzetti" [sergio.manzetti(a)gmx.com]
> Dear all, as earth metal oxides, such as ZnO are particles, how can =
these be represented correctly as single molecules for calculations? =
Considering their charge, for instance, Mg2+ and O2-, their bonding =
should be ionic, however this is not clearly represented in the gaussian =
outputs when running simple MgO calculations and Mg can assimilate =
multiple bonds to other neighbouring atoms.
>=20
> How can this be correctly defined? Should open shell calculations be =
used?
>=20
> Thanks
> There is a bit of a culture and language issue here. We are taught all =
sorts of models of bonding and electron behavior in our chemical =
education, and it is sometimes dificult to realise that an electronic =
structure model, as implemented by an ab initio program such as the one =
you mentioned, is a deeper model where the language of interation which =
we inherit from the simpler descriptions, may no longer be the most =
acurate way of describing what is happening. By all means try open shell =
calculations, but be prepared for the eventuality that they may not =
clarify the picture in terms of a simpler understanding.
> All the best
> Laurence Cuffethe strange characters on the top line to the ]^[ sign. =
You can alsoE-mail to subscribers:  CHEMISTRY%5D%5E%5Bccl.net  or =
use:E-mail to administrators:  CHEMISTRY-REQUEST%5D%5E%5Bccl.net  or =
usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers=
.txt--=3D=3D=3D=3D=3D=3D=3D=3DGMXBoundary208791385716574266531
> Content-Type: text/html; charset=3D"utf-8"
> Content-Transfer-Encoding: quoted-printable
>=20
> <span style=3D3D'font-family:Verdana'><span =
style=3D3D'font-size:12px'>How does=3D
>  one distingusih from a calculation of:<br /><br />1. One Table salt =
molecu=3D
> le.<br /><br />2. One Sodium atom and one Chloride atom next to each =
other,=3D
>  spaced by 1.2 =3DC3=3D85.<br /><br /><br /><br />Sergio<p =
style=3D3D"margin:0px;=3D
>  padding:0px;" >=3DC2=3DA0</p><blockquote style=3D3D"border-left: 1px =
solid #CCC;=3D
>  padding-left: 5px; margin-left: 5px; margin-bottom: 0px; margin-top: =
0px; =3D
> margin-right: 0px;" type=3D3D"cite"><p style=3D3D"margin:0px; =
padding:0px;" ><s=3D
> pan style=3D3D"font-family:Verdana"><span =
style=3D3D"font-size:12px">----- Orig=3D
> inal Message -----</span></span></p><p style=3D3D"margin:0px; =
padding:0px;" >=3D
> <span style=3D3D"font-family:Verdana"><span =
style=3D3D"font-size:12px">From: La=3D
> urence Cuffe cuffe(~)mac.com</span></span></p><p style=3D3D"margin:0px; =
paddi=3D
> ng:0px;" ><span style=3D3D"font-family:Verdana"><span =
style=3D3D"font-size:12px=3D
> ">Sent: 11/28/13 10:29 PM</span></span></p><p style=3D3D"margin:0px; =
padding:=3D
> 0px;" ><span style=3D3D"font-family:Verdana"><span =
style=3D3D"font-size:12px">T=3D
> o: Manzetti, Sergio </span></span></p><p style=3D3D"margin:0px; paddi=3D=

> ng:0px;" ><span style=3D3D"font-family:Verdana"><span =
style=3D3D"font-size:12px=3D
> ">Subject: CCL:G: Earth metal oxides in =
Gaussian</span></span></p>=3DC2=3DA0<di=3D
> v><div>=3DC2=3DA0</div><div><pre style=3D3D"white-space: pre-wrap; =
word-wrap: bre=3D
> ak-word; font-size:11;font-family: 'Helvetica Neue', Helvetica, =
sans-serif;=3D
>  font-size: 15px; white-space: pre-wrap">Sent from =
QCloud</pre></div><div><=3D
> br />On Nov 28, 2013, at 05:03 AM, "Sergio Manzetti =
sergio.manzetti:gmx.com=3D
> " &lt;owner-chemistry]^[ccl.net&gt; wrote:<br />=3DC2=3DA0<div><blockquo=
te type=3D
> =3D3D"cite"><div class=3D3D"msg-quote"><div class=3D3D"_stretch"><br =
/>Sent to CC=3D
> L by: "Sergio Manzetti" [sergio.manzetti(a)gmx.com]<br />Dear all, as =
earth=3D
>  metal oxides, such as ZnO are particles, how can these be represented =
corr=3D
> ectly as single molecules for calculations? Considering their charge, =
for i=3D
> nstance, Mg2+ and O2-, their bonding should be ionic, however this is =
not c=3D
> learly represented in the gaussian outputs when running simple MgO =
calculat=3D
> ions and Mg can assimilate multiple bonds to other neighbouring =
atoms.<br /=3D
> ><br />How can this be correctly defined? Should open shell =
calculations be=3D
>  used?<br /><br =
/>Thanks</div></div></blockquote><span>&nbsp;</span><br />T=3D
> here is a bit of a culture and language issue here. We are taught all =
sorts=3D
>  of models of bonding and electron behavior in our chemical education, =
and =3D
> it is sometimes dificult to realise that an electronic structure =
model, as =3D
> implemented by an ab initio program such as the one you mentioned, is =
a dee=3D
> per model where the language of interation which we inherit from the =
simple=3D
> r descriptions, may no longer be the most acurate way of describing =
what is=3D
>  happening. By all means try open shell calculations, but be prepared =
for t=3D
> he eventuality that they may not clarify the picture in terms of a =
simpler =3D
> understanding.<br />All the best<br />Laurence Cuffe<br /><br =
/>=3DC2=3DA0<bloc=3D
> kquote type=3D3D"cite"><div class=3D3D"msg-quote"><div =
class=3D3D"_stretch"><br /=3D
> ><br /><br />-=3D3D This is automatically added to each message by the =
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> g script =3D3D-<br />To recover the email address of the author of the =
messag=3D
> e, please change<br />the strange characters on the top line to the =
]^[ sig=3D
> n. You can also<br /<=3D
> br /><br />E-mail to subscribers: <a =
href=3D3D"mailto:CHEMISTRY%5D%5E%5Bccl.n=3D
> et">CHEMISTRY]^[ccl.net</a> or use:<br /><a =
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> a><br /><br />E-mail to administrators: <a =
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> cl/send_ccl_message</a><br /><br />Subscribe/Unsubscribe:<br /><a =
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> ub_unsub.shtml</a><br /><br />Before posting, check wait time at: <a =
href=3D
> =3D3D"http://www.ccl.net">http://www.ccl.net</a><br /><br />Job: <a =
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> ttp://www.ccl.net/jobs">http://www.ccl.net/jobs</a><br />Conferences: =
<a hr=3D
> =
ef=3D3D"http://server.ccl.net/chemistry/announcements/conferences/">http:/=
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> rver.ccl.net/chemistry/announcements/conferences/</a><br /><br =
/>Search Mes=3D
> sages: <a =
href=3D3D"http://www.ccl.net/chemistry/searchccl/index.shtml">http:=3D
> //www.ccl.net/chemistry/searchccl/index.shtml</a><br /><br /><a =
href=3D3D"htt=3D
> p://www.ccl.net/spammers.txt">http://www.ccl.net/spammers.txt</a><br =
/><br =3D
> />RTFI: <a =
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> p://www.ccl.net/chemistry/aboutccl/instructions/</a><br /><br =
/>=3DC2=3DA0</div=3D
> ></div></blockquote></div></div></div></blockquote><p =
style=3D3D"margin:0px; =3D
> padding:0px;" >=3DC2=3DA0</p></span></span>
>=20


=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
Prof. Dr. Marcel Swart

ICREA Research Professor at
Institut de Qu=EDmica Computacional i Cat=E0lisi
Universitat de Girona

Facultat de Ci=E8ncies
Campus Montilivi
17071 Girona
Catalunya (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mail
marcel.swart~~icrea.cat
marcel.swart~~udg.edu
web
http://www.marcelswart.eu
vCard
addressbook://www.marcelswart.eu/MSwart.vcf
=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






--Apple-Mail=_88816C54-2A40-418E-920D-C993C2C393EE
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html;
	charset=iso-8859-1

<html><head><meta http-equiv=3D"Content-Type" content=3D"text/html =
charset=3Diso-8859-1"><meta http-equiv=3D"Content-Type" =
content=3D"text/html charset=3Diso-8859-1"></head><body =
style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space;">I would say a cluster model of =
real atoms embedded in the Madelung potential<div>of surrounding crystal =
environment. This is standard practice with people =
using</div><div>MOLCAS such as Coen de Graaf, Ria Broer, Francesc Illas, =
Carmen Sousa</div><div>to name just a few. For MgO, see =
e.g.</div><div><a =
href=3D"http://prb.aps.org/abstract/PRB/v62/i15/p10013_1">http://prb.aps.o=
rg/abstract/PRB/v62/i15/p10013_1</a></div><div><br></div><div>Marcel</div>=
<div><br><div><div>On 29 Nov 2013, at 15:15, Brian Skinn =
brian.skinn---<a href=3D"http://gmail.com">gmail.com</a> &lt;<a =
href=3D"mailto:owner-chemistry~~ccl.net">owner-chemistry~~ccl.net</a>&gt; =
wrote:</div><br class=3D"Apple-interchange-newline"><blockquote =
type=3D"cite"><div dir=3D"ltr"><div><div>Or:<br><br></div>3) One Na atom =
next to a Cl atom in a three-dimensional matrix of Na and Cl =
atoms.<br><br></div>Gas phase simulations of crystal unit cells do not, =
in general, represent a good model for the extended phase properties of =
that crystal.&nbsp; If I'm understanding what you're seeking to =
investigate, you should probably consider something more like CPMD or =
CASINO (quantum Monte Carlo), using an infinitely repeating simulation =
box.&nbsp; These should allow more ready examination of the extended =
system of, e.g., your MgO particle or the surface of that particle, and =
also of the various geometrical configurations/microstates accessible to =
that system at your temperature of interest.<br>

<br>-Brian<br><br></div><div class=3D"gmail_extra"><br><br><div =
class=3D"gmail_quote">On Fri, Nov 29, 2013 at 4:16 AM, Sergio Manzetti =
sergio.manzetti%x%<a href=3D"http://gmx.com/">gmx.com</a> <span =
dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry%C3%8Cl.net" =
target=3D"_blank">owner-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:1ex">How does one =
distingusih from a calculation of:<br>
<br>
1. One Table salt molecule.<br>
<br>
2. One Sodium atom and one Chloride atom next to each other, spaced by =
1.2 =C5.<br>
<br>
<br>
<br>
Sergio<br>
<div class=3D"im">----- Original Message -----<br>
&gt; From: Laurence Cuffe cuffe(~)<a href=3D"http://mac.com/" =
target=3D"_blank">mac.com</a><br>
Sent: 11/28/13 10:29 PM<br>
To: Manzetti, Sergio<br>
Subject: CCL:G: Earth metal oxides in Gaussian<br>
<br>
Sent from QCloud<br>
On Nov 28, 2013, at 05:03 AM, "Sergio Manzetti sergio.manzetti:<a =
href=3D"http://gmx.com/" target=3D"_blank">gmx.com</a>" =
&lt;owner-chemistry]^[<a href=3D"http://ccl.net/" =
target=3D"_blank">ccl.net</a>&gt; wrote:<br>
<br>
Sent to CCL by: "Sergio Manzetti" [sergio.manzetti(a)<a =
href=3D"http://gmx.com/" target=3D"_blank">gmx.com</a>]<br>
Dear all, as earth metal oxides, such as ZnO are particles, how can =
these be represented correctly as single molecules for calculations? =
Considering their charge, for instance, Mg2+ and O2-, their bonding =
should be ionic, however this is not clearly represented in the gaussian =
outputs when running simple MgO calculations and Mg can assimilate =
multiple bonds to other neighbouring atoms.<br>


<br>
How can this be correctly defined? Should open shell calculations be =
used?<br>
<br>
Thanks<br>
There is a bit of a culture and language issue here. We are taught all =
sorts of models of bonding and electron behavior in our chemical =
education, and it is sometimes dificult to realise that an electronic =
structure model, as implemented by an ab initio program such as the one =
you mentioned, is a deeper model where the language of interation which =
we inherit from the simpler descriptions, may no longer be the most =
acurate way of describing what is happening. By all means try open shell =
calculations, but be prepared for the eventuality that they may not =
clarify the picture in terms of a simpler understanding.<br>


All the best<br>
</div>Laurence Cuffethe strange characters on the top line to the ]^[ =
sign. You can alsoE-mail to subscribers: &nbsp;CHEMISTRY%5D%5E%<a =
href=3D"http://5Bccl.net">5Bccl.net</a> &nbsp;or use:E-mail to =
administrators: &nbsp;CHEMISTRY-REQUEST%5D%5E%<a =
href=3D"http://5Bccl.net">5Bccl.net</a> &nbsp;or usehttp://<a =
href=3D"http://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spa=
mmers.txt--=3D=3D=3D=3D=3D=3D=3D=3DGMXBoundary208791385716574266531Content=
-Type" =
target=3D"_blank">www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/=
spammers.txt--=3D=3D=3D=3D=3D=3D=3D=3DGMXBoundary208791385716574266531<br>=

Content-Type</a>: text/html; charset=3D"utf-8"<br>
Content-Transfer-Encoding: quoted-printable<br>
<br>
&lt;span style=3D3D'font-family:Verdana'&gt;&lt;span =
style=3D3D'font-size:12px'&gt;How does=3D<br>
&nbsp;one distingusih from a calculation of:&lt;br /&gt;&lt;br /&gt;1. =
One Table salt molecu=3D<br>
le.&lt;br /&gt;&lt;br /&gt;2. One Sodium atom and one Chloride atom next =
to each other,=3D<br>
&nbsp;spaced by 1.2 =3DC3=3D85.&lt;br /&gt;&lt;br /&gt;&lt;br =
/&gt;&lt;br /&gt;Sergio&lt;p style=3D3D"margin:0px;=3D<br>
&nbsp;padding:0px;" &gt;=3DC2=3DA0&lt;/p&gt;&lt;blockquote =
style=3D3D"border-left: 1px solid #CCC;=3D<br>
&nbsp;padding-left: 5px; margin-left: 5px; margin-bottom: 0px; =
margin-top: 0px; =3D<br>
margin-right: 0px;" type=3D3D"cite"&gt;&lt;p style=3D3D"margin:0px; =
padding:0px;" &gt;&lt;s=3D<br>
pan style=3D3D"font-family:Verdana"&gt;&lt;span =
style=3D3D"font-size:12px"&gt;----- Orig=3D<br>
inal Message -----&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p =
style=3D3D"margin:0px; padding:0px;" &gt;=3D<br>
&lt;span style=3D3D"font-family:Verdana"&gt;&lt;span =
style=3D3D"font-size:12px"&gt;From: La=3D<br>
urence Cuffe cuffe(~)<a href=3D"http://mac.com/" =
target=3D"_blank">mac.com</a>&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p =
style=3D3D"margin:0px; paddi=3D<br>
ng:0px;" &gt;&lt;span style=3D3D"font-family:Verdana"&gt;&lt;span =
style=3D3D"font-size:12px=3D<br>
"&gt;Sent: 11/28/13 10:29 PM&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p =
style=3D3D"margin:0px; padding:=3D<br>
0px;" &gt;&lt;span style=3D3D"font-family:Verdana"&gt;&lt;span =
style=3D3D"font-size:12px"&gt;T=3D<br>
o: Manzetti, Sergio &lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p =
style=3D3D"margin:0px; paddi=3D<br>
ng:0px;" &gt;&lt;span style=3D3D"font-family:Verdana"&gt;&lt;span =
style=3D3D"font-size:12px=3D<br>
"&gt;Subject: CCL:G: Earth metal oxides in =
Gaussian&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;=3DC2=3DA0&lt;di=3D<br>
v&gt;&lt;div&gt;=3DC2=3DA0&lt;/div&gt;&lt;div&gt;&lt;pre =
style=3D3D"white-space: pre-wrap; word-wrap: bre=3D<br>
ak-word; font-size:11;font-family: 'Helvetica Neue', Helvetica, =
sans-serif;=3D<br>
&nbsp;font-size: 15px; white-space: pre-wrap"&gt;Sent from =
QCloud&lt;/pre&gt;&lt;/div&gt;&lt;div&gt;&lt;=3D<br>
br /&gt;On Nov 28, 2013, at 05:03 AM, "Sergio Manzetti =
sergio.manzetti:<a href=3D"http://gmx.com/" =
target=3D"_blank">gmx.com</a>=3D<br>
" &amp;lt;owner-chemistry]^[<a href=3D"http://ccl.net/" =
target=3D"_blank">ccl.net</a>&amp;gt; wrote:&lt;br =
/&gt;=3DC2=3DA0&lt;div&gt;&lt;blockquote type=3D<br>
=3D3D"cite"&gt;&lt;div class=3D3D"msg-quote"&gt;&lt;div =
class=3D3D"_stretch"&gt;&lt;br /&gt;Sent to CC=3D<br>
L by: "Sergio Manzetti" [sergio.manzetti(a)<a href=3D"http://gmx.com/" =
target=3D"_blank">gmx.com</a>]&lt;br /&gt;Dear all, as earth=3D<br>
&nbsp;metal oxides, such as ZnO are particles, how can these be =
represented corr=3D<br>
ectly as single molecules for calculations? Considering their charge, =
for i=3D<br>
nstance, Mg2+ and O2-, their bonding should be ionic, however this is =
not c=3D<br>
learly represented in the gaussian outputs when running simple MgO =
calculat=3D<br>
ions and Mg can assimilate multiple bonds to other neighbouring =
atoms.&lt;br /=3D<br>
&gt;&lt;br /&gt;How can this be correctly defined? Should open shell =
calculations be=3D<br>
&nbsp;used?&lt;br /&gt;&lt;br =
/&gt;Thanks&lt;/div&gt;&lt;/div&gt;&lt;/blockquote&gt;&lt;span&gt;&amp;nbs=
p;&lt;/span&gt;&lt;br /&gt;T=3D<br>
here is a bit of a culture and language issue here. We are taught all =
sorts=3D<br>
&nbsp;of models of bonding and electron behavior in our chemical =
education, and =3D<br>
it is sometimes dificult to realise that an electronic structure model, =
as =3D<br>
implemented by an ab initio program such as the one you mentioned, is a =
dee=3D<br>
per model where the language of interation which we inherit from the =
simple=3D<br>
r descriptions, may no longer be the most acurate way of describing what =
is=3D<br>
&nbsp;happening. By all means try open shell calculations, but be =
prepared for t=3D<br>
he eventuality that they may not clarify the picture in terms of a =
simpler =3D<br>
understanding.&lt;br /&gt;All the best&lt;br /&gt;Laurence Cuffe&lt;br =
/&gt;&lt;br /&gt;=3DC2=3DA0&lt;bloc=3D<br>
kquote type=3D3D"cite"&gt;&lt;div class=3D3D"msg-quote"&gt;&lt;div =
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From owner-chemistry@ccl.net Fri Nov 29 14:24:00 2013
From: "Torstein Fjermestad torstein.fjermestad++unito.it" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL:G: Optimizing only the shell coordinates in GULP
Message-Id: <-49390-131129133829-20063-98CTpUEdMzEXUEqITZh1sQ]![server.ccl.net>
X-Original-From: "Torstein  Fjermestad" <torstein.fjermestad,unito.it>
Date: Fri, 29 Nov 2013 13:38:26 -0500


Sent to CCL by: "Torstein  Fjermestad" [torstein.fjermestad(-)unito.it]
Dear CCL Subscribers,

I am planing to do an ONIOM calculation on a zeolite system. DFT is going to 
be the high level method, and a shell model force field implemented in GULP 
is going to be the low level method. The ONIOM energy evaluation and 
optimization is going to be done with Gaussian and GULP is going to be 
interfaced through the "External" keyword. 

For such a calculation to work, GULP must provide the total energy and the 
gradients of the atom coordinates. In a shell model force field there are 
also shell coordinates. Gaussian does not know about shell coordinates, and 
the solution I have been thinking about is to freeze the atom coordinates 
(provided by Gaussian through the "External" mechanism) and optimize ONLY the 
shell coordinates. With the shell coordinates optimized, I would like to 
compute the gradients of the atom coordinates and feed these back to 
Gaussian. 
Does anyone know if this is possible with GULP? 

> From the manual and the help function, I have got the impression that this is 
possible, but still I have not succeeded. An attempt I made was to include 
the keywords 

shell gradient conv

This computes the gradients, but the shell coordinates do not seem to be 
optimized (the numerical values of the gradients are far from zero). 

Any help in solving this problem is appreciated. 

Regards,
Torstein Fjermestad