Re: [Jmol-users] ionic radii
And here are my notes, in
http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/util/Elements.java
The note about O- and N+ refers to the fact that we use the covalent
bonding radius for these, not the crystal ionic radius, because those
number are just so not useful for organic compounds and pretty unusual in
any crystal structure as well. We are talking about *isolated* ions for
that HCP table: N+ (0.25 A), O- (1.76 A). In the 54th Edition (dates, me,
huh?) I read, "may have been calculated from wavefunctions" with no
additional references, so I'm guessing that's the case for N+ and O- as
isolated ions.
Bob
* This data is from
* Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143
* (scanned for Jmol by Phillip Barak, Jan 2004)
*
* Reorganized from two separate arrays 9/2006 by Bob Hanson, who thought
* it was just too hard to look these up and, if necessary, add or modify.
* At the same time, the table was split into cations and anions for
easier
* retrieval.
*
* O- and N+ removed 9/2008 - BH. The problem is that
* the formal charge is used to determine bonding radius.
* But these formal charges are different than the charges used in
* compilation of HCP data (which is crystal ionic radii).
* Specifically, because O- and N+ are very common in organic
* compounds, I have removed their radii from the table FOR OUR PURPOSES
HERE.
*
* I suppose there are some ionic compounds that have O- and N+ as
* isolated ions, but what they would be I have no clue. Better to
* be safe and go with somewhat more reasonable values.
*
On Fri, Apr 18, 2014 at 5:04 PM, Phillip Barak wrote:
> These are ionic radii in the sense that Linus Pauling used them for
> multiple oxidation states, extended a number of times in the literature,
> and probably reaching their pinnacle in the work of Shannon et al, who
> calculated ionic radii as a functional of coordination number. See
> http://en.wikipedia.org/wiki/Ionic_radius for a bit more.
>
> They work tolerably well for help in calculating bonding in Jmol,
> particularly for the inorganic components...values for carbon, for example,
> vary considerably depending on whether it is +4 (as in carbonate) or -4
> (organic carbon). They are of course just another way of visualizing atoms,
> so they are not 'right'.
>
>
>
>
> On 04/18/14, *Robert Hanson * wrote:
>
> "ionic" in Jmol is a bit of a misnomer. I have never liked it. It refers
> to a mix of covalent bonding radii and ionic radii, and really there is no
> "turning it off". The spreadsheet detailing this is online. See
> http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/_documents/
>
> perhaps ionicradia11.xls
>
> Note that for these ionic values to apply, you need formal charges:
>
> load http://chemapps.stolaf.edu/jmol/docs/examples-12/data/nacl.cif packed
> {_Na}.formalCharge = 1
> {_Cl}.formalCharge = -1
> spacefill ionic
>
>
>
>
>
>
>
>
>
>
>
> On Fri, Apr 18, 2014 at 9:19 AM, Pshemak Maslak wrote:
>
>> On 4/18/2014 5:47 AM, Angel Herráez wrote:
>>
>> Hi Pshemak
>>
>> try this:
>>
>> spacefill ionic;
>> print {*}.radius.all;
>>
>> If you want the full list of original values used, you probably need to
>> check
>> the source code. The Scripting Doc page has a link to an Excel table (it may
>> be not up to date, I know there was a recent change in something related to
>> bonding radii) athttp://chemapps.stolaf.edu/jmol/docs/misc/radii.xls
>>
>>
>>
>> Thanks! That helps.. It looks like there are some unusual
>> discrepancies. For example:
>>
>> Br(-1) 1.96 A on the xls list and 1.21 A in Jmol when read from KBr,cif
>> file
>> Cl(-1) 1.81 A on the xls list and 0.99 A in Jmol when read from CsCl.cif
>> file (it shows correctly at 1.81 A from NaCl.cif file)
>>
>> Any idea of what is happening?
>>
>> PM
>>
>> PS. (Can I enclose the cif files with the email?).
>>
>>
>> --
>> Learn Graph Databases - Download FREE O'Reilly Book
>> "Graph Databases" is the definitive new guide to graph databases and their
>> applications. Written by three acclaimed leaders in the field,
>> this first edition is now available. Download your free book today!
>> http://p.sf.net/sfu/NeoTech
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
> --
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and
Re: [Jmol-users] ionic radii
These are ionic radii in the sense that Linus Pauling used them for multiple
oxidation states, extended a number of times in the literature, and probably
reaching their pinnacle in the work of Shannon et al, who calculated ionic
radii as a functional of coordination number. See
http://en.wikipedia.org/wiki/Ionic_radius for a bit more.
They work tolerably well for help in calculating bonding in Jmol, particularly
for the inorganic components...values for carbon, for example, vary
considerably depending on whether it is +4 (as in carbonate) or -4 (organic
carbon). They are of course just another way of visualizing atoms, so they are
not 'right'.
On 04/18/14, Robert Hanson wrote:
> "ionic" in Jmol is a bit of a misnomer. I have never liked it. It refers to a
> mix of covalent bonding radii and ionic radii, and really there is no
> "turning it off". The spreadsheet detailing this is online. See
> http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/_documents/
>
>
>
> perhaps ionicradia11.xls
>
>
> Note that for these ionic values to apply, you need formal charges:
>
> load http://chemapps.stolaf.edu/jmol/docs/examples-12/data/nacl.cif packed
>
> {_Na}.formalCharge = 1
> {_Cl}.formalCharge = -1
> spacefill ionic
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Fri, Apr 18, 2014 at 9:19 AM, Pshemak Maslak wrote:
>
>
> > On 4/18/2014 5:47 AM, Angel Herráez wrote:
> >
> >
> > >
> > > Hi Pshemak try this: spacefill ionic;
> > > print {*}.radius.all; If you want the full list of original values used,
> > > you probably need to check the source code. The Scripting Doc page has a
> > > link to an Excel table (it may be not up to date, I know there was a
> > > recent change in something related to bonding radii) at
> > > http://chemapps.stolaf.edu/jmol/docs/misc/radii.xls
> > >
> >
> >
> >
> > Thanks! That helps.. It looks like there are some unusual discrepancies.
> > For example:
> >
> > Br(-1) 1.96 A on the xls list and 1.21 A in Jmol when read from KBr,cif
> > file
> > Cl(-1) 1.81 A on the xls list and 0.99 A in Jmol when read from CsCl.cif
> > file (it shows correctly at 1.81 A from NaCl.cif file)
> >
> > Any idea of what is happening?
> >
> > PM
> >
> > PS. (Can I enclose the cif files with the email?).
> >
> > --
> >
> > Learn Graph Databases - Download FREE O'Reilly Book
> >
> > "Graph Databases" is the definitive new guide to graph databases and their
> >
> > applications. Written by three acclaimed leaders in the field,
> >
> > this first edition is now available. Download your free book today!
> >
> > http://p.sf.net/sfu/NeoTech
> > ___
> >
> > Jmol-users mailing list
> >
> > Jmol-users@lists.sourceforge.net
> >
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
> >
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
>
>
--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] ionic radii
"ionic" in Jmol is a bit of a misnomer. I have never liked it. It refers to
a mix of covalent bonding radii and ionic radii, and really there is no
"turning it off". The spreadsheet detailing this is online. See
http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/_documents/
perhaps ionicradia11.xls
Note that for these ionic values to apply, you need formal charges:
load http://chemapps.stolaf.edu/jmol/docs/examples-12/data/nacl.cif packed
{_Na}.formalCharge = 1
{_Cl}.formalCharge = -1
spacefill ionic
On Fri, Apr 18, 2014 at 9:19 AM, Pshemak Maslak wrote:
> On 4/18/2014 5:47 AM, Angel Herráez wrote:
>
> Hi Pshemak
>
> try this:
>
> spacefill ionic;
> print {*}.radius.all;
>
> If you want the full list of original values used, you probably need to check
> the source code. The Scripting Doc page has a link to an Excel table (it may
> be not up to date, I know there was a recent change in something related to
> bonding radii) athttp://chemapps.stolaf.edu/jmol/docs/misc/radii.xls
>
>
>
> Thanks! That helps.. It looks like there are some unusual
> discrepancies. For example:
>
> Br(-1) 1.96 A on the xls list and 1.21 A in Jmol when read from KBr,cif
> file
> Cl(-1) 1.81 A on the xls list and 0.99 A in Jmol when read from CsCl.cif
> file (it shows correctly at 1.81 A from NaCl.cif file)
>
> Any idea of what is happening?
>
> PM
>
> PS. (Can I enclose the cif files with the email?).
>
>
> --
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/NeoTech
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] ionic radii
On 4/18/2014 5:47 AM, Angel Herráez wrote:
Hi Pshemak
try this:
spacefill ionic;
print {*}.radius.all;
If you want the full list of original values used, you probably need to check
the source code. The Scripting Doc page has a link to an Excel table (it may
be not up to date, I know there was a recent change in something related to
bonding radii) at
http://chemapps.stolaf.edu/jmol/docs/misc/radii.xls
Thanks! That helps.. It looks like there are some unusual
discrepancies. For example:
Br(-1) 1.96 A on the xls list and 1.21 A in Jmol when read from
KBr,cif file
Cl(-1) 1.81 A on the xls list and 0.99 A in Jmol when read from
CsCl.cif file (it shows correctly at 1.81 A from NaCl.cif file)
Any idea of what is happening?
PM
PS. (Can I enclose the cif files with the email?).
--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] ionic radii
Hi Pshemak
try this:
spacefill ionic;
print {*}.radius.all;
If you want the full list of original values used, you probably need to check
the source code. The Scripting Doc page has a link to an Excel table (it may
be not up to date, I know there was a recent change in something related to
bonding radii) at
http://chemapps.stolaf.edu/jmol/docs/misc/radii.xls
--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] ionic radii
Is it possible to print out ionic radii used by Jmol? PM -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
