ChemWiki - User contributions [en]

User:Njm08

2015-03-24T22:53:46Z

Njm08:

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The [http://www.mediawiki.org/wiki/Extension:Jmol mediawiki Jmol extension] comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter and confusion of countless individual Jmol applets, Jmol applet links/buttons or static 2D images, making them a great way to concisely display computational results.

Below is an interactive table for visualising vibrational modes. The Jmol applet loads the log file for a caculation performed in Gaussian. The buttons send scripts to the applet which load the appropriate models for the corresponding frequencies. Animation can be turned on or off via the labelled checkbox.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Mode
! Description
! Frequency
! lit. [http://dx.doi.org/10.1021/ja00738a008]
! Intensity
! Symmetry (D3h point group)
! Form of vibration
|-
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolCheckbox><scriptWhenChecked>vibration 5;</scriptWhenChecked><scriptWhenUnchecked>vibration OFF;</scriptWhenUnchecked><target>BH3_vibrations</target><text> Animation</text></jmolCheckbox></jmol>
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>4</text></jmolButton></jmol>
|
| 2598 || (2693 [http://dx.doi.org/10.1063/1.448805]) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

Here is an interactive table for visualising molecular orbitals in the style of the Gaussview MO editor dialog. The isosurface for each orbital (.jvxl file) is loaded via the push buttons. A further push button clears the applet of isosurfaces. Alternatively, the isosurfaces could be toggled between using a radio button group or even a drop down menu.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of H<sub>2</sub>O
| align="center" |
<jmol>
<jmolApplet>
<name>H2O_orbitals</name>
<color>white</color>
<size>300</size>
<script>frame 12; rotate z -27.7; rotate y 77.29; rotate z 88.65; zoom 115.03; translate x -5.71; translate y 1.71;</script>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24954/logfile.log</urlContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol>
<jmolButton>
<script>isosurface "images/3/36/Njm08-water-mo1.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>1</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/d/d5/Njm08-water-mo2.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>2</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/7/73/Njm08-water-mo3.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>3</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/b/b7/Njm08-water-mo4.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>4</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/9/90/Njm08-water-mo5.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>5</text>
</jmolButton>
<jmolButton>
<script>isosurface OFF</script>
<target>H2O_orbitals</target>
<text>clear</text>
</jmolButton>
</jmol>
| [[File:Njm08-water-mo-diagram.svg‎|140px|SVG Molecular orbitals of H2O]]
|}

View the page source to see how each table has been constructed. Documentation for the Jmol extension, including handy code snippets and a useful reference, can be found at http://wiki.jmol.org/index.php/MediaWiki.

==Loading Jmol files from the D-Space repository==

As well as loading files that have been uploaded to the wiki, Jmol can be used to load files from other URLs. This means that if you have published your calculation through the HPC web portal, it is possible to load your file directly from the digital repository.

URLs for files on the Imperial D-Space repository have the following structure:
<nowiki>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/</nowiki>''handle-prefix''/''handle-suffix''/''filename''

To load a file from a URL you must use the <code><nowiki><urlContents></nowiki></code> tag instead of the <code><nowiki><uploadedFileContents></nowiki></code> tag.

For example, the following code will produce a Jmol link that will load the log file from the D-Space calculation archive resolved by {{DOI|10042/24956}}:
<pre><nowiki>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

===Loading files from DSpace into Jmol using their Handle===

A better way of loading the file is to use a URL derived from the file-set's [http://handle.net Handle] (a type of persistent identifier). This helps to avoid future "link rot", which is where the URL of a webpage changes resulting in a dead link (404 File not found!).

Handles are resolved using the http://hdl.handle.net/ or http://doi.org/ proxy servers.
http://doi.org/10042/24956

The DSpace Handles can resolve directly to a specific file by appending a ''[http://www.handle.net/overviews/handle_type_10320_loc.html locatt]'' query string:
*<code><nowiki>http://doi.org/10042/24956?locatt=filename:logfile.log</nowiki></code>
*<code><nowiki>http://doi.org/10042/24956?locatt=mimetype:chemical/x-gaussian-log</nowiki></code>
*<code><nowiki>http://doi.org/10042/24956?locatt=mimetype:chemical/x-cml</nowiki></code>

Thus, the following code will create a Jmol link for the log file archived at {{DOI|10042/24956}}:
<pre><nowiki>
<jmol>
<jmolAppletLink>
<urlContents>http://doi.org/10042/24956?locatt=filename:logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>http://doi.org/10042/24956?locatt=filename:logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

===Loading files from DSpace into Jmol using their DOI===

Imperial's SPECTRa DSpace repository also assigns file-sets a [http://doi.org DOI]. DOIs are based on the Handle system and have a Handle-prefix that always start with "10.".

The DOIs do not have the ''locatt'' functionality described above. However, one can use [http://data.datacite.org DataCite services] to link directly to a file.

URLs must be constructed as follows:
<nowiki>http://data.datacite.org/</nowiki>''MIME_media_type''/''MIME_subtype''/''DOI-prefix''/''DOI-suffix''

Currently only the CML file (MIME = chemical/x-cml) can be loaded in this way.

Thus, the following code will create a Jmol link for the CML file archived at {{DOI|10.14469/CH/18917}}:
<pre><nowiki>
<jmol>
<jmolAppletLink>
<urlContents>http://data.datacite.org/chemical/x-cml/10.14469/CH/18917</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>http://data.datacite.org/chemical/x-cml/10.14469/CH/18917</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

User:Njm08

2015-03-24T21:55:18Z

Njm08:

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The [http://www.mediawiki.org/wiki/Extension:Jmol mediawiki Jmol extension] comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter and confusion of countless individual Jmol applets, Jmol applet links/buttons or static 2D images, making them a great way to concisely display computational results.

Below is an interactive table for visualising vibrational modes. The Jmol applet loads the log file for a caculation performed in Gaussian. The buttons send scripts to the applet which load the appropriate models for the corresponding frequencies. Animation can be turned on or off via the labelled checkbox.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Mode
! Description
! Frequency
! lit. [http://dx.doi.org/10.1021/ja00738a008]
! Intensity
! Symmetry (D3h point group)
! Form of vibration
|-
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolCheckbox><scriptWhenChecked>vibration 5;</scriptWhenChecked><scriptWhenUnchecked>vibration OFF;</scriptWhenUnchecked><target>BH3_vibrations</target><text> Animation</text></jmolCheckbox></jmol>
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>4</text></jmolButton></jmol>
|
| 2598 || (2693 [http://dx.doi.org/10.1063/1.448805]) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><target>BH3_vibrations</target><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

Here is an interactive table for visualising molecular orbitals in the style of the Gaussview MO editor dialog. The isosurface for each orbital (.jvxl file) is loaded via the push buttons. A further push button clears the applet of isosurfaces. Alternatively, the isosurfaces could be toggled between using a radio button group or even a drop down menu.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of H<sub>2</sub>O
| align="center" |
<jmol>
<jmolApplet>
<name>H2O_orbitals</name>
<color>white</color>
<size>300</size>
<script>frame 12; rotate z -27.7; rotate y 77.29; rotate z 88.65; zoom 115.03; translate x -5.71; translate y 1.71;</script>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24954/logfile.log</urlContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol>
<jmolButton>
<script>isosurface "images/3/36/Njm08-water-mo1.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>1</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/d/d5/Njm08-water-mo2.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>2</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/7/73/Njm08-water-mo3.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>3</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/b/b7/Njm08-water-mo4.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>4</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/9/90/Njm08-water-mo5.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>5</text>
</jmolButton>
<jmolButton>
<script>isosurface OFF</script>
<target>H2O_orbitals</target>
<text>clear</text>
</jmolButton>
</jmol>
| [[File:Njm08-water-mo-diagram.svg‎|140px|SVG Molecular orbitals of H2O]]
|}

View the page source to see how each table has been constructed. Documentation for the Jmol extension, including handy code snippets and a useful reference, can be found at http://wiki.jmol.org/index.php/MediaWiki.

==Loading Jmol files from the D-Space repository==

As well as loading files that have been uploaded to the wiki, Jmol can be used to load files from other URLs. This means that if you have published your calculation through the HPC web portal, it is possible to load your file directly from the digital repository.

URLs for files on the Imperial D-Space repository have the following structure:
<nowiki>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/</nowiki>''handle-prefix''/''handle-suffix''/''filename''

To load a file from a URL you must use the <code><nowiki><urlContents></nowiki></code> tag instead of the <code><nowiki><uploadedFileContents></nowiki></code> tag.

For example, the following code will produce a Jmol link that will load the log file from the D-Space calculation archive resolved by {{DOI|10042/24956}}:
<pre><nowiki>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

===Loading files from DSpace into Jmol using their Handle===

A better way of loading the file is to use a URL derived from the file-set's Handle (a type of persistent identifier). This helps to avoid future "link rot", which is where the URL of a webpage changes resulting in a dead link (404 File not found!).

Handles are resolved using the http://hdl.handle.net/ or http://doi.org/ proxy servers.
http://doi.org/10042/24956

The DSpace Handles can resolve directly to a specific file by appending a ''locatt'' query string:
*<code><nowiki>http://doi.org/10042/24956?locatt=filename:logfile.log</nowiki></code>
*<code><nowiki>http://doi.org/10042/24956?locatt=mimetype:chemical/x-gaussian-log</nowiki></code>
*<code><nowiki>http://doi.org/10042/24956?locatt=mimetype:chemical/x-cml</nowiki></code>

Thus, the following code will create a Jmol link for log file archived at {{DOI|10042/24956}}:
<pre><nowiki>
<jmol>
<jmolAppletLink>
<urlContents>http://doi.org/10042/24956?locatt=filename:logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>http://doi.org/10042/24956?locatt=filename:logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

===Loading files from DSpace into Jmol using their DOI===

Imperial's SPECTRa DSpace repository also assigns file-sets a DOI. DOIs are based on the Handle system and have a Handle-prefix that always start with "10.".

The DOIs do not have the ''locatt'' functionality described above. However, one can use DataCite services the link directly to a file.

URLs must be constructed as follows:
<nowiki>http://data.datacite.org/</nowiki>''MIME_media_type''/''MIME_subtype''/''DOI-prefix''/''DOI-suffix''

Currently only the CML file (MIME = chemical/x-cml) can be loaded in this way.

Thus, the following code will create a Jmol link for the CML file archived at {{DOI|10.14469/CH/18917}}:
<pre><nowiki>
<jmol>
<jmolAppletLink>
<urlContents>http://data.datacite.org/chemical/x-cml/10.14469/CH/18917</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>http://data.datacite.org/chemical/x-cml/10.14469/CH/18917</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

User:Njm08

2015-03-24T20:08:44Z

Njm08:

User:Njm08

2013-08-20T17:18:34Z

Njm08: /* Interactive tables */

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The [http://www.mediawiki.org/wiki/Extension:Jmol mediawiki Jmol extension] comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter and confusion of countless individual Jmol applets, Jmol applet links/buttons or static 2D images, making them a great way to concisely display computational results.

Below is an interactive table for visualising vibrational modes. The Jmol applet loads the log file for a caculation performed in Gaussian. The buttons send scripts to the applet which load the appropriate models for the corresponding frequencies. Animation can be turned on or off via the labelled checkbox.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! lit. [http://dx.doi.org/10.1021/ja00738a008]
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolCheckbox><scriptWhenChecked>vibration 5;</scriptWhenChecked><scriptWhenUnchecked>vibration OFF;</scriptWhenUnchecked><text> Animation</text></jmolCheckbox></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>4</text></jmolButton></jmol>
|
| 2598 || (2693 [http://dx.doi.org/10.1063/1.448805]) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

Here is an interactive table for visualising molecular orbitals in the style of the Gaussview MO editor dialog. The isosurface for each orbital (.jvxl file) is loaded via the push buttons. A further push button clears the applet of isosurfaces. Alternatively, the isosurfaces could be toggled between using a radio button group or even a drop down menu.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of H<sub>2</sub>O
| align="center" |
<jmol>
<jmolApplet>
<name>H2O_orbitals</name>
<color>white</color>
<size>300</size>
<script>frame 12; rotate z -27.7; rotate y 77.29; rotate z 88.65; zoom 115.03; translate x -5.71; translate y 1.71;</script>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24954/logfile.log</urlContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol>
<jmolButton>
<script>isosurface "images/3/36/Njm08-water-mo1.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>1</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/d/d5/Njm08-water-mo2.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>2</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/7/73/Njm08-water-mo3.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>3</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/b/b7/Njm08-water-mo4.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>4</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/9/90/Njm08-water-mo5.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>5</text>
</jmolButton>
<jmolButton>
<script>isosurface OFF</script>
<target>H2O_orbitals</target>
<text>clear</text>
</jmolButton>
</jmol>
| [[File:Njm08-water-mo-diagram.svg‎|140px|SVG Molecular orbitals of H2O]]
|}

View the page source to see how each table has been constructed. Documentation for the Jmol extension, including handy code snippets and a useful reference, can be found at http://wiki.jmol.org/index.php/MediaWiki.

==Loading Jmol files from the D-Space repository==

As well as loading files that have been uploaded to the wiki, Jmol can be used to load files from other URLs. This means that if you have published your calculation through the HPC web portal, it is possible to load your file directly from the digital repository.

URLs for files on the Imperial D-Space repository have the following structure:
<nowiki>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/</nowiki>''handle-prefix''/''handle-suffix''/''filename''

To load a file from a URL you must use the <code><nowiki><urlContents></nowiki></code> tag instead of the <code><nowiki><uploadedFileContents></nowiki></code> tag.

For example, the following code will produce a Jmol link that will load the log file from the D-Space calculation archive resolved by {{DOI|10042/24956}}:
<pre><nowiki>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

File:Njm08-water-mo-diagram.svg

2013-08-20T17:16:13Z

Njm08: uploaded a new version of "File:Njm08-water-mo-diagram.svg"

File:Njm08-water-mo-diagram.svg

2013-08-20T17:11:46Z

Njm08: uploaded a new version of "File:Njm08-water-mo-diagram.svg"

User:Njm08

2013-08-20T17:02:12Z

Njm08: /* Interactive tables */

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The [http://www.mediawiki.org/wiki/Extension:Jmol mediawiki Jmol extension] comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter and confusion of countless individual Jmol applets, Jmol applet links/buttons or static 2D images, making them a great way to concisely display computational results.

Below is an interactive table for visualising vibrational modes. The Jmol applet loads the log file for a caculation performed in Gaussian. The buttons send scripts to the applet which load the appropriate models for the corresponding frequencies. Animation can be turned on or off via the labelled checkbox.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! lit. [http://dx.doi.org/10.1021/ja00738a008]
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolCheckbox><scriptWhenChecked>vibration 5;</scriptWhenChecked><scriptWhenUnchecked>vibration OFF;</scriptWhenUnchecked><text> Animation</text></jmolCheckbox></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>4</text></jmolButton></jmol>
|
| 2598 || (2693 [http://dx.doi.org/10.1063/1.448805]) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

Here is an interactive table for visualising molecular orbitals in the style of the Gaussview MO editor dialog. The isosurface for each orbital (.jvxl file) is loaded via the push buttons. A further push button clears the applet of isosurfaces. Alternatively, the isosurfaces could be toggled between using a radio button group or even a drop down menu.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of H<sub>2</sub>O
| align="center" |
<jmol>
<jmolApplet>
<name>H2O_orbitals</name>
<color>white</color>
<size>350</size>
<script>frame 12; rotate z -27.7; rotate y 77.29; rotate z 88.65; zoom 115.03; translate x -5.71; translate y 1.71;</script>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24954/logfile.log</urlContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol>
<jmolButton>
<script>isosurface "images/3/36/Njm08-water-mo1.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>1</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/d/d5/Njm08-water-mo2.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>2</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/7/73/Njm08-water-mo3.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>3</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/b/b7/Njm08-water-mo4.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>4</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/9/90/Njm08-water-mo5.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>5</text>
</jmolButton>
<jmolButton>
<script>isosurface OFF</script>
<target>H2O_orbitals</target>
<text>clear</text>
</jmolButton>
</jmol>
| [[File:Njm08-water-mo-diagram.svg‎|200px|SVG Molecular orbitals of H2O]]
|}

View the page source to see how each table has been constructed. Documentation for the Jmol extension, including handy code snippets and a useful reference, can be found at http://wiki.jmol.org/index.php/MediaWiki.

==Loading Jmol files from the D-Space repository==

As well as loading files that have been uploaded to the wiki, Jmol can be used to load files from other URLs. This means that if you have published your calculation through the HPC web portal, it is possible to load your file directly from the digital repository.

URLs for files on the Imperial D-Space repository have the following structure:
<nowiki>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/</nowiki>''handle-prefix''/''handle-suffix''/''filename''

To load a file from a URL you must use the <code><nowiki><urlContents></nowiki></code> tag instead of the <code><nowiki><uploadedFileContents></nowiki></code> tag.

For example, the following code will produce a Jmol link that will load the log file from the D-Space calculation archive resolved by {{DOI|10042/24956}}:
<pre><nowiki>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

User:Njm08

2013-08-20T16:54:27Z

Njm08:

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The [http://www.mediawiki.org/wiki/Extension:Jmol mediawiki Jmol extension] comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter and confusion of countless individual Jmol applets, Jmol applet links/buttons or static 2D images, making them a great way to concisely display computational results.

Below is an interactive table for visualising vibrational modes. The Jmol applet loads the log file for a caculation performed in Gaussian. The buttons send scripts to the applet which load the appropriate models for the corresponding frequencies. Animation can be turned on or off via the labelled checkbox.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! lit. [http://dx.doi.org/10.1021/ja00738a008]
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolCheckbox><scriptWhenChecked>vibration 5;</scriptWhenChecked><scriptWhenUnchecked>vibration OFF;</scriptWhenUnchecked><text> Animation</text></jmolCheckbox></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>4</text></jmolButton></jmol>
|
| 2598 || (2693 [http://dx.doi.org/10.1063/1.448805]) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

Here is a "Gaussview"-style interactive table for visualising molecular orbitals. The isosurface for each orbital (.jvxl file) is loaded via the push buttons. A further push button clears the applet of isosurfaces. Alternatively, the isosurfaces could be toggled between using a radio button group or even a drop down menu.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of H<sub>2</sub>O
| align="center" |
<jmol>
<jmolApplet>
<name>H2O_orbitals</name>
<color>white</color>
<size>350</size>
<script>frame 12; rotate z -27.7; rotate y 77.29; rotate z 88.65; zoom 115.03; translate x -5.71; translate y 1.71;</script>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24954/logfile.log</urlContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol>
<jmolButton>
<script>isosurface "images/3/36/Njm08-water-mo1.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>1</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/d/d5/Njm08-water-mo2.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>2</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/7/73/Njm08-water-mo3.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>3</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/b/b7/Njm08-water-mo4.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>4</text>
</jmolButton>
<jmolButton>
<script>isosurface "images/9/90/Njm08-water-mo5.jvxl" translucent</script>
<target>H2O_orbitals</target>
<text>5</text>
</jmolButton>
<jmolButton>
<script>isosurface OFF</script>
<target>H2O_orbitals</target>
<text>clear</text>
</jmolButton>
</jmol>
| [[File:Njm08-water-mo-diagram.svg‎|200px|SVG Molecular orbitals of H2O]]
|}

View the page source to see how each table has been constructed. Documentation for the Jmol extension, including handy code snippets and a useful reference, can be found at http://wiki.jmol.org/index.php/MediaWiki.

==Loading Jmol files from the D-Space repository==

As well as loading files that have been uploaded to the wiki, Jmol can be used to load files from other URLs. This means that if you have published your calculation through the HPC web portal, it is possible to load your file directly from the digital repository.

URLs for files on the Imperial D-Space repository have the following structure:
<nowiki>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/</nowiki>''handle-prefix''/''handle-suffix''/''filename''

To load a file from a URL you must use the <code><nowiki><urlContents></nowiki></code> tag instead of the <code><nowiki><uploadedFileContents></nowiki></code> tag.

For example, the following code will produce a Jmol link that will load the log file from the D-Space calculation archive resolved by {{DOI|10042/24956}}:
<pre><nowiki>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

File:Njm08-water-mo5.jvxl

2013-08-20T16:05:11Z

Njm08:

File:Njm08-water-mo4.jvxl

2013-08-20T16:05:10Z

Njm08:

File:Njm08-water-mo3.jvxl

2013-08-20T16:05:10Z

Njm08:

File:Njm08-water-mo2.jvxl

2013-08-20T16:05:10Z

Njm08:

File:Njm08-water-mo1.jvxl

2013-08-20T16:05:10Z

Njm08:

File:Njm08-water-mo-diagram.svg

2013-08-20T16:05:09Z

Njm08:

File:Water-mo5.jvxl

2013-08-20T16:00:26Z

Njm08:

File:Water-mo4.jvxl

2013-08-20T16:00:25Z

Njm08:

File:Water-mo3.jvxl

2013-08-20T16:00:24Z

Njm08:

File:Water-mo2.jvxl

2013-08-20T16:00:24Z

Njm08:

File:Water-mo1.jvxl

2013-08-20T16:00:23Z

Njm08:

File:MO-diagram.svg

2013-08-20T16:00:22Z

Njm08:

User:Njm08

2013-08-10T13:37:26Z

Njm08: /* Interactive tables */

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The [http://www.mediawiki.org/wiki/Extension:Jmol mediawiki Jmol extension] comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter and confusion of countless individual Jmol applets, Jmol applet links/buttons or static 2D images, making them a great way to concisely display computational results.

Below is an interactive table for visualising vibrational modes. The Jmol applet loads the log file for a caculation performed in Gaussian. The buttons send scripts to the applet which load the appropriate models for the corresponding frequencies. Animation can be turned on or off via the labelled checkbox.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! lit. [http://dx.doi.org/10.1021/ja00738a008]
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolCheckbox><scriptWhenChecked>vibration 5;</scriptWhenChecked><scriptWhenUnchecked>vibration OFF;</scriptWhenUnchecked><text> Animation</text></jmolCheckbox></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>4</text></jmolButton></jmol>
|
| 2598 || (2693 [http://dx.doi.org/10.1063/1.448805]) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

Here is a "Gaussview"-style interactive table for visualising molecular orbitals. The isosurface for each orbital (.jvxl file) is loaded via the push buttons. A further push button clears the applet of isosurfaces. Alternatively, the isosurfaces could be toggled between using a radio button group or even a drop down menu.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of BH<sub>3</sub>
| align="center" |<jmol>
<jmolApplet>
<name>BH3_orbitals</name><color>white</color><size>350</size>
<script>zoom 78.85;
</script><uploadedFileContents>BH3_njm08.mol</uploadedFileContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol><jmolButton><script>isosurface "images/f/ff/BH3_mo1_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>1</text></jmolButton>
<jmolButton><script>isosurface "images/4/41/BH3_mo2_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>2</text></jmolButton>
<jmolButton><script>isosurface "images/3/32/BH3_mo3_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>3</text></jmolButton>
<jmolButton><script>isosurface "images/3/3d/BH3_mo4_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>4</text></jmolButton>
<jmolButton><script>isosurface "images/d/d7/BH3_mo5_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>5</text></jmolButton>
<jmolButton><script>isosurface "images/4/4b/BH3_mo6_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>6</text></jmolButton>
<jmolButton><script>isosurface "images/f/f9/BH3_mo7_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>7</text></jmolButton>
<jmolButton><script>isosurface "images/5/5f/BH3_mo8_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>8</text></jmolButton>
<jmolButton><script>isosurface OFF</script><name>BH3_orbitals</name><text>clear</text></jmolButton></jmol>
| [[File:MOs_of_BH3_njm08.jpg|400px|]]
|}

View the page source to see how each table has been constructed. Documentation for the Jmol extension, including handy code snippets and a useful reference, can be found at http://wiki.jmol.org/index.php/MediaWiki.

==Loading Jmol files from the D-Space repository==

As well as loading files that have been uploaded to the wiki, Jmol can be used to load files from other URLs. This means that if you have published your calculation through the HPC web portal, it is possible to load your file directly from the digital repository.

URLs for files on the Imperial D-Space repository have the following structure:
<nowiki>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/</nowiki>''handle-prefix''/''handle-suffix''/''filename''

To load a file from a URL you must use the <code><nowiki><urlContents></nowiki></code> tag instead of the <code><nowiki><uploadedFileContents></nowiki></code> tag.

For example, the following code will produce a Jmol link that will load the log file from the D-Space calculation archive resolved by {{DOI|10042/24956}}:
<pre><nowiki><jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

User:Njm08

2013-08-10T13:14:35Z

Njm08: /* Loading Jmol files from the D-Space repository */

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The [http://www.mediawiki.org/wiki/Extension:Jmol mediawiki Jmol extension] comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter and confusion of countless individual Jmol applets, Jmol applet links/buttons or static 2D images, making them a great way to concisely display computational results.

Below is an interactive table for visualising the vibrational modes of water. The Jmol applet loads the log file for a caculation performed in Gaussian. The buttons send scripts to the applet which load the appropriate models for the corresponding frequencies. Animation can be turned on or off via the labelled checkbox.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! lit. [http://dx.doi.org/10.1021/ja00738a008]
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolCheckbox><scriptWhenChecked>vibration 5;</scriptWhenChecked><scriptWhenUnchecked>vibration OFF;</scriptWhenUnchecked><text> Animation</text></jmolCheckbox></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>4</text></jmolButton></jmol>
|
| 2598 || (2693 [http://dx.doi.org/10.1063/1.448805]) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

Here is a "Gaussview"-style interactive table for visualising molecular orbitals. The isosurface for each orbital (.jvxl file) is loaded via the push buttons. A further push button clears the applet of isosurfaces. Alternatively, the isosurfaces could be toggled between using a radio button group or even a drop down menu.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of BH<sub>3</sub>
| align="center" |<jmol>
<jmolApplet>
<name>BH3_orbitals</name><color>white</color><size>350</size>
<script>zoom 78.85;
</script><uploadedFileContents>BH3_njm08.mol</uploadedFileContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol><jmolButton><script>isosurface "images/f/ff/BH3_mo1_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>1</text></jmolButton>
<jmolButton><script>isosurface "images/4/41/BH3_mo2_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>2</text></jmolButton>
<jmolButton><script>isosurface "images/3/32/BH3_mo3_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>3</text></jmolButton>
<jmolButton><script>isosurface "images/3/3d/BH3_mo4_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>4</text></jmolButton>
<jmolButton><script>isosurface "images/d/d7/BH3_mo5_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>5</text></jmolButton>
<jmolButton><script>isosurface "images/4/4b/BH3_mo6_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>6</text></jmolButton>
<jmolButton><script>isosurface "images/f/f9/BH3_mo7_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>7</text></jmolButton>
<jmolButton><script>isosurface "images/5/5f/BH3_mo8_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>8</text></jmolButton>
<jmolButton><script>isosurface OFF</script><name>BH3_orbitals</name><text>clear</text></jmolButton></jmol>
| [[File:MOs_of_BH3_njm08.jpg|400px|]]
|}

View the page source to see how each table has been constructed. Documentation for the Jmol extension, including handy code snippets and a useful reference, can be found at http://wiki.jmol.org/index.php/MediaWiki.

==Loading Jmol files from the D-Space repository==

As well as loading files that have been uploaded to the wiki, Jmol can be used to load files from other URLs. This means that if you have published your calculation through the HPC web portal, it is possible to load your file directly from the digital repository.

URLs for files on the Imperial D-Space repository have the following structure:
<nowiki>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/</nowiki>''handle-prefix''/''handle-suffix''/''filename''

To load a file from a URL you must use the <code><nowiki><urlContents></nowiki></code> tag instead of the <code><nowiki><uploadedFileContents></nowiki></code> tag.

For example, the following code will produce a Jmol link that will load the log file from the D-Space calculation archive resolved by {{DOI|10042/24956}}:
<pre><nowiki><jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24956/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

User:Njm08

2013-08-10T13:12:04Z

Njm08: /* Interactive tables */

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The [http://www.mediawiki.org/wiki/Extension:Jmol mediawiki Jmol extension] comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter and confusion of countless individual Jmol applets, Jmol applet links/buttons or static 2D images, making them a great way to concisely display computational results.

Below is an interactive table for visualising the vibrational modes of water. The Jmol applet loads the log file for a caculation performed in Gaussian. The buttons send scripts to the applet which load the appropriate models for the corresponding frequencies. Animation can be turned on or off via the labelled checkbox.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! lit. [http://dx.doi.org/10.1021/ja00738a008]
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolCheckbox><scriptWhenChecked>vibration 5;</scriptWhenChecked><scriptWhenUnchecked>vibration OFF;</scriptWhenUnchecked><text> Animation</text></jmolCheckbox></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>4</text></jmolButton></jmol>
|
| 2598 || (2693 [http://dx.doi.org/10.1063/1.448805]) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

Here is a "Gaussview"-style interactive table for visualising molecular orbitals. The isosurface for each orbital (.jvxl file) is loaded via the push buttons. A further push button clears the applet of isosurfaces. Alternatively, the isosurfaces could be toggled between using a radio button group or even a drop down menu.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of BH<sub>3</sub>
| align="center" |<jmol>
<jmolApplet>
<name>BH3_orbitals</name><color>white</color><size>350</size>
<script>zoom 78.85;
</script><uploadedFileContents>BH3_njm08.mol</uploadedFileContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol><jmolButton><script>isosurface "images/f/ff/BH3_mo1_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>1</text></jmolButton>
<jmolButton><script>isosurface "images/4/41/BH3_mo2_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>2</text></jmolButton>
<jmolButton><script>isosurface "images/3/32/BH3_mo3_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>3</text></jmolButton>
<jmolButton><script>isosurface "images/3/3d/BH3_mo4_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>4</text></jmolButton>
<jmolButton><script>isosurface "images/d/d7/BH3_mo5_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>5</text></jmolButton>
<jmolButton><script>isosurface "images/4/4b/BH3_mo6_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>6</text></jmolButton>
<jmolButton><script>isosurface "images/f/f9/BH3_mo7_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>7</text></jmolButton>
<jmolButton><script>isosurface "images/5/5f/BH3_mo8_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>8</text></jmolButton>
<jmolButton><script>isosurface OFF</script><name>BH3_orbitals</name><text>clear</text></jmolButton></jmol>
| [[File:MOs_of_BH3_njm08.jpg|400px|]]
|}

View the page source to see how each table has been constructed. Documentation for the Jmol extension, including handy code snippets and a useful reference, can be found at http://wiki.jmol.org/index.php/MediaWiki.

==Loading Jmol files from the D-Space repository==

As well as loading files that have been uploaded to the wiki, Jmol can be used to load files from other URLs. This means that if you have published your calculation through the HPC web portal, it is possible to load your file directly from the digital repository.

URLs for files on the Imperial D-Space repository have the following structure:
<nowiki>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/</nowiki>''handle-prefix''/''handle-suffix''/''filename''

To load a file from a URL you must use the <code><nowiki><urlContents></nowiki></code> tag instead of the <code><nowiki><uploadedFileContents></nowiki></code> tag.

For example, the following code will produce a Jmol link that will load the log file from the D-Space calculation archive resolved by {{DOI|10042/24952}}:
<pre><nowiki><jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24952/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24952/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

User:Njm08

2013-08-10T13:11:05Z

Njm08: /* Interactive tables */

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The [http://www.mediawiki.org/wiki/Extension:Jmol mediawiki Jmol extension] comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter and confusion of countless individual Jmol applets, Jmol applet links/buttons or static 2D images, making them a great way to concisely display computational results.

Below is an interactive table for visualising the vibrational modes of water. The Jmol applet loads the log file for an <code>opt freq</code> caculation performed in Gaussian. The buttons send scripts to the applet which load the appropriate models for the corresponding frequencies. Animation can be turned on or off via the labelled checkbox.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! lit. [http://dx.doi.org/10.1021/ja00738a008]
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolCheckbox><scriptWhenChecked>vibration 5;</scriptWhenChecked><scriptWhenUnchecked>vibration OFF;</scriptWhenUnchecked><text> Animation</text></jmolCheckbox></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>4</text></jmolButton></jmol>
|
| 2598 || (2693 [http://dx.doi.org/10.1063/1.448805]) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

Here is a "Gaussview"-style interactive table for visualising molecular orbitals. The isosurface for each orbital (.jvxl file) is loaded via the push buttons. A further push button clears the applet of isosurfaces. Alternatively, the isosurfaces could be toggled between using a radio button group or even a drop down menu.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of BH<sub>3</sub>
| align="center" |<jmol>
<jmolApplet>
<name>BH3_orbitals</name><color>white</color><size>350</size>
<script>zoom 78.85;
</script><uploadedFileContents>BH3_njm08.mol</uploadedFileContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol><jmolButton><script>isosurface "images/f/ff/BH3_mo1_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>1</text></jmolButton>
<jmolButton><script>isosurface "images/4/41/BH3_mo2_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>2</text></jmolButton>
<jmolButton><script>isosurface "images/3/32/BH3_mo3_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>3</text></jmolButton>
<jmolButton><script>isosurface "images/3/3d/BH3_mo4_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>4</text></jmolButton>
<jmolButton><script>isosurface "images/d/d7/BH3_mo5_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>5</text></jmolButton>
<jmolButton><script>isosurface "images/4/4b/BH3_mo6_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>6</text></jmolButton>
<jmolButton><script>isosurface "images/f/f9/BH3_mo7_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>7</text></jmolButton>
<jmolButton><script>isosurface "images/5/5f/BH3_mo8_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>8</text></jmolButton>
<jmolButton><script>isosurface OFF</script><name>BH3_orbitals</name><text>clear</text></jmolButton></jmol>
| [[File:MOs_of_BH3_njm08.jpg|400px|]]
|}

View the page source to see how each table has been constructed. Documentation for the Jmol extension, including handy code snippets and a useful reference, can be found at http://wiki.jmol.org/index.php/MediaWiki.

==Loading Jmol files from the D-Space repository==

As well as loading files that have been uploaded to the wiki, Jmol can be used to load files from other URLs. This means that if you have published your calculation through the HPC web portal, it is possible to load your file directly from the digital repository.

URLs for files on the Imperial D-Space repository have the following structure:
<nowiki>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/</nowiki>''handle-prefix''/''handle-suffix''/''filename''

To load a file from a URL you must use the <code><nowiki><urlContents></nowiki></code> tag instead of the <code><nowiki><uploadedFileContents></nowiki></code> tag.

For example, the following code will produce a Jmol link that will load the log file from the D-Space calculation archive resolved by {{DOI|10042/24952}}:
<pre><nowiki><jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24952/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>
</nowiki></pre>
<jmol>
<jmolAppletLink>
<urlContents>https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24952/logfile.log</urlContents>
<text>Load Jmol from D-Space</text>
</jmolAppletLink>
</jmol>

User:Njm08

2013-08-10T00:00:48Z

Njm08: /* Loading Jmol files from the D-Space repository */

User:Njm08

2013-08-09T23:59:38Z

Njm08: /* Loading Jmol files from the D-Space repository */

User:Njm08

2013-08-09T23:40:09Z

Njm08: /* Loading Jmol files from the D-Space repository */

User:Njm08

2013-08-09T23:32:04Z

Njm08: /* Interactive tables */

User:Njm08

2013-08-09T23:23:02Z

Njm08: /* Loading Jmol files from the D-Space repository */

User:Njm08

2013-08-09T22:56:35Z

Njm08: /* Interactive tables */

User:Njm08

2013-08-09T22:12:54Z

Njm08: /* Interactive tables */

User:Njm08

2013-08-09T22:03:11Z

Njm08:

User:Njm08

2013-08-09T21:46:06Z

Njm08: /* Interactive tables */

User:Njm08

2013-08-09T21:33:10Z

Njm08: /* Interactive tables */

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The mediawiki Jmol extension comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter of countless Jmol windows, Jmol links or static 2D images, making them a great way to concisely display computational results.

Below is an interactive table for visualising the vibrational modes of water. The Jmol applet loads the log file for an <code>opt freq</code> caculation performed in Gaussian. The buttons send scripts to the applet which load the appropriate models for the corresponding frequencies. Animation can be turned on or off via the labelled checkbox.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! lit.
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolCheckbox><scriptWhenChecked>vibration 5;</scriptWhenChecked><scriptWhenUnchecked>vibration OFF;</scriptWhenUnchecked><text> Animation</text></jmolCheckbox></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>4</text></jmolButton></jmol>
|
| 2598 || (2693) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

Here is a "Gaussview style" interactive table for visualising the molecular orbitals for a calculation performed on water. The isosurface for each orbital is loaded via the push buttons. A further push button clears the applet of isosurfaces. Alternatively, the isosurfaces could be toggled between using a radio button group or even a drop down menu.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of BH<sub>3</sub>
| align="center" |<jmol>
<jmolApplet>
<name>BH3_orbitals</name><color>white</color><size>350</size>
<script>zoom 78.85;
</script><uploadedFileContents>BH3_njm08.mol</uploadedFileContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol><jmolButton><script>isosurface "images/f/ff/BH3_mo1_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>1</text></jmolButton>
<jmolButton><script>isosurface "images/4/41/BH3_mo2_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>2</text></jmolButton>
<jmolButton><script>isosurface "images/3/32/BH3_mo3_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>3</text></jmolButton>
<jmolButton><script>isosurface "images/3/3d/BH3_mo4_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>4</text></jmolButton>
<jmolButton><script>isosurface "images/d/d7/BH3_mo5_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>5</text></jmolButton>
<jmolButton><script>isosurface "images/4/4b/BH3_mo6_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>6</text></jmolButton>
<jmolButton><script>isosurface "images/f/f9/BH3_mo7_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>7</text></jmolButton>
<jmolButton><script>isosurface "images/5/5f/BH3_mo8_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>8</text></jmolButton>
<jmolButton><script>isosurface OFF</script><name>BH3_orbitals</name><text>clear</text></jmolButton></jmol>
| [[File:MOs_of_BH3_njm08.jpg|400px|]]
|}

User:Njm08

2013-08-09T21:30:54Z

Njm08: /* Interactive tables */

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The mediawiki Jmol extension comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter of countless Jmol windows, Jmol links or static 2D images, making them a great way to concisely display computational results.

Below is an interactive table for visualising the vibrational modes of water. The Jmol applet loads the log file for an <code>opt freq</code> caculation performed in Gaussian. The buttons send scripts to the applet which load the appropriate models for the corresponding frequencies. Animation can be turned on or off via the labelled checkbox.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! lit.
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolCheckbox><scriptWhenChecked>vibration 5;</scriptWhenChecked><scriptWhenUnchecked>vibration OFF;</scriptWhenUnchecked><text> Animation</text></jmolCheckbox></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>4</text></jmolButton></jmol>
|
| 2598 || (2693<ref>{{DOI|10.1063/1.448805}}</ref>) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

Here is a "Gaussview style" interactive table for visualising the molecular orbitals for a calculation performed on water. The isosurface for each orbital is loaded via the push buttons. A further push button clears the applet of isosurfaces. Alternatively, the isosurfaces could be toggled between using a radio button group or even a drop down menu.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of BH<sub>3</sub>
| align="center" |<jmol>
<jmolApplet>
<name>BH3_orbitals</name><color>white</color><size>350</size>
<script>zoom 78.85;
</script><uploadedFileContents>BH3_njm08.mol</uploadedFileContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol><jmolButton><script>isosurface "images/f/ff/BH3_mo1_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>1</text></jmolButton>
<jmolButton><script>isosurface "images/4/41/BH3_mo2_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>2</text></jmolButton>
<jmolButton><script>isosurface "images/3/32/BH3_mo3_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>3</text></jmolButton>
<jmolButton><script>isosurface "images/3/3d/BH3_mo4_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>4</text></jmolButton>
<jmolButton><script>isosurface "images/d/d7/BH3_mo5_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>5</text></jmolButton>
<jmolButton><script>isosurface "images/4/4b/BH3_mo6_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>6</text></jmolButton>
<jmolButton><script>isosurface "images/f/f9/BH3_mo7_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>7</text></jmolButton>
<jmolButton><script>isosurface "images/5/5f/BH3_mo8_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>8</text></jmolButton>
<jmolButton><script>isosurface OFF</script><name>BH3_orbitals</name><text>clear</text></jmolButton></jmol>
| [[File:MOs_of_BH3_njm08.jpg|400px|]]
|}

User:Njm08

2013-08-09T21:13:58Z

Njm08: /* Interactive tables */

User:Njm08

2013-08-09T20:57:46Z

Njm08: /* Nicholas Mason */

=== Nicholas Mason ===

MSci chemistry graduate

==Interactive tables==

The mediawiki Jmol extension comes with several useful widgets (GUI elements) that can be used to send scripts to an embedded Jmol applet. These widgets include push buttons, checkboxes, radio buttons and drop-down menus. Used creatively, these allow for the construction of interactive tables. Using interactive tables avoids the clutter of countless Jmol windows, Jmol links or static 2D images, making them a great way to concisely display computational results.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! lit. <ref>{{DOI|10.1021/ja00738a008}}</ref>
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
Animation: <jmol><jmolButton><script>vibration 5;</script><name>BH3_vibrations</name><text>ON</text></jmolButton>
<jmolButton><script>vibration OFF;</script><name>BH3_vibrations</name><text>OFF</text></jmolButton></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>4</text></jmolButton></jmol>
|
| 2598 || (2693<ref>{{DOI|10.1063/1.448805}}</ref>) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of BH<sub>3</sub>
| align="center" |<jmol>
<jmolApplet>
<name>BH3_orbitals</name><color>white</color><size>350</size>
<script>zoom 78.85;
</script><uploadedFileContents>BH3_njm08.mol</uploadedFileContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol><jmolButton><script>isosurface "images/f/ff/BH3_mo1_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>1</text></jmolButton>
<jmolButton><script>isosurface "images/4/41/BH3_mo2_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>2</text></jmolButton>
<jmolButton><script>isosurface "images/3/32/BH3_mo3_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>3</text></jmolButton>
<jmolButton><script>isosurface "images/3/3d/BH3_mo4_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>4</text></jmolButton>
<jmolButton><script>isosurface "images/d/d7/BH3_mo5_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>5</text></jmolButton>
<jmolButton><script>isosurface "images/4/4b/BH3_mo6_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>6</text></jmolButton>
<jmolButton><script>isosurface "images/f/f9/BH3_mo7_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>7</text></jmolButton>
<jmolButton><script>isosurface "images/5/5f/BH3_mo8_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>8</text></jmolButton>
<jmolButton><script>isosurface OFF</script><name>BH3_orbitals</name><text>clear</text></jmolButton></jmol>
| [[File:MOs_of_BH3_njm08.jpg|400px|]]
|}

{| class="wikitable"
|+ Optimised geometries of 2A, 2E and 2P
!2A
!2E
!2P
|-
|
<jmol>
<jmolApplet>
<name>acetonitrile</name><color>white</color><size>300</size>
<script>rotate z -80.89; rotate y 120.84; rotate z -95.89; zoom 110.41;
</script><uploadedFileContents>P4_opt_1acetonitrile_SDD.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<name>ethene</name><color>white</color><size>300</size>
<script> rotate z -105.77; rotate y 55.08; rotate z 87.91; zoom 100.0;
</script><uploadedFileContents>P4_opt_1ethene_SDD.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<name>PCl3</name><color>white</color><size>300</size>
<script>rotate z -107.47; rotate y 51.26; rotate z 89.06; zoom 110.41;
</script><uploadedFileContents>P4_opt_1PCl3_SDD.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|- valign="top"
|
Selected bond lengths (nm):
<jmol>
<jmolRadioGroup>
<item>
<script>measure OFF; measure 1 4;</script>
<text>Pd1-Pd4 = 0.402</text>
</item>
<item>
<script>measure OFF; measure 2 3;</script>
<text>Pd2-Pd3 = 0.378</text>
</item>
<item>
<script>measure OFF; measure 4 39;</script>
<text>Pd4-N39 = 0.226</text>
</item>
<item>
<script>measure OFF; measure 39 40;</script>
<text>N39-C40 = 0.116</text>
</item>
<target>acetonitrile</target>
<vertical>true</vertical>
</jmolRadioGroup>
</jmol>
|
Selected bond lengths (nm):
<jmol>
<jmolRadioGroup>
<item>
<script>measure OFF; measure 1 4;</script>
<text>Pd1-Pd4 = 0.415</text>
</item>
<item>
<script>measure OFF; measure 2 3;</script>
<text>Pd2-Pd3 = 0.368</text>
</item>
<item>
<script>measure OFF; measure 39 40;</script>
<text>C39-C40 = 0.137</text>
</item>
<target>ethene</target>
<vertical>true</vertical>
</jmolRadioGroup>
</jmol>
| align="top" |
Selected bond lengths (nm):
<jmol>
<jmolRadioGroup>
<item>
<script>measure OFF; measure 1 4;</script>
<text>Pd1-Pd4 = 0.411</text>
</item>
<item>
<script>measure OFF; measure 2 3;</script>
<text>Pd2-Pd3 = 0.372</text>
</item>
<target>PCl3</target>
<vertical>true</vertical>
</jmolRadioGroup>
</jmol>
|-
| Distortion factor = 1.06 || Distortion factor = 1.13 || Distortion factor = 1.11
|}

User:Njm08/MSci research

2013-07-31T17:44:59Z

Njm08:

Documentation of MSci research project

[[Category:Njm08]]

User:Njm08

2013-07-31T17:42:48Z

Njm08: /* Nicholas Mason */

=== Nicholas Mason ===

MSci chemistry graduate

User:Njm08/MSci research

2012-11-07T21:56:13Z

Njm08:

Documentation of MSci research project

==Phase 1==

===HPESW reaction===

{| class="wikitable"

|-

! reaction scheme

! reaction conditions

! yield

! ee

|-

|

|

|

|

|}

[[Category:Njm08]]

File:HPESW-reaction1.gif

2012-11-07T21:36:17Z

Njm08:

User:Njm08

2012-10-10T22:31:04Z

Njm08:

=== Nicholas Mason ===

4th year chemistry undergraduate

User:Njm08/MSci research

2012-10-10T22:29:21Z

Njm08:

Documentation of MSci research project

[[Category:Njm08]]

User:Njm08

2012-10-10T22:28:47Z

Njm08:

=== Nicholas Mason ===

4th year chemistry undergraduate

[[Category:Njm08]]

Category:Njm08

2012-10-10T22:28:21Z

Njm08: Blanked the page

Category:MSci research

2012-10-10T22:27:26Z

Njm08: Blanked the page

Category:3rd year computational lab

2012-10-10T22:27:05Z

Njm08: Blanked the page

Rep:Mod:1101927

2012-10-10T22:26:30Z

Njm08: /* References and links */

'''Computational lab - module 1''' organic

==Modeling using molecular mechanics==

=== The Hydrogenation of Cyclopentadiene ===

[[Image:Production_of_JP-10_njm08.png|thumb|upright=2.5|Scheme 1. Commercial production of JP-10]]
''Exo''-tetrahydrodicyclopentadiene is a high performance single-component fuel, known as JP-10. It has found application as a jet fuel, used in aircrafts and missiles <ref>http://dx.doi.org/10.1002/prep.200600043</ref>, having several desirable properties such as high thermal stability, high energy density and low cost<ref>http://dx.doi.org/10.1021/jp8081479</ref>. Industrially, it is made from the isomerisation of ''endo''-tetrahydrodicyclopentadiene, which is in turn made from the hydrogenation of ''endo''-dicyclopentadiene, typically with a Pd/C catalyst <ref>http://worldwide.espacenet.com/publicationDetails/biblio?FT=D&date=19851022&DB=EPODOC&locale=en_EP&CC=JP&NR=60209536A&KC=A&ND=6</ref> <ref>http://dx.doi.org/10.1021/jp9060363</ref> ('''Scheme 1.''').
''Endo''-dicyclopentadiene is the product of the Diels Alder π4s + π2s cycloaddition between two molecules of cyclopentadiene. The reactions involved in this process, notably the dimeristion of cyclopentadiene and the hydrogenation of dicyclopentadiene, ('''Scheme 2. and 4.''') show pronounced stereo- and regio- control. It is the intention to use molecular mechanics to model the products of these two reactions in an attempt to rationalise their stereo- and regio-chemical outcomes.

====Part 1. Dimerisation of cyclopentadiene====

[[Image:dimerisation njm08.png|thumb|upright=2.5|Scheme 2. Dimerisation of cyclopentadiene]]
Cyclopentadiene undergoes a π4s + π2s cycloaddition to dicyclopentadiene. This reaction has two potential products, the ''exo''- isomer ('''1''') and the ''endo''- isomer ('''2'''), shown in '''Scheme 2''' (relative sterochemistry). However, only formation of the ''endo''- isomer is observed.

The selectivity of a reaction may be guided by kinetic of thermodynamic control. Kinetically controlled reactions are generally irreversible under the reaction conditions and the observed major product is that with the lowest barrier to formation. In other words, the outcome is determined by the stability of the transition state rather than the stability of the product. Thermodynamically controlled reactions are reversible under the reaction conditions resulting in an equilibrium. Therefore, the outcome of a thermodynamically controlled reaction is determine by the stability of the products.
Molecular mechanics may be used to find the relative energies of '''1''' and '''2'''. Depending on whether the ''endo''- isomer ('''2''') is higher or lower in energy, one can determine whether the reaction is under thermodynamic or kinetic control.

[[Image:Frontial_mol_cyclopent_njm08.png|thumb|upright=1.8|Scheme 3. Frontier molecular orbital justification for ''endo''-selectivity]]
{| class="wikitable"
|+ Table 1. Results of MM2 energy minimisation: 1 and 2
|-
! rowspan="2" |
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
|-
! <jmolFile text="1">Molecule_1_njm08.mol</jmolFile>
! <jmolFile text="2">Molecule_2_njm08.mol</jmolFile>
|-
! Stretch
| 1.2850 || 1.2508 || 0.0342
|-
! Bend
| 20.5805 || 20.8477 || -0.2672
|-
! Stretch-Bend
| -0.8380 ||-0.8358 ||-0.0022
|-
! Torsion
| 7.6555 || 9.5109 ||-1.8554
|-
! Non-1,4 VDW
| -1.4174 || -1.5440 ||0.1266
|-
! 1,4 VDW
| 4.2333 ||4.3202 || -0.0869
|-
! Dipole/Dipole
| 0.3775 || 0.4477 ||-0.0702
|-
! Total Energy
| '''31.8764''' || '''33.9975''' ||'''-2.1211'''
|}

Models of dimers '''1''' and '''2''' were constructed in ChemBio3D ultra. Geometry minimisation was performed on both molecules using the MM2 force field. The results of both calculations can be seen in '''Table 1''' (click on molecule numbers for Jmol).

The calculations found the ''exo''-product ('''1''') to be the lowest energy isomer of the two by ≈2.1 kcal/mol. However, this is not the observed product of the dimerisation of cyclopentadiene. Therefore, one can conclude that the reaction is not under thermodynamic control, but rather kinetic control. This can be rationalised by the additional orbital overlap of the frontier molecular orbitals on formation of '''2''', stabilising the transition state ('''Scheme 3.'''). Further calculations could test this prediction by calculating both transition states by density function theory.

====Part 2. Hydrogenation====

[[Image:hydrogenation_scheme_njm08.png|thumb|upright=2.5|Scheme 4. Hydrogenation of dimer]]

The product ('''2''') of the dimerisation undergoes hydrogenation to initially give only one of the two dihydro derivatives, '''3''' and '''4''', as shown is '''Scheme 4'''. After prolonged hydrogenation this eventually gives the tetrahydro derivative. Again, molecular mechanics can be used to calculate the relative energies of '''3''' and '''4'''. By analysing the relative contributions to the total energy of each molecule, one can attempt to rationalise their relative stabilities and use this to predict which of the two molecules is formed.

{| class="wikitable"
|+ Table 2. Results of MM2 energy minimisation: 3 and 4
|-
! rowspan="2" |
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
|-
! <jmolFile text="3">Molecule_3_njm08.mol</jmolFile>
! <jmolFile text="4">Molecule_4_njm08.mol</jmolFile>
|-
! Stretch
| 1.2349 || 1.0964 ||0.1385
|-
! Bend
| 18.9384 || 14.5246 ||'''4.4138'''
|-
! Stretch-Bend
| -0.7609 ||-0.5494||-0.2115
|-
! Torsion
| 12.1240 || 12.4973 ||-0.3733
|-
! Non-1,4 VDW
| -1.5017 || -1.0702 ||-0.4315
|-
! 1,4 VDW
| 5.7289 || 4.5127 ||1.2162
|-
! Dipole/Dipole
| 0.1631 || 0.1406 ||0.0225
|-
! Total Energy
| '''35.9266''' || '''31.1520''' ||'''4.7746'''
|}

Models of dimers '''3''' and '''4''' were constructed in ChemBio3D ultra. Geometry minimisation was performed on both molecules using the MM2 force field. The results of both calculations can be seen in '''Table 2'''.

The calculation showed that molecule '''4''', with the remaining double bond on the ''endo''-ring, is lowest in energy by ≈4.8 kcal/mol. The largest contributing factor to the difference in stability is the ''Bend'' term, which is 4.4 kcal/mol higher for '''3''' than '''4'''. This term alone almost accounts for the difference in energy entirely and corresponds to strain arising from non-ideal molecular angles.

Examination of the detailed MM2 reports show that the largest contributors to the bend energy in both '''3''' and '''4''' are the C-C-C bond angles associated with the unsaturated components of the 5 membered rings. This is because the angles are closer to ideality for the sp3 carbon centres (ideal = 109.5°) present in the saturated rings, than the sp2 carbon centres (ideal = 120°) in the unsaturated rings. The difference between '''3''' and '''4''' is that the reduced bond angle across the bridging carbon has the effect of squeezing and reducing the opposite bond angles in the corresponding 5-membered ring. This means the angles across the double bond in '''3''' are even further from ideality than those across the double bond in '''4''', which is why '''3''' is the higher energy mono unsaturated derivative.

Kinetic and mechanistic studies <ref>http://dx.doi.org/10.1021/jp9060363</ref> have shown that compound '''3''' is simply not formed. This would appear to agree with the results from the MM2 calculations. However, this is because hydrogenation of the alkene to give '''3''' is found to have a much higher barrier to formation then hydrogenation of the alkene to give '''4'''. In other words, even though compound '''4''' is more stable, the reaction is still under kinetic control. This explains why '''4''' is formed quickly, but the tetrahedro derivative is only formed after prolonged hydrogenation.

<references/>

===Stereochemistry of a proposed synthetic intermediate towards the synthesis of taxanes===

[[Image:Taxol_scheme.njm08.png|thumb|Scheme 6. Atropisomers 9and 10 of proposed Taxol intermediate]]
The reaction, as shown in Scheme 6., is an atropselective oxyanionic Cope rearrangement reported by Paquette<ref>{{DOI|10.1016/S0040-4039(00)92617-0}}</ref>. Products of this reaction have been proposed as synthetic analogues and potential intermediates towards the synthesis of taxanes <ref>{{DOI|10.1021/np990176i}}</ref>, a class of diterpenoids isolated from the ''Taxus'' (Yew) genus. Perhaps the most well known example in this family of natural products is Taxol, originally isolated from the bark of the pacific yew tree<ref>{{DOI|10.1021/ja00738a045}}</ref>, that has become a commercially and clinically successful anti-cancer drug.

The reaction, as shown in Scheme 6., constitutes the key step in a construction of the fused cyclic framework that forms the basic carbon skeleton of the majority of taxanes. Several studies have been published that attempt to incorporate the functionality required for application of this scheme to the total synthesis of Taxol<ref>{{DOI|10.1021/jo00109a020}}</ref><ref>{{DOI|10.1021/jo00070a036}}</ref> and Taxusin<ref>{{DOI|10.1021/ja9805371}}</ref>. However, a complete total synthesis utilising this strategy has not yet been reported.

====Part 1.====

Products of the oxyanionic Cope rearrangement such as those shown in Scheme 6., or substituted derivatives, are initially formed with the carbonyl group either facing upwards ('''9''') or downwards ('''10'''). One standing this converts to the alternative atropisomer. As this process is under thermodynamic control, molecular mechanics may be used to determine the relative energies to find the most stable atropisomer.

Models of '''9''' and '''10''' were constructed in ChemBio3D and minimised using both the MM2 and MMFF94 force fields. The results of these calculations can be seen in tables 3 and 4.

{| class="wikitable"
|+ Table 3. Results of MM2 energy minimisation: 9 and 10
|-
! rowspan="2" |
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
|-
! <jmolFile text="9">9_A_njm08.mol</jmolFile>
! <jmolFile text="9'">9_B_njm08.mol</jmolFile>
! <jmolFile text="10">10_A_njm08.mol</jmolFile>
! <jmolFile text="10'">10_B_njm08.mol</jmolFile>
|-
! Stretch
| 2.7848 || 3.3221 || -0.5373 || 2.6204 || 3.3096 || -0.6892
|-
! Bend
| 16.5415 || 20.4884 || -3.9469 || 11.3388||16.8295 || -5.4907
|-
! Stretch-Bend
| 0.4305 ||0.4980 || -0.0675 || 0.3432|| 0.4352 || -0.0920
|-
! Torsion
| 18.2507|| 22.0138 || -3.7631 || 19.6719|| 20.1054 || -0.4335
|-
! Non-1,4 VDW
| -1.5524 || -1.0696 || -0.4828 || -2.1613 || -0.1289 || -2.0324
|-
! 1,4 VDW
| 13.1093 || 14.9656 || -1.8563 || 12.8721|| 13.7744 || -0.9023
|-
! Dipole/Dipole
| -1.7248 || -1.8326 || 0.1078 || -2.0023 || -1.7834 || -0.2189
|-
! Total Energy
| '''47.8395''' || '''58.3856''' || '''-10.5461''' || '''42.6828''' ||'''52.5418'''|| '''-9.8590'''
|}

{| class="wikitable"
|+ Table 4. Results of MMFF94 energy minimisation: 9 and 10
|-
! rowspan="2" |
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
|-
! <jmolFile text="9">9_A_MMFF94_njm08.mol</jmolFile>
! <jmolFile text="9'">9_B_MMFF94_njm08.mol</jmolFile>
! <jmolFile text="10">10_A_MMFF94_njm08.mol</jmolFile>
! <jmolFile text="10'">10_B_MMFF94_njm08.mol</jmolFile>
|-
! Total Energy
| 70.5284 || 82.6200 || -12.0916 || 66.2783 || 74.7125 || -8.4342
|}

{| class="wikitable"
|+Table 5. Comparison of MM2 and MMFF94 for 9 and 10
! rowspan="2" |
! colspan="2" | Total energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
|-
! 9
! 10
|-
!MM2
| 47.8395 || 42.6828 || 5.1567
|-
!MMFF94
| 70.5284 || 66.2783 || 4.2501
|}

The energy minimisation by MM2 and MMFF94 force field revealed that anitropisomer '''10''', with the ketone facing downwards was more stable by 5.1567 and 4.2501 kcal/mol respectively, as summarised in '''Table 5'''. Therefore, one would expect, given thermally equilibrating conditions, for '''9''' to eventually convert to '''10'''. The fused cyclohexane ring was found to adopt the chair conformation in both atropisomers. However, it was noticed on comparison of the structures, that '''9''' and '''10''' had opposite chair conformations. This can be visualised in Jmol (click links in tables 3 or 4). Given this, each antropisomer was modelled with the alternative chair conformation ('''9'''' and '''10''''). These were found to be higher in energy by approximately 10 kcal/mol for both methods. What this shows is that in order for one antropisomer to convert to the lowest energy conformation of the other, the cyclohexane ring must ring flip to the alternative chair. This would be difficult since the cyclohexane ring is highly restricted by its fused nature and this may explain why atropisomerism is observed.

====Part 2.====

An interesting finding reported by Paquette <ref name="sub">{{DOI|10.1021/ja00004a040}}</ref>, was that whilst the atropisomer with the downwards facing carbonyl was usually the the thermodynamic product, this was not always the case. It was noted that the atropselectivity of the reaction was particularly sensitive to substitution at the *-carbon. For instance, in methylated derviatives, substitution with a protected OH group, such as OMOM or OTBS, favours the carbonyl pointing downwards for ''R'', and upwards for ''S''.

[[File:Updown_njm08.png|400px]]

To examine this interesting result, methylated models of '''9''' and '''10''' ('''9"''' and '''10"''') were constructed in ChemBio3D with an OMe group substituted in the * position with ''R'' and ''S'' configurations. The were subjected to MM2 minimisation, the results of which are summerised in '''table 6'''.

{| class="wikitable"
|+ Table 6. MM2 minimisation of 9"R, 10"R, 9"S, 10"S
! rowspan="2" |
! colspan="4" | Energies (kcal/mol)
|-
! <jmolFile text="9''R">9subup_njm08.mol</jmolFile>
! <jmolFile text="10''R">10subup_njm08.mol</jmolFile>
! <jmolFile text="9''S">9subdown_njm08.mol</jmolFile>
! <jmolFile text="10''S">10subdown_njm08.mol</jmolFile>
|-
! Stretch
| 4.6146||4.7903||4.5607||4.821
|-
! Bend
| 20.2844||18.6454||19.7901||20.0545
|-
! Stretch-Bend
| 0.8961||0.9116||0.8728||0.9877
|-
! Torsion
| 22.131||22.4621||21.3192||23.116
|-
! Non-1,4 VDW
| 0.3158||0.5344||0.4282||-0.7809
|-
! 1,4 VDW
| 17.4661||17.5659||17.0709||18.0639
|-
! Dipole/Dipole
| -1.7532||-2.554||-1.7091||-0.2735
|-
! '''Total Energy'''
| 63.9548||'''62.3558'''||'''62.3328'''||65.9886
|}

The MM2 minimisation shows that whilst '''10"R''', with the carbonyl facing down, is the thermodynamic atropisomer for ''R''-substitution; '''9"S''', with the carbonyl facing up, is the thermodynamic atropisomer for ''S''- substitution. This is consistent with the experimental results reported by Paquette <ref name="sub" />. Visualisation of the structures in Jmol (click links in table) shows that, once again, this is to do with the conformation of the cyclohexane ring. For '''9"R''', the OMe is in an axial position, resulting in a 1,3-diaxial clash with the methyl group. On the other hand, '''10"R''' has the opposite chair conformation so the OMe is positioned equatorially, avoiding such unfavourable interactions. Similarly, '''10"S''' positions the OMe in an axial position; whereas '''9"S''', with the carbonyl pointing upwards, places the OMe in an equatorial position. This is why '''9"S''' is the thermodynamically favoured atropisomer for ''S''- substitution.

<references/>

==Modeling using semi-empirical molecular orbital theory==

===Regioselective Addition of Dichlorocarbene===

[[Image:Chlorocarbene_njm08.png|thumb|upright=2|Scheme 5. Regioselectivity of the addition of dichlorocarbene to '''12''']]
It was reported by Halton and Russell<ref>http://dx.doi.org/10.1021/jo00019a015</ref>, that only one mono-adduct was isolated from the electrophilic addition of dichlorocarbene to molecule '''12''', as shown in '''Scheme. 5'''. The carbene adds exclusively to the double bond ''endo'' to the chlorine, attacking from the sterically-unhindered opposite face of the molecule.

Semi-empirical molecular orbital theory and density functional theory can offer insights as to whether it is electronic effects that are influencing the regioselectivity of the addition. Appropriate semi-empirical models such as PM6 or RM1 can be implemented through MOPAC, and DFT calculations through Gaussian 09.

====Part 1.====

A model of molecule '''12''' was constructed using ChemBio3D Ultra. The geometry was optimised using the MM2 force field to a maximum RMS gradient of 0.001 (click to view [[Media:MM2_12_njm08.txt|results]] and <jmolFile text="Jmol">12_A_MM2_njm08.mol</jmolFile>).

From the MM2 optimized geometry, an energy minimisation was performed and the molecular surfaces calculated using the MOPAC/PM6 semi-empirical method. When the molecular orbitals were visualised, it was noticed that whilst most of the lobes were symmetric, there were elements of asymmetry about the σ-plane. It was initially assumed that this was due to asymmetry in the MM2 optimised geometry.
In MOPAC, the symmetry of the molecule can be constrained by adding the keyword AUTOSYM<ref>http://openmopac.net/manual/autosym.html</ref>. By specifying this keyword, symmetry in the starting material is automatically detected using the following rules:
* All bond-lengths which are within 0.0001Å are set equal.
* All bond-angles which are within 0.0057° are set equal.
* All dihedral angles which are within 0.0057° are set equal.
* All dihedral angles which are within 0.0057° of the negative of an existing dihedral are set equal to the negative of the existing dihedral.
[[Image:12_asymmetric_PM6_autosym_HOMO_njm08.png|thumb|Asymmetry of the MOPAC/PM6 generated HOMO]]
The point point group is detected and is displayed in the output file at the start and end of the calculation<ref>http://openmopac.net/manual/point_group_theory.html</ref>.
Therefore, the MOPAC/PM6 calculation was repeated using the AUTOSYM keyword. As you can see from the [[Media:12_PM6_AUTOSYM_njm08.txt|output file]] the point group was correctly identified as Cs. However, the orbitals were still asymmetric about the molecule's plane of symmetry. It was concluded that this must be a bug in the calculation and a different method must be chosen. The view shown of the HOMO, looking down the σ-plane, is a good example of the asymmetry generated by MOPAC/PM6 through ChemBio3D.

From the original MM2 optimised geometry, an energy minimisation was performed and the molecular surfaces calculated using the MOPAC/RM1 method with the AUTOSYM keyword (view [[Media:12_RM1_AUTOSYM_njm08.txt|output]]). The point group was again correctly identified as Cs and inspection of the molecular orbitals revealed symmetry about the σ-plane.
The same calculation was then repeated using the additional keyword GRAPHF<ref>http://openmopac.net/manual/graph.html</ref>, generating a MOPAC graphics file, allowing the orbitals to be visulaised in Jmol.

{| class="wikitable"
|+ RM1 generated Molecular Orbitals
| align="center" | <jmol>
<jmolApplet>
<name>RM1_Molecular_Orbitals</name><color>white</color><size>400</size>
<script> rotate z -68.78; rotate y 141.9; rotate z 131.44;
</script><uploadedFileContents>12_RM1_njm08.mgf</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolButton><script>MO 31</script><name>RM1_Molecular_Orbitals</name><text>HOMO-1</text></jmolButton>
<jmolButton><script>MO 32</script><name>RM1_Molecular_Orbitals</name><text>HOMO</text></jmolButton>
<jmolButton><script>MO 33</script><name>RM1_Molecular_Orbitals</name><text>LUMO</text></jmolButton>
<jmolButton><script>MO 34</script><name>RM1_Molecular_Orbitals</name><text>LUMO+1</text></jmolButton>
<jmolButton><script>MO 35</script><name>RM1_Molecular_Orbitals</name><text>LUMO+2</text></jmolButton>

<jmolButton><script>MO OFF</script><name>RM1_Molecular_Orbitals</name><text>clear</text></jmolButton></jmol>
'''Ring Distortion:'''
<jmol><jmolCheckbox><scriptWhenChecked> measure 2 11; measure 8 11;</scriptWhenChecked><scriptWhenUnchecked>measure OFF;</scriptWhenUnchecked><name>RM1_Molecular_Orbitals</name><text>View distances</text></jmolCheckbox></jmol>
|}

Inspection of the molecular orbitals reveal that the electron density of the HOMO is located on the ''endo'' alkene π bond. One would expect this to be the most reactive orbital towards electrophilic attack, which is consistent with the regioselectivity of the addition of dichlorocarbene. Electron density of the HOMO-1 is located on the ''exo'' alkene, which is 0.5884eV lower in energy. This means there would be a greater ΔE for any incoming electrophile for the HOMO-1 than that of the HOMO.
The additional stability of the ''exo'' π bond can be rationalised by examining the favourable orbital alignment between the HOMO-1 and the LUMO, which corresponds to the σ* of the C-Cl bond. Donation of electron density from the ''exo'' π into the σ* may account for the stabilisation and reduced electron density on the ''exo'' alkene. This interaction manifests itself in a slight distortion of the ''exo'' ring upwards, towards the σ*. As you can see in the model above, the distance between the alkene carbons to the bridging cyclopropane carbon is 0.017nm shorter for the ''exo'' alkene than the ''endo''.
There also appears to be an unfavourable interaction in the HOMO between the ''endo'' π bond and a chlorine p-orbital, which may be raising the energy relative to the ''exo'' alkene.

====Part 2.====
[[Image:13_njm08.png|thumb| Structure of '''13''' ]]
The .mol file from the MM2 optimised geometry of '''12''' was opened in Gaussview 5. A gaussian input file was set up to perform an energy minimisation and frequency calculation using the B3LYP hybrid-DFT functional and the 6-31G(d,p) basis set, with the point group symmetry contrained to Cs.
The structure was then edited to give the ''exo''-hydrogenated structure '''13''', in order to examine what effect the presence of the ''exo''- double bond has on the C-Cl stretching frequency. Again, a gaussian input file was set up to perform the same calculation (B3LYP/6-31G(d,p) opt freq), although this time without constraining to a point group.
Both files were run on Gaussian 09 through the SCAN cluster.

The .log output files were saved and molecular vibrations visualised on Gaussview 5. The results are summerised in '''Table 7''' (click links for GIF animation).

[[Image:12_IR.svg|thumb|400px| Computed IR spectra of '''12''' ]]
[[Image:13_IR.svg|thumb|400px| Computed IR spectra of '''13''' ]]

{| class="wikitable"
|+ Table 7. Selected molecular vibrations for B3LYP/6-31G(d,p) optimised structures, 12 and 13
! rowspan="2" |
! colspan="2" | Frequency (cm<sup>-1</sup>)
|-
! 12 <ref name=12optfreq>{{DOI|10042/to-12853}}</ref>
! 13 <ref>{{DOI|10042/to-12854}}</ref>
|-
! C-Cl
| [[Media:12_C-Cl_770.89.gif|770.89]] || [[Media:13_C-Cl_780.00.gif|780.00]]
|-
! C=C ''exo''
| [[Media:12_C--C_1737.07.gif|1737.07]] || align="center" | -
|-
! C=C ''endo''
| [[Media:12_C--C_1757.35.gif|1757.35]] || [[Media:13_C--C_1753.76.gif|1753.76]]
|}

The vibrational mode corresponding to the C-Cl stretch was found to increase in wavenumber for molecule '''13''', with the ''exo''-double bond replaced by a single bond. This indicates a stronger C-Cl bond for '''13''' than for '''12'''. This is consistant with the semi-empiracal orbital analysis, whereby donation from the π-bond of the ''exo'' alkene into the σ* C-Cl would decrease the strength of the C-Cl bond and result in a weaker stretching frequency. Absence of this interaction would result in less anti bonding character, a stronger C-Cl bond and, hence, a stronger stretching frequency as is observed.

The C=C stretches have also been identified. The C=C stretch for the ''endo'' bond is higher in wavenumber than that of the ''exo'' bond in molecule '''12'''. This is consistent with the ''endo'' bond having greater electron density than that of the ''exo'', making it more amenable to electrophilic attack. The ''exo'' bond's stretching frequency is much lower that of the ''endo'' bond in either '''12''' or '''13''', further supporting the notion of π-donation into the σ*. Interestingly, the stretching frequency of the ''endo'' bond in '''12''' is higher than that of '''13'''. From this, one might predict that '''12''' would be slightly more reactive towards electrophiles that its hydrogenated derivative, '''13'''.
{| class="wikitable"
|+ B3LYP/6-31G(d,p) Molecular Orbitals
| align="center" | <jmol>
<jmolApplet>
<name>B3LYP_Molecular_Orbitals</name><color>white</color><size>400</size>
<script>rotate z -127.29;rotate y 154.64; rotate z 133.31;
</script><uploadedFileContents>12_mol_njm08.mol</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolButton><script>isosurface "images/f/f2/HOMOminus1_njm08.jvxl"</script><name>B3LYP_Molecular_Orbitals</name><text>HOMO-1</text></jmolButton>
<jmolButton><script>isosurface "images/4/4a/HOMO_njm08.jvxl"</script><name>B3LYP_Molecular_Orbitals</name><text>HOMO</text></jmolButton>
<jmolButton><script>isosurface "images/1/1f/LUMO_njm08.jvxl"</script><name>B3LYP_Molecular_Orbitals</name><text>LUMO</text></jmolButton>
<jmolButton><script>isosurface "images/c/c6/LUMOplus1_njm08.jvxl"</script><name>B3LYP_Molecular_Orbitals</name><text>LUMO+1</text></jmolButton>
<jmolButton><script>isosurface "images/1/11/LUMOplus2_njm08.jvxl"</script><name>B3LYP_Molecular_Orbitals</name><text>LUMO+2</text></jmolButton>

<jmolButton><script>isosurface OFF</script><name>B3LYP_Molecular_Orbitals</name><text>clear</text></jmolButton></jmol>
'''Ring Distortion:'''
<jmol><jmolCheckbox><scriptWhenChecked> measure 2 11; measure 8 11;</scriptWhenChecked><scriptWhenUnchecked>measure OFF;</scriptWhenUnchecked><name>B3LYP_Molecular_Orbitals</name><text>View distances</text></jmolCheckbox></jmol>
|}

Out of curiosity, the molecular orbitals generated by B3LYP/6-31G(d,p) were visualised for comparison with the orbitals generated by MOPAC/RM1. This was to see how well the semi-empirical method matches up to the higher level, DFT method. As the cube files generated by Gaussian are large in size, they were converted to the .jvxl format using the desktop Jmol app.
The main difference between the two sets of orbitals is that the ordering is slightly different. Whilst the HOMO-1 and HOMO remain the same, the C-Cl σ* orbital is now the LUMO+2, rather than the LUMO. As the orbitals are generated through a higher level of theory, it is most likely that the B3LYP/6-31G(d,p) ordering is correct. This ordering is also consistent with that reported in the literature <ref>http://dx.doi.org/10.1039/P29920000447</ref>. The distortion of the ''exo''-ring is still observed in the DFT-optimised geometry , with the ''exo''-alkene carbons 25nm closer than the ''endo''-alkene carbons to the bridging cyclopropane carbon.

====Part 3.====

To explore the effect of the ''exo''-double bond on the C-Cl stretching frequency further, several molecules were prepared with various electron donating and electron withdrawing substituents on the ''exo''-alkene. One would assume, based on the analysis above, that electron donating substituents would increase electron density on the alkene resulting in a decrease in Cl-C stretching frequency in comparison to '''12'''. Similarly, one would expect electron withdrawing substituents to decrease electron density on the alkene resulting in an increase in stretching frequency in comparison to '''12'''.

The results of the frequency calculation are summerised in the '''table 8'''.

{| class="wikitable sortable"
|+ Table 8. Effect of ''exo''-alkene substituents on stretching frequencies.
!substituent
!νC=C (endo)(cm<sup>-1</sup>)
!νC=C (exo)(cm<sup>-1</sup>)
!νC-Cl(cm<sup>-1</sup>)
|-
| ('''12''') H <ref name=12optfreq /> || 1757.35 || 1737.07 || 770.89
|-
| ('''14''') OMe <ref>{{DOI|10042/to-12853}}</ref> || 1755.78 || 1762.39 || 775.70
|-
| ('''15''') CN <ref>{{DOI|10042/to-12853}}</ref>|| 1757.13 || 1670.36 || 772.62
|-
| ('''16''') Me <ref>{{DOI|10042/to-12853}}</ref>|| 1755.59 || 1747.08 || 768.16
|}

Ranking by ''exo''-alkene stretching frequency gives a good indication of the electron density on the ''exo''-alkene. The electron withdrawing substituent, CN ('''15'''), gives a lower ''exo''-alkene stretch of 1670 cm<sup>-1</sup> compared to '''12'''. Whereas, the moderately electron donating Me ('''16''') gives a higher stretching frequency of 1747 cm<sup>-1</sup> and the strongly electron donating OMe ('''14''') gives and even higher stretch of 1762 cm<sup>-1</sup>. This order is as one would expect for the selected substituents. The effect of this electron density on the C-Cl stretch follows the rationale outlined above, for '''15''' and '''16'''. The reduced electron density on the ''exo''-alkene of '''15''' results in an increase in the C-Cl stretching frequency in comparison to '''12'''. Similarly, the increased electron density on the ''exo''-alkene of '''16''' results in a decrease in the C-Cl stretching frequency in comparison to '''12'''. However, '''14''' does not appear to fit this trend. The OMe substituent clearly imparts the most electron density to the ''exo''-alkene. So much so, that the stretching frequency is higher that that of the ''endo''-alkene. Examination of the molecular orbitals reveals that for '''14''', the ''exo''-alkene π-bond is now the highest occupied molecular orbital. Yet, the stretching frequency for C-Cl is higher than that of '''12''' and even that of '''15'''. This is a surprising result as is does not appear to fit with the previous analysis where greater electron density leads to greater donation into C-Cl σ*, an increase in C-Cl antibonding character and a reduction in the C-Cl stretching frequency.

One observation is that, in '''12''', both the HOMO and HOMO-1 are significantly delocalised across the C-Cl bond. This arises from orbital mixing with the HOMO-3, which appears to correspond to a π*-type orbital across the C-Cl bond. In '''14''', significant orbital mixing with HOMO-3 is only observed with the HOMO-1, now corresponding to the ''endo''-π bond. It appears that the increased electron density from the OMe substituents in '''14''' has raised the energy of the ''exo''-π bond to such an extent that orbital mixing with the HOMO-3 is greatly reduced. If this outways any increase in donation to the C-Cl σ*, then the net effect will be a reduction in antibonding character across the C-Cl bond and an increase in the stretching frequency, as is observed. In fact, it may be that donation into the C-Cl σ* from the ''exo''-π is a minor effect when it comes to the stabilisation of the HOMO-1 compared to the HOMO in '''12''', especially considering the large ΔE between the participating orbitals. It may be better explained by a greater extent of orbital mixing between the ''exo''-π and the HOMO-3.

{| class="wikitable"
|+ A comparison of orbital mixing between '''12''' and '''14'''
!12
!14
|-
| align="center" | <jmol>
<jmolApplet>
<name>12_MO</name><color>white</color><size>300</size>
<script>rotate z -127.29;rotate y 154.64; rotate z 133.31;
</script><uploadedFileContents>12_mol_njm08.mol</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolButton><script>isosurface "images/c/cd/12_HOMO-3_njm08.jvxl"</script><name>12_MO</name><text>HOMO-3</text></jmolButton>
<jmolButton><script>isosurface "images/f/f2/HOMOminus1_njm08.jvxl"</script><name>12_MO</name><text>HOMO-1</text></jmolButton>
<jmolButton><script>isosurface "images/4/4a/HOMO_njm08.jvxl"</script><name>12_MO</name><text>HOMO</text></jmolButton>
<jmolButton><script>isosurface OFF</script><name>12_MO</name><text>clear</text></jmolButton></jmol>
| align="center" | <jmol>
<jmolApplet>
<name>14_MO</name><color>white</color><size>300</size>
<script>rotate z -73.39; rotate y 67.76; rotate z 77.48;
</script><uploadedFileContents>14_mol_njm08.mol</uploadedFileContents>
</jmolApplet>
</jmol>
<jmol><jmolButton><script>isosurface "images/c/c5/14_HOMO-3_njm08.jvxl"</script><name>14_MO</name><text>HOMO-3</text></jmolButton>
<jmolButton><script>isosurface "images/1/1f/14_HOMO-1_njm08.jvxl"</script><name>14_MO</name><text>HOMO-1</text></jmolButton>
<jmolButton><script>isosurface "images/e/e3/14_HOMO_njm08.jvxl"</script><name>14_MO</name><text>HOMO</text></jmolButton>
<jmolButton><script>isosurface OFF</script><name>14_MO</name><text>clear</text></jmolButton></jmol>
|}

<references/>

===Monosaccharide chemistry: glycosidation===
[[File:SchemeA_njm08.png|thumb|Scheme 7. Glycosidation]]
In glycosidation reactions, leaving group X is substituted by an incoming nucleophile. Neighbouring group participation from the O-acetyl group, in position 2 of the pyranose ring, directs the face of attack, resulting in a 1,2-trans relationship in the product. Hence, stereoselectivity for either the α- or β-anomer is seen to depend on the stereochemistry of O-acetyl group (Scheme 7). However, these reactions often deliver less than 99% selectivity for the 1,2-trans product, which is a requirement to efficient solid phase synthesis <ref>{{DOI|10.1016/j.carres.2007.03.030}}</ref>. This may be because certain conformations allow for neighbouring group participation to the other face of the ring, or that certain conformations do not allow for neighbouring group participation to occur and the directing effect is lost.

The aim is to examine the facial preference for incoming nucleophilic attack by modelling the oxonium cation with and without neighbouring group participation with MM2 and MOPAC/PM6. The conventional mode of participation will be examined ('''A''', '''C''', '''B''' and '''D''') as well as a possible alternative mode of participation ('''A'''', '''C'''', '''B'''' and '''D'''') a illustrated in Scheme 8.

[[File:SchemeB_njm08.png|thumb|Scheme 8. Models]]
{| class="wikitable"
|+ Table 9. Results of MM2 minimisation: A, A', B, B'
|-
! rowspan="2" |
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
|-
! <jmolFile text="A">A_MM2_njm08.mol</jmolFile>
! <jmolFile text="A'">A_prime_MM2_njm08.mol</jmolFile>
! <jmolFile text="B">B_MM2_njm08.mol</jmolFile>
! <jmolFile text="B'">B_prime_MM2_njm08.mol</jmolFile>
|-
! Stretch
| 2.6283 || 2.2373 || 0.3910 || 2.6405 || 2.4157 || 0.2248
|-
! Bend
| 12.7740 || 9.2852 || 3.4888 || 11.4460||11.1836 || 0.2624
|-
! Stretch-Bend
| 0.9398 || 0.7834 || 0.1564 || 0.8744|| 0.7869|| 0.0875
|-
! Torsion
| 1.7303|| 1.7000 || 0.0303 || 0.9854|| 0.9499 || 0.0355
|-
! Non-1,4 VDW
| 2.1704 || -2.7354 || 4.9058 || 1.4499 || -0.5396 || 1.9895
|-
! 1,4 VDW
| 19.5306 || 19.7049 || -0.1743 || 19.4758|| 19.9537 || -0.4779
|-
!Charge/Dipole
| -40.0090 || -8.1852 || -31.8238 || -34.4282 || -27.0912 || -7.337
|-
! Dipole/Dipole
| 7.9847 || 3.9058 || 4.0789 || 6.9932 || 6.5677 || 0.4255
|-
! Total Energy
| '''7.7491''' || '''26.6960''' || '''-18.9469''' || '''9.4370''' ||'''14.2267'''|| '''-4.7897'''
|}

{| class="wikitable"
|+ Table 10. Results of PM6 minimisation: A, A', B, B'
|-
! rowspan="2" |
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
|-
! <jmolFile text="A">A_PM6_njm08.mol</jmolFile>
! <jmolFile text="A'">A_prime_PM6_njm08.mol</jmolFile>
! <jmolFile text="B">B_PM6_njm08.mol</jmolFile>
! <jmolFile text="B'">B_prime_PM6_njm08.mol</jmolFile>
|-
! Heat of formation
| -91.66313 || -85.75198 || -5.91115 || -88.53126 || -76.54449 || -11.98677
|}

The results of minimisation of '''A''', '''A'''', '''B''', '''B'''' can be seen above in tables 9 and 10. The aim was to find two stable conformations for '''A''' and '''B''' where the O-acetyl group pointed above or below the plane of the oxonium cation. The structures found by MM2 minimisation were used as starting structures for MOPAC/PM6 minimisation. The most stable conformations, '''A''' and '''B''', corresponded to positioning of the O-acetyl group towards the face that would lead to conventional neighbouring group participation and 1,2-trans products. '''A'''' and '''B'''', which corresponded to positioning of the O-acetyl group towards the alternative face, were found to be considerably higher in energy for both methods. So much so, that the population of these species in solution would be negligible (a difference of 3kcal/mol ≈ 99:1).

It must be said the flexibility in orientation of the methanol groups about the ring made finding the lowest energy conformations with MM2 very time consuming. This is because each orientation of the groups gave local minima, which had to individually screened. Great difficulty was often experienced in re-locating previously found minima with particularly low energies. Quite often this resulted in settling for higher energy conformations. This problem was not experienced with PM6, with MOPAC consistently optimising to the same low energy conformation. This is perhaps not surprising, considering that molecular mechanics is not well suited to chemical problems where charge delocalisation or other electronic effects are present. This is because the atom types, charges associated with atoms and their bond types are specified before the minimisation and are not subject to change, which can often give an unrealistic picture. In this respect, whilst MM2 may be useful for screening conformations to provide approximate geometries for further optimisation, the focus for chemical analysis should be on the results of the MOPAC/PM6 energy minimisation.

The positioning of the O-acetyl group in the MOPAC/PM6 optimised '''A''' and '''B''', and lengthening of the O+=C bond, show that the structures have optimised to a geometry where the participating neighboring group, O-acetyl, is already participating, despite not being specified in the starting structure. This clearly shows that participation and delocalisation of the charge to the O-acetyl group is a spontaneous and favourable process for these conformations.

Interestingly, for '''A'''' where the O-acetyl group is not in an appropriate orientation to participate, the C-6 OMe oxygen has bent over to stabilise the charge. This may explain why the difference in energy is less than for '''B'''', where no neighbouring group participation is observed. This would mean that there would be no facial directing effects, although as previously mentioned, the energy is so much higher that one would expect a negligible population in solution.

The same molecules were then minimised with MM2 followed by MOPAC/PM6, this time with neighbouring group participation specified in the starting geometries. The results are summarised in tables 11 and 12.

{| class="wikitable"
|+ Table 11. Results of MM2 minimisation: C, C', D, D'
|-
! rowspan="2" |
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
|-
! <jmolFile text="C">C_MM2_njm08.mol</jmolFile>
! <jmolFile text="C'">C_prime_MM2_njm08.mol</jmolFile>
! <jmolFile text="D">D_MM2_njm08.mol</jmolFile>
! <jmolFile text="D'">D_prime_MM2_njm08.mol</jmolFile>
|-
! Stretch
| 1.9288 || 2.9390 || -1.0102 || 1.8209 || 2.8121|| -0.9912
|-
! Bend
| 12.7809 || 19.6974 || -6.9165 || 18.1083||17.8415 || 0.2668
|-
! Stretch-Bend
| 0.6520 || 0.8005 || -0.1485 || 0.7141|| 0.7922|| -0.0781
|-
! Torsion
| 7.8528|| 7.1132 || 0.7396 || 7.9961|| 7.2672 || 0.7289
|-
! Non-1,4 VDW
| -2.6503 || -3.6699 || 1.0196 || -3.4525 || -2.5673 || -0.8852
|-
! 1,4 VDW
| 18.0099 || 19.0698 || -1.0599 || 17.8207|| 19.2775 || -1.4568
|-
!Charge/Dipole
| -10.5383 || 2.0865 || -12.6248 || -7.4090 || -2.7178 || -4.6912
|-
! Dipole/Dipole
| -1.1068 || 0.0239 || -1.1307 || -1.5858 || 0.1099 || -1.6957
|-
! Total Energy
| '''26.9291''' || '''48.0603''' || '''-21.1312''' || '''34.0127''' ||'''42.8154'''|| '''-8.8027'''
|}

{| class="wikitable"
|+ Table 12. Results of PM6 minimisation: C, C', D, D'
|-
! rowspan="2" |
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
! colspan="2" | energies (kcal/mol)
! rowspan="2" | energy difference (kcal/mol)
|-
! <jmolFile text="C">C_PM6_njm08.mol</jmolFile>
! <jmolFile text="C'">C_prime_PM6_njm08.mol</jmolFile>
! <jmolFile text="D">D_PM6_njm08.mol</jmolFile>
! <jmolFile text="D'">D_prime_PM6_njm08.mol</jmolFile>
|-
! Heat of formation
| -91.65991 || -65.49634 || -26.1636 || -88.53397 || -66.67342 || -21.8606
|}

The heat formations for '''C''' and '''D''' are practically identical to the heat of formations for '''A''' and '''B''', which confirms that '''A''' and '''B''' had minimised to geometries where the O-acetyl group was participating in charge delocalisation. '''C'''' and '''D'''' are both considerably higher in energy that '''C'''' and '''D'''', where neighboring group participation was not specified in the starting material. This indicates that for these conformations, neighbouring group participation to the alternative face of the oxonium cation is not favourable.

In conclusion, these calculations show that neighboring group participation is a favourable and spontaneous process and results in the lowest energy conformations for each monosaccharide. Conformations where neighboring group participation does not occur are higher in energy and would have low populations in solution. Neighboring group participation to the alternative face of the oxonium cation is not favourable. These findings explain why there is a high preference for 1,2-trans products in glycosidation reactions where neighboring group participation can occur. However, further calculations are needed to provide a satisfactory answer as to why selectivity for 1,2-trans products are usually less that 99%.

<references/>

==Structure based Mini project using DFT-based Molecular orbital methods==
===The structure and conformers of Stagonolide D===

====Introduction====

[[File:Cirsium arvense with Bees Richard Bartz.jpg|thumb|The "creeping thistle" ''Cirsium arvense'']]
''Cirsium arvense'', otherwise known as the creeping thistle or the Canada thistle, is a perennial weed. As an invasive species, it competes with crops and, as such, has become a problem in North America and Europe <ref>http://www.wildflowers-and-weeds.com/weedsinfo/Cirsium_arvense.htm</ref>. In 2007, the isolation and characterisation of Stagonolide A was reported <ref name="stanA">{{DOI|10.1021/jf070742c}}</ref>. This small molecule was a pytotoxic metabolite isolated from a liquid culture of ''Stagonospora cirsii'', a fungal pathogen of ''Cirsium arvense''. It was shown to inhibit root growth, and was identified as a possible candidate for a biological herbicide<ref>
http://dx.doi.org/10.1016/S0261-2194(00)00092-2</ref> to control the weed.
In 2008, the isolation and characterisation of nine more metabolites, Stagonolide B-F <ref name="stanB-F">{{DOI|10.1021/np0703038}}</ref>and Stagonolide G-I and Modiolite A <ref name="stanG-I">{{DOI|10.1021/np800415w}}</ref>, were reported from solid cultures of ''Stagonospora cirsii''.

A recently published total synthesis of Stagonolide D by Ramana ''et al'' <ref name="Ramana">{{DOI|10.1021/jo202138g}}</ref>, found that the <sup>1</sup>H-NMR and <sup>13</sup>C-NMR of the structure, as proposed by the original characterisation ('''1'''), did not match up to the <sup>1</sup>H-NMR and <sup>13</sup>C-NMR of the isolated natural product. They went on to synthesise an alternative isomer ('''2''''), of which the NMR data did match with that of the isolated natural product. This new structure was found to have an optical rotation of opposite sign to that of natural stagonolide D. Therefore, they proposed an appropriate structural revision ('''2'''). Interestingly, the NMR spectra of both the synthesised proposed structure and revised structure showed two sets of peaks with slightly different chemical shifts. These were attributed to two slowly equilibrating, major and minor conformers. It was only the major conformer of the revised structure that matched the NMR data of the isolated natural product. If they are correct, it suggests that the final step of the synthesis, the ring closing metathesis, generated two antropisomers of the molecule.

However, another total synthesis of Stagonolide D was publish shortly before this paper, by Nanda ''et al'' <ref name="Nanda">http://dx.doi.org/10.1246/bcsj.20100197</ref>. They too synthesised the originally proposed structure, yet the <sup>1</sup>H-NMR and <sup>13</sup>C-NMR data they report in the paper matches well with the isolated natural product, confirming the original structure. Curiously, the attached <sup>1</sup>H-NMR spectra in the supplementary information does not match the peak data given in the experimental section of the paper. This spectra, labeled as that of Stagonolide D, does not match that of the isolated natural product or the revised structure reported by Ramana. The final step in the Nanda synthesis was also a ring closing metathesis, although no evidence of antropisomerism was observed in the NMR.

[[File:Possible_structures_of_stagonolide_D_njm08.png|460px]]

This project aims to investigate the uncertainties surrounding the structure of Stagonolide D. Firstly, the low energy conformation(s) of the originally proposed structure ('''1''') and the alternative synthetic isomer ('''2'''') will be identified, using semi-empirical moleular orbital theory and DFT geometry minimisations. Once the low energy conformer(s) are found, prediction of the <sup>1</sup>H-NMR and <sup>13</sup>C-NMR spectra should allow for identification of the major and minor antropisomers observed by Ramana. These calculation should also resolve the contradiction between the confirmation of the originally proposed structure by Nanda, and the rejection of the originally proposed structure by Ramana.

====Location of low energy conformers====

Models of '''1''' (given the label O) and '''2'''' (given the label I) were constructed using chembio3D, as well as a plastic physical model to aid visualisation. Eight conformers were found for both '''1''' and '''2'''' by inspection, the geometries of which were minimised by MOPAC/PM6. These were categorized into four main-conformers (labeled 1 - 4) resulting from the relative orientation of the double bond and ester bond, each with two chair-like or twist-boat-like sub-conformers (labeled a and b) resulting from carbon-3 pointing up or down.

The structures of each of these conformations can be seen in '''table 13'''.

{| class="wikitable"
|+ Table 13. Conformations of 1 and 2' minimised by MOPAC/PM6
!
! <jmolFile text="O1a">O1a_njm08.mol</jmolFile>
! <jmolFile text="O1b">O1b_njm08.mol</jmolFile>
! <jmolFile text="O2a">O2a_njm08.mol</jmolFile>
! <jmolFile text="O2b">O2b_njm08.mol</jmolFile>
! <jmolFile text="O3a">O3a_njm08.mol</jmolFile>
! <jmolFile text="O3b">O3b_njm08.mol</jmolFile>
! <jmolFile text="O4a">O4a_njm08.mol</jmolFile>
! <jmolFile text="O4b">O4b_njm08.mol</jmolFile>
|-
| || [[Image:O1a.jpg|50px]] || [[Image:O1b.jpg|50px]] || [[Image:O2a.jpg|50px]] || [[Image:O2b.jpg|50px]] || [[Image:O3a.jpg|50px]] || [[Image:O3b.jpg|50px]] || [[Image:O4a.jpg|50px]] || [[Image:O4b.jpg|50px]]
|-
|ΔH <br />(kcal/mol) || -141.37423 || -139.87433 || -138.76809 || -139.53815 || -138.06490 || -140.03708 || -140.84378 || -139.19046
|-
!
! <jmolFile text="I1a">I1a.mol</jmolFile>
! <jmolFile text="I1b">I1b.mol</jmolFile>
! <jmolFile text="I2a">I2a.mol</jmolFile>
! <jmolFile text="I2b">I2b.mol</jmolFile>
! <jmolFile text="I3a">I3a.mol</jmolFile>
! <jmolFile text="I3b">I3b.mol</jmolFile>
! <jmolFile text="I4a">I4a.mol</jmolFile>
! <jmolFile text="I4b">I4b.mol</jmolFile>
|-
| || [[Image:I1a_njm08.jpg|50px]] || [[Image:I1b_njm08.jpg|50px]] || [[Image:I2a_njm08.jpg|50px]] || [[Image:I2b_njm08.jpg|50px]] || [[Image:I3a_njm08.jpg|50px]] || [[Image:I3b_njm08.jpg|50px]] || [[Image:I4a_njm08.jpg|50px]] || [[Image:I4b_njm08.jpg|50px]]
|-
|ΔH <br />(kcal/mol) || -142.32658 || -140.70779 ||-140.03046 || -137.51099 || -136.78381 || -139.34324 || -138.02835 || -139.56015
|}

==== Calculation of <sup>13</sup>C-NMR ====

A gaussian input file was prepared, based on the MOPAC/PM6 optimised geometries of each of the above conformations, to perform a DFT optimisation, as specified by:
*<nowiki># opt mpw1pw91/6-31G(d,p) scrf=(cpcm,solvent=chloroform)</nowiki>
A gaussian input file was then prepared from the formatted checkpoint file of each of the DFT optimised geometries to perform a GAIO NMR calculation as specified by:
*<nowiki># nmr=giao mpw1pw91/6-31g(d,p) scrf=(cpcm,solvent=chloroform)</nowiki>
This method was chosen as it has been shown to predict <sup>13</sup>C-NMR shifts to an acceptable accuracy whilst using the modest and inexpensive 6-31G(d,p) basis set <ref name="NMRmethod">{{DOI|10.1021/np0705918}}</ref>. A solvation model was chosen to minimise potential errors in the optimised geometries, relative energies and calculated chemical shifts in comparison to the experimental data, measured in CDCl<sub>3</sub>. Both sets of calculations were implemented using Gaussian 09 on the SCAN cluster. The PM6 geometries were further optimised using density functional theory prior to the NMR calculation, as accurate relative energies are crucial for calculating NMR data in molecules with several low energy conformations. This is because each conformation that interconverts faster than the NMR timescale will have an effect on the experimentally observed chemical shifts if it has a significant population. Therefore, using the calculated energies for each conformation relative to the lowest energy conformation of each molecule, the Boltzmann populations in solution were obtained <ref name="NMRreview">{{DOI|10.1021/cr200106v}}</ref>.

This data is summarised in '''Table 14'''.

{| class="wikitable"
|+ Table 14. Energies, populations and NMR peak data for mpw1pw91/6-31G(d,p) optimised conformations: O1-4, I1-4
!
! O1a <ref>{{DOI|10042/to-12858}}</ref> <ref>{{DOI|10042/to-12874}}</ref>
! O1b <ref>{{DOI|10042/to-12859}}</ref> <ref>{{DOI|10042/to-12875}}</ref>
! O2a <ref>{{DOI|10042/to-12860}}</ref> <ref>{{DOI|10042/to-12876}}</ref>
! O2b <ref>{{DOI|10042/to-12861}}</ref> <ref>{{DOI|10042/to-12877}}</ref>
! O3a <ref>{{DOI|10042/to-12862}}</ref> <ref>{{DOI|10042/to-12878}}</ref>
! O3b <ref>{{DOI|10042/to-12863}}</ref> <ref>{{DOI|10042/to-12879}}</ref>
! O4a <ref>{{DOI|10042/to-12864}}</ref> <ref>{{DOI|10042/to-12880}}</ref>
! O4b <ref>{{DOI|10042/to-12865}}</ref> <ref>{{DOI|10042/to-12881}}</ref>
|-
| Total energy (Hartrees)
| -690.19707265 || -690.19304602 || -690.18205613 || -690.18531163 || -690.18772229 || -690.19218504 || -690.19511334 || -690.19736046
|-
| Relative energy (kcal/mol)
| 0.1806035 || 2.707351953 || 9.603611992 || 7.560754915 || 6.048042939 || 3.247625056 || 1.410089078 || 0
|-
| Boltzmann population
| '''0.399731''' || 0.005619 || 4.95056E-08 || 1.55625E-06 || 2E-05 || 0.002257 || 0.050182 || '''0.542189'''
|-
| NMR peak data
| [[Media:O1a NMR njm08.txt|link]] || [[Media:O1b NMR njm08.txt|link]] || [[Media:O2a-nmr njm08.txt|link]] || [[Media:O2b-nmr njm08.txt|link]] || [[Media:O3a-nmr njm08.txt|link]] || [[Media:O3b-nmr njm08.txt|link]] || [[Media:O4a-nmr njm08.txt|link]] || [[Media:O4b-nmr njm08.txt|link]]
|-
!
! I1a <ref>{{DOI|10042/to-12866}}</ref> <ref>{{DOI|10042/to-12882}}</ref>
! I1b <ref>{{DOI|10042/to-12867}}</ref> <ref>{{DOI|10042/to-12889}}</ref>
! I2a <ref>{{DOI|10042/to-12868}}</ref> <ref>{{DOI|10042/to-12883}}</ref>
! I2b <ref>{{DOI|10042/to-12869}}</ref> <ref>{{DOI|10042/to-12884}}</ref>
! I3a <ref>{{DOI|10042/to-12870}}</ref> <ref>{{DOI|10042/to-12885}}</ref>
! I3b <ref>{{DOI|10042/to-12871}}</ref> <ref>{{DOI|10042/to-12886}}</ref>
! I4a <ref>{{DOI|10042/to-12872}}</ref> <ref>{{DOI|10042/to-12887}}</ref>
! I4b <ref>{{DOI|10042/to-12873}}</ref> <ref>{{DOI|10042/to-12888}}</ref>
|-
| Total energy (Hartrees)
| -690.198975 || -690.1953307 || -690.1817656 || -690.1847384 || -690.1868985 || -690.1918577 || -690.1970615 || -690.1941203
|-
| Relative energy (kcal/mol)
| 0 || 2.286801382 || 10.79908028 || 8.933576206 || 7.578093002 || 4.466141768 || 1.200707993 || 3.046376494
|-
| Boltzmann population
| '''0.86263''' || 0.01818 || 1.04723E-08 || 2.44044E-07 || 2.4E-06 || 0.000459 || '''0.113684''' || 0.005044
|-
| NMR peak data
| [[Media:I1a-nmr njm08.txt|link]] || [[Media:I1b-nmr njm08.txt|link]] || [[Media:I2a-nmr njm08.txt|link]] || [[Media:I2b-nmr njm08.txt|link]] || [[Media:I3a-nmr njm08.txt|link]] || [[Media:I3b-nmr njm08.txt|link]] || [[Media:I4a-nmr njm08.txt|link]] || [[Media:I4b-nmr njm08.txt|link]]
|}

As you can see, there are two conformations for both '''1''' and '''2'''' with significant populations in solution (bold). In both molecules, these correspond to conformations where the ester carbonyl is pointing up. Conformations where the ester carbonyl is pointing down (O2-O3, I2-I3) are markedly higher in energy and have very low, in some cases insignificant, populations. The two pairs of low energy conformations differ in the orientation of the double bond. If rotation of the E-alkene occurs faster than the NMR timescale, then both of the pairs would contribute towards the observed NMR shifts. However, if rotation of the alkene is restricted so that it occurs slower that the NMR timescale, then two sets of peaks would be observed.

{| class="wikitable"
|+ Table 15. Boltzmann weighted chemical shifts of O1-4 and I1-4 in comparison to natural stagonolide D
! rowspan="2" | carbon number
! natural stagonolide D
! colspan="2" | O1-4
! colspan="2" | I1-4
|-
! shift (ppm)
! shift (ppm)
! difference
! shift (ppm)
! difference
|-
| 1 (3)||173.5||167.90||5.60||169.10||4.40
|-
| 5 (5)||134.2||134.90||-0.70||133.97||0.23
|-
| 6 (10)||128.1||121.14||6.96||126.13||1.97
|-
| 4 (6)||75.1||71.28||3.82||74.15||0.95
|-
| 9 (7)||65.7||66.73||-1.03||66.34||-0.64
|-
| 8 (8)||58.2||57.35||0.85||58.26||-0.06
|-
| 7 (9)||55.4||56.18||-0.78||55.83||-0.43
|-
| 3 (1)||35||35.34||-0.34||37.43||-2.43
|-
| 2 (2)||31.2||31.50||-0.30||32.53||-1.33
|-
| 10 (13)||16.2||18.38||-2.18||17.86||-1.66
|}

[[File:Graph dev 1 njm08.pdf|400px|center|]]

The Boltzmann weighted <sup>13</sup>C-NMR shifts for both molecules '''1''' and '''2'''' were calculated and compared to the experimentally observed shifts for the natural Stagonolide D. The deviations in ppm for each carbon are shown in '''table 15''' (Gaussian atom numbers in brackets) and the corresponding chart. An error of about 5ppm was observed for carbon 1 in both molecules. A systematic error for ester carbonyl carbons of 4-5 ppm for mpw1pw91/6-31g(d,p) GAIO calculations has been reported in the literature; indeed, a suitable correction brings these calculated shifts in line with that of the natural product. The largest deviation in chemical shift is around 7 ppm for carbon 6 of '''O1-4''', compared to just 2 ppm for '''I1-4'''. Interestingly, this corresponds to the alkene carbon nearest to the epoxide ring. For O4b, the highest populated conformation of O1-4, the alkene is oriented in the opposite direction to that of I1a, the highest populated conformation of I1-4. This may suggest that in the natural product the alkene is oriented as in I1a. The second largest deviation, apart from carbon-1, is for carbon-4, which corresponds to that of the secondary alcohol who's stereochemistry is in dispute. As before, '''I1-4''' has a much lower deviation that '''O1-4''', which may suggest that the natural product does indeed have the structure of '''2''' as reassigned by Ramana.

The calculated shifts were then grouped into two for each molecule, entertaining the possibility of atropisomers separated by the orientation of the double bond. The relative energies and Boltzmann populations were re-calculated for each individual atropisomer (O1-O2, O3-O4, I1-I2, I3-I4), the results of which are summerised in '''table 16.'''.

{| class="wikitable"
|+ Table 16. Energies and populations of mpw1pw91/6-31G(d,p) optimised conformations: O1-2, O3-4, I1-2, I3-4
!
! O1a
! O1b
! O2a
! O2b
|-
| Total energy (Hartrees)
| -690.19707265 || -690.19304602 || -690.18205613 || -690.18531163
|-
| Relative energy (kcal/mol)
| 0 || 2.526748453 || 9.423008491 || 7.380151415
|-
| Boltzmann population
| '''0.986134''' || 0.013862 || 1.2213E-07 || 3.83926E-06
|-
!
! O3a
! O3b
! O4a
! O4b
|-
| Total energy (Hartrees)
| -690.18772229 || -690.19218504 || -690.19511334 || -690.19736046
|-
| Relative energy (kcal/mol)
| 6.048042939 || 3.247625056 || 1.410089078 || 0
|-
| Boltzmann population
| 3.36236E-05 || 0.003796 || 0.084389 || '''0.911781'''
|-
!
! I1a
! I1b
! I2a
! I2b
|-
| Total energy (Hartrees)
| -690.198975 || -690.1953307 || -690.1817656 || -690.1847384
|-
| Relative energy (kcal/mol)
| 0 || 2.286801382 || 10.79908028 || 8.933576206
|-
| Boltzmann population
| '''0.97936''' || 0.02064 || 1.18894E-08 || 2.77067E-07
|-
!
! I3a
! I3b
! I4a
! I4b
|-
| Total energy (Hartrees)
| -690.1868985 || -690.1918577 || -690.1970615 || -690.1941203
|-
| Relative energy (kcal/mol)
| 6.377385009 || 3.265433775 || 0 || 1.845668501
|-
| Boltzmann population
| 2.01745E-05 || 0.003854 || '''0.953803''' || 0.042323
|}

{| class="wikitable"
|+ Table 17. Boltzmann weighted chemical shifts of O1-2, O3-4, I1-2 and I3-4 in comparison to natural stagonolide D
! rowspan="2" | carbon number
! natural stagonolide D
! colspan="2" | O1-2
! colspan="2" | O3-4
! colspan="2" | I1-2
! colspan="2" | I3-4
|-
! shift (ppm)
! shift (ppm)
! difference
! shift (ppm)
! difference
! shift (ppm)
! difference
! shift (ppm)
! difference
|-
| 1 (3) ||173.5||168.74||4.76||167.34||6.16||169.22||4.28||168.20||5.30
|-
| 5 (5) ||134.2||134.33||-0.13||135.29||-1.09||133.83||0.37||134.95||-0.75
|-
| 6 (10) ||128.1||123.77||4.33||119.35||8.75||127.40||0.70||116.73||11.37
|-
| 4 (6) ||75.1||69.35||5.75||72.59||2.51||74.75||0.35||69.71||5.39
|-
| 9 (7) ||65.7||66.39||-0.69||66.95||-1.25||66.23||-0.53||67.10||-1.40
|-
| 8 (8) ||58.2||56.50||1.70||57.94||0.26||58.37||-0.17||57.47||0.73
|-
| 7 (9) ||55.4||56.11||-0.71||56.23||-0.83||55.76||-0.36||56.35||-0.95
|-
| 3 (1) ||35||35.65||-0.65||35.12||-0.12||38.26||-3.26||31.32||3.68
|-
| 2 (2) ||31.2||28.74||2.46||33.38||-2.18||32.76||-1.56||30.81||0.39
|-
| 10 (13) ||16.2||17.57||-1.37||18.93||-2.73||17.58||-1.38||19.87||-3.67
|}

[[File:Graph dev 2 njm08.pdf|400px|center|]]

Out of the four calculated atopisomers, I1-2 stands out as matching the experimental NMR data of stagonolide D markedly better than the others. The error in ppm for carbon 5, 6, 4, 9, 8 and 7 is less that 1ppm, with a maximum deviation of 3ppm corresponding to carbon 3. The fit to the experimental data is better than for I1-4, and each of the other atropisomers have much larger maximum deviations, especially at key carbons such as 6 and 4.

Examination of the molecular orbitals of the various conformations reveals that there is significant transannular overlap between that HOMO, which corresponds to the π-orbital of the alkene, and the unoccupied π* of the ester carbonyl; particularly with the lobe positioned over the carbonyl carbon (carbon 1). It is difficult to compare the extent of overlap between conformations, but frequency analysis and examination of the C=O stretch would be a good method of quantifying the interaction. This transannular interaction may be one of the key factors that restricts rotation of the alkene bond as a poor alignment of the π-faces would cause reduction in orbital overlap. It would be interesting to see whether how the frequency of the C=O stretch changes for the higher energy conformations such as I2a, where the ester carbonyl group is pointing downwards.

====Assignment of atropisomers====

An interesting observation made by Ramana in the synthesis of '''1''' and '''2'''', was that the NMR spectra for both compounds showed two sets of peaks, assigned as slowly equilibrating major and minor conformers <ref name="Ramana" />. For '''2'''', only the chemical shifts of the major conformer matched that of the natural product. This may suggest that the final ring closing metathesis generated two sets of atropisomers or, as suggested by Ramana, that there exists two conformations which interconvert slower than the NMR timescale.

The calculated chemical shifts for O1-2, O3-4, I1-2 and I3-4 were compared to the reported chemical shifts of the major and minor conformations for '''1''' and '''2'''', as synthesised by Ramana. The average deviation (excluding carbon-1) was used to quantify the fit and the results are summarised in '''table 18'''.

{| class="wikitable"
|+ Table 18. Average deviation of O1-2, O3-4, I1-2, I3-4 compared to 1 major, 1 minor, 2' major, 2' minor
!
! 1 major
! 1 minor
! 2' major
! 2' minor
|-
! O1-2
|'''1.21'''||1.70||2.00||1.67
|-
! O3-4
|2.83||'''0.94'''||2.21||2.08
|-
! I1-2
|2.40||2.01||'''0.97'''||3.42
|-
! I3-4
|2.60||1.45||3.17||'''1.17'''
|}

{| align="center"
|+ '''Deviations from experimental'''
| [[File:Omajor_njm08.pdf|200px]] || [[File:Ominor_njm08.pdf|200px]]
|-
| [[File:Imajor_njm08.pdf|200px]] || [[File:Iminor_njm08.pdf|200px]]
|}

For each set of major and minor peaks, one set of calculated chemical shifts matched noticeably better than the others, especially for '''1 minor''' and '''2' major'''. This suggests that the two sets of peaks found in Ramana's spectra are indeed due to conformations of the same molecule. Interestingly, the relative peak heights observed by Ramana do not correspond to the Boltzmann populations as determined by the relative energies from the calculated structures. For example, the lowest energy conformation of '''1''' was calculated to be O4b. But O3-4, where O4b has a 91% population, matches the NMR of the minor conformer. This suggests that the conformations observed in the experimental spectra are not at thermodynamic equilibrium, which implies that they are true atropisomers, unable to intervonvert. Its feasible to see how these atropisomers could have come about from the final ring closing metathesis, especially as it appears they differ by the orientation of the double bond.

The other explanation is that the relative energies from the DFT optimised structure are inaccurate. This is quite likely since the modest 6-31G(d,p) basis set was used. The relative total energies were also approximated to be representative of the relative Gibbs free energies, which of course is not necessarily the case. By performing a frequency analysis, the entropy corrected energies can be obtained which would give more accurate populations.

The feasibility of repeating the optimisations and NMR calculations using methods that have been shown to give lower errors, was evaluated. The NMR for I1a was calculated from the mpw1pw91/6-31g(d,p) optimised structure using the following methods:
* # nmr=giao mpw1pw91/aug-cc-pvdz scrf=(cpcm,solvent=chloroform) <ref>{{DOI|10042/to-128990}}</ref>
* # nmr=giao b3lyp/aug-cc-pvdz scrf=(cpcm,solvent=chloroform) iop(3/76=1000001189,3/77=0961409999,3/78=0000109999) <ref>{{DOI|10042/to-128991}}</ref>
The first of these methods simply replaces the 6-31G(d,p) basis set with the aug-cc-pvdz basis set and has shown to reduce many of the systematic errors such as with the ester carbonyl carbon <ref name="NMRmethod" />. The second uses the WP04 functional, a version of the popular B3LYP functional that has been re-parametised specifically for calculating NMR shifts in chloroform <ref name="WP04">{{DOI|10.1021/jo900482q}}</ref>. Both methods took approximately 40 minutes of wall time on the SCAN, compared to ≈5 minutes with mpw1pw91/6-31g(d,p). Each of the 16 conformations would have to be re-optimised by the same method (ideally with frequency analysis) prior to NMR calculations, which took between 20-60 minutes of wall time for mpw1pw91/6-31g(d,p). Therefore, it was decided that these methods were too expensive given the limited time frame and requirement of the SCAN by other colleagues.

Even so, the errors were seen to be low enough to assign the structure of each of the atropisomers for '''1''' and '''2'''' as represented by the lowest energy conformation. These structures can be seen below.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Atropisomers of 1 and 2' as represented by their lowest energy conformation
!1 major ('''1''')
!1 minor ('''1''')
|-
|
<jmol>
<jmolApplet>
<name>Omajor</name><color>white</color><size>200</size>
<script>rotate z -108.96; rotate y 54.67; rotate z 89.98;</script>
<uploadedFileContents>O1a_checkpoint_56266.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<name>Ominor</name><color>white</color><size>200</size>
<script>rotate z 78.46; rotate y 61.31; rotate z 79.84;</script>
<uploadedFileContents>O4b_checkpoint_56273.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|-
!2' major ('''2'''')
!2' minor ('''2'''')
|-
|
<jmol>
<jmolApplet>
<name>Imajor</name><color>white</color><size>200</size>
<script>rotate z -108.96; rotate y 54.67; rotate z 89.98;</script>
<uploadedFileContents>I1a_checkpoint_56274.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<name>Iminor</name><color>white</color><size>200</size>
<script>rotate z -108.96; rotate y 54.67; rotate z 89.98;</script>
<uploadedFileContents>I4a_checkpoint_56280.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|}

====Calculation of optical rotation====

A Gaussian input file was prepared from the formatted checkpoint file of the DFT optimised structure of I1a to calculate its optical rotation, specified by:

* # cam-b3lyp/aug-cc-pvdz polar(optrot) scrf=(cpcm,solvent=chloroform) CPHF=RdFreq

The frequency was specified as 589nm in the input file to correspond to the sodium D lines. A similar input file was prepared for its enantiomer, I1a'.

The purpose of this calculation is to determine the sign of the optical rotation for I1a, which the calculations suggest is a representative structure for '''2''''; and the enantiomer I1a', which if correct would correspond to '''2''', or natural Stagonolide D. Ramana reported an [α]<sup>25</sup><sub>D</sub> of +76.8 for '''2'''', compared to a reported [α]<sup>25</sup><sub>D</sub> of -82 for the natural product, leading to the reassignment of Stagonolide D as '''2'''.

{| class="wikitable"
|+ Optical rotation of I1a and I1a'
!
!I1a <ref>{{DOI|10042/to-12892}}</ref>
!I1a' <ref>{{DOI|10042/to-12893}}</ref>
|-
| '''[α]<sup>25</sup><sub>D</sub> (calc.)'''
| +114.97
| -114.86
|-
| '''[α]<sup>25</sup><sub>D</sub> (lit.)'''
| +76.8 <ref name="Ramana" />
| -82 <ref name="stanB-F" />
|}

The optical rotation of I1a was found to be the same direction as that of '''2'''', and the I1a' to be the same direction as natural stagonolide D. This supports the absolute sterochemistry of the reassigned structure of Stagonolide D ('''2''').

====Conclusions====
[[File:Possible_structures_of_stagonolide_D_njm08.png|460px]]

The calculated 13C-NMR spectra and calculated optical rotation appear to support the reassignment of the structure of Stagonolide D by Ramana. The major and minor conformers found in the spectra of '''1''' and '''2'''' were assigned to pairs of Boltzmann weighted conformers, differing in the orientation of the double bond. The relative peak heights observed in the experimental spectra do not reflect the populations of the conformers as calculated by Boltzmann statistics. This may suggest that the pairs are not at thermodynamic equilibrium and are atropisomers generated by the final synthetic step - the ring closing metathesis. This is also supported by the observation that only the major conformer of '''2'''', I1-2, matches well with the NMR data of the natural product.

For a more definitive assignment, calculations should be repeated using higher levels of theory as described in previous sections. This is particularly true of the geometry optimisations to ensure accurate relative energies and representative populations.

It would be interesting to carry out further calculations to rationalise the relative stability and instability of the low and higher energy conformations. This would be done using molecular mechanics to evaluate the steric factors, and frequency analysis of the C=O stretch to assess the extent of the transannular interaction between the π- bond of the alkene and the π* of the ester carbonyl.

An issue not addressed was the confirmation of the originally proposed structure, '''1''', by Nanda <ref name="Nanda" />. There is definitely something odd about the paper. One point to note is that stagonolide D is one of the only isolated stagonolides that is a crystalline solid. Ramana's synthesis of '''1''' gave a yellow oil, whereas his synthesis of '''2'''' gave a crystalline solid. The nature of the product synthesised by Nanda is not stated in the paper. The other point is that the <sup>1</sup>H-NMR spectra attached in the supplementary information labeled as "stagonolide D" does not match the <sup>1</sup>H-NMR peak data given in the experimental section of the paper. One of the reasons for repeating the NMR calculations at a higher level of theory such as WP04/aug-cc-pvdz, is that it has been shown to give acceptable predictions of <sup>1</sup>H-NMR shifts <ref name="WP04" />, which may shed light on this problem.

The lack of any X-ray crystallography data may suggest a difficulty in obtaining high quality crystals, although this would allow for a definitive answer to the structure.

==== References and links ====
<references/>

[[Category:Njm08]]

Rep:Mod:8039662

2012-10-10T22:26:05Z

Njm08:

'''Computational lab, module 3''' inorganic

== Getting to grips with Gaussian ==

===BH<sub>3</sub>===

====Optimisation====

A model of BH<sub>3</sub> was constructed using the Gaussview 5 graphical user interface using the trigonal planar boron fragment from the ''element fragment'' palette. Each of the B-H bond lengths were extended to 1.5Å. A gaussian input file was prepared, through the ''Gaussian calculation setup'' menu, to perform an optimisation, specified by:

<code># opt b3lyp/3-21g geom=connectivity</code>

The input file was saved as BH3_opt.gjf and submitted to Gaussian.

https://wiki.ch.ic.ac.uk/wiki/images/4/41/BH3_opt_wiki_njm08.log

Once the calculation was complete, the .log file was opened in Gaussview 5 with the ''read intermediate geometries'' checkbox ticked. The final set of forces and displacements printed in the output final were checked to ensure the optimisation had converged. A summary of the calculation can be seen in '''table 1'''.

[[File:Total_energy_graph_njm08.svg|thumb|upright=1.8|Plot of total energy]]
[[File:RMS_gradient_graph_njm08.svg|thumb|upright=1.8|Plot of RMS gradient]]
{| class="wikitable"
|+ Table 1. Summary
! colspan="2" | BH<sub>3</sub> optimisation
|-
| File Name || BH3_OPT.out
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 3-21G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -26.46226338 a.u.
|-
| RMS Gradient Norm || 0.00020672 a.u.
|-
| Imaginary Freq || -
|-
| Dipole Moment || 0.0000 Debye
|-
| Point Group || D3H
|-
| Job cpu time || 0 days 0 hours 0 minutes 11.0 seconds.
|}

The path of the optimisation was visualised using the animation, which showed the bond lengths shrinking from the starting structure to the final geometry. Plots of ''Total energy'' and ''RMS gradient norm'' can be seen below.

The optimisation converged in four steps. Inspection of the optimised geometry revealed B-H bond lengths of 1.19Å (lit. 1.19Å<ref>{{DOI|10.1063/1.461942}}</ref>) and H-B-H bond angles of 120.000°.

====Frequency analysis====

From the B3LYP/3-21G optimised geometry, an input file was prepared, through the ''Gaussian calculation setup'' menu to perform a frequency analysis specified by:

<code> # freq b3lyp/3-21g geom=connectivity pop=(full,nbo)</code>

The keyword ''freq'' <ref name="freq">http://www.gaussian.com/g_tech/g_ur/k_freq.htm</ref> requests calculation of the force constants from the second dervatives of the energy. From this, vibrational frequencies and thermochemical corrections may be obtained. Since the second derivative of a function indicates the nature of a stationary point, frequency calculations should only be done on fully optimised geometries, otherwise the results are meaningless. This requires that the same method, including basis set, be used for the optimisation and fequency analysis. If all the force constants and subsequent vibrational frequencies are positive, then the structure has optimised to a minimum. This means that movement along all of the 3N-6 degrees of freedom results in an increase in energy. If there is one negative (or imaginary) frequency, then the structure has optimised to a transition state. This can be thought of as a saddle point on the potential energy surface connecting two local minima, where movement along one degree of freedom results in a decrease in energy but movement in any other degree of freedom sees an increase in energy.

https://wiki.ch.ic.ac.uk/wiki/images/4/4f/BH3_FREQ_NJM08.LOG

<pre><nowiki>Low frequencies --- -66.7625 -66.3592 -66.3589 -0.0020 0.0031 0.2123
Low frequencies --- 1144.1483 1203.6413 1203.6424</nowiki></pre>

The six ''low frequencies'' printed in the output file, shown in '''table 3''', correspond to the three translational and rotational motions of the molecule. They should all be close to ''zero'' cm<sup>-1</sup> (ideally < 10cm<sup>-1</sup> <ref name="lowfreq">http://www.gaussian.com/g_whitepap/vib.htm</ref>) and their magnitude can give an indication of the quality of the optimisation. The rotational frequencies for the B3LYP/3-21G optimised structure are on the large side at around 60cm<sup>-1</sup>. This is indicative of the low level method used. All of the normal vibrational frequencies are positive, which confirms that the structure has optimised to a minima.

The form and frequency of the normal vibrational modes can be seen in '''table 4'''. The vibrations may be visualised using the Jmol applet and Jmol script bottons in the table.

{| class="wikitable"
|+ Table 4. Frequencies of BH<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! lit. <ref>{{DOI|10.1021/ja00738a008}}</ref>
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>BH3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>BH3_FREQ_NJM08.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
Animation: <jmol><jmolButton><script>vibration 5;</script><name>BH3_vibrations</name><text>ON</text></jmolButton>
<jmolButton><script>vibration OFF;</script><name>BH3_vibrations</name><text>OFF</text></jmolButton></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>1</text></jmolButton></jmol>
|
| 1144 || 1125 || 93 || A"
|-
| align="center" |
<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>2</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>3</text></jmolButton></jmol>
|
| 1204 || 1604 || 12 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>4</text></jmolButton></jmol>
|
| 2598 || (2693<ref>{{DOI|10.1063/1.448805}}</ref>) || 0 || A'
|-
| align="center" |
<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>5</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|-
| align="center" |
<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>BH3_vibrations</name><text>6</text></jmolButton></jmol>
|
| 2737 || 2808 || 100 || E'
|}

[[File:BH3_IR_njm08.svg|thumb|upright=2|Calculated IR spectrum of BH<sub>3</sub>]]
Examination of the predicted IR spectra reveals only three peaks despite there being six vibrational modes. A' is totally symmetric and does not results in a change in dipole moment, unlike the other vibrational modes present for D3h symmetry. This makes the A' stretch at 2598 cm<sup>-1</sup> IR inactive, hence why it does not appear on the spectra. The two pairs of E' modes are degenerate, which means each of the component vibrations occur at the same frequency and intensity, appearing as a single peak on the spectra. The outcome is a peak at 1144 cm<sup>-1</sup> corresponding to A", a peak at 1204 cm<sup>-1</sup> corresponding to the first E' pair and a peak at 2737 cm<sup>-1</sup> corresponding to the second E' pair.

For DFT methods, including B3LYP, the default is to calculate second derivatives analytically<ref name="freq" />. This means that the magnitude of the rotational ''low frequencies'' may be reduced by specifying tighter optimisation criteria in the input file <ref name="lowfreq" />. For example;

<code># freq opt=verytight b3lyp/3-21G</code>

====Molecular Orbitals====

From the formatted checkpoint file of the B3LYP/3-21G optimised structure of BH<sub>3</sub>, an input file was prepared to perform population analysis, atomic charge assignments and full Natural Bond Orbital analysis, using NBO version 3, specified by:

<code># b3lyp/3-21g pop=(nbo,full) geom=connectivity</code>

{{DOI|10042/to-12907}}

The calculation was run through Gaussian 09 on the SCAN cluster and took 12.6 seconds. From the formatted checkpoint file, cube files for the first eight molecular orbitals were generated through Gaussview 5.0 and converted to the .jxvl format using the Jmol java app. These can be visualised using the Jmol applet and Jmol script buttons below.

{| class="wikitable"
|+ B3LYP/3-21G Molecular Orbitals of BH<sub>3</sub>
| align="center" |<jmol>
<jmolApplet>
<name>BH3_orbitals</name><color>white</color><size>350</size>
<script>zoom 78.85;
</script><uploadedFileContents>BH3_njm08.mol</uploadedFileContents>
</jmolApplet>
</jmol>
Molecular Orbitals:

<jmol><jmolButton><script>isosurface "images/f/ff/BH3_mo1_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>1</text></jmolButton>
<jmolButton><script>isosurface "images/4/41/BH3_mo2_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>2</text></jmolButton>
<jmolButton><script>isosurface "images/3/32/BH3_mo3_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>3</text></jmolButton>
<jmolButton><script>isosurface "images/3/3d/BH3_mo4_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>4</text></jmolButton>
<jmolButton><script>isosurface "images/d/d7/BH3_mo5_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>5</text></jmolButton>
<jmolButton><script>isosurface "images/4/4b/BH3_mo6_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>6</text></jmolButton>
<jmolButton><script>isosurface "images/f/f9/BH3_mo7_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>7</text></jmolButton>
<jmolButton><script>isosurface "images/5/5f/BH3_mo8_njm08.jvxl" translucent</script><name>BH3_orbitals</name><text>8</text></jmolButton>
<jmolButton><script>isosurface OFF</script><name>BH3_orbitals</name><text>clear</text></jmolButton></jmol>
| [[File:MOs_of_BH3_njm08.jpg|400px|]]
|}

The molecular orbital diagram for BH<sub>3</sub> can be seen below, constructed from the boron atomic orbitals and the D3h H<sub>3</sub> fragment. Snapshots of the B3LYP/3-21G calculated molcecular orbitals can be seen along side the "LCAO" molecular orbitals for comparison. Ordering of the molecular orbitals was assisted by the quantitative relative energies of the B3LYP/3-21G calculated orbitals.

[[File:Modiagram_njm08.png|800px]]

Qualitative molecular orbital theory can be used to gain insight into the relative energies and shapes of molecular orbitals without resorting to quantum mechanical calculations. Comparison of the "LCAO" MOs with the calculated MOs shows that, for simple molecules of high symmetry such as BH<sub>3</sub>, this qualitative approach gives reasonable predictions.

====Natural Bond Orbital analysis====

As described above, Natural Bond Orbital analysis, using NBO version 3, was requested on the B3LYP/3-21G optimised geometry of BH<sub>3</sub>. The full NBO analysis, as printed in the output file, can viewed [[Media:BH3_NBO_analysis_njm08.txt|here]].

The NBO charge distribution was visualised using Gaussview 5.0.

{|
| [[File:BH3_NBOcharges_njm08.png|300px|]]
| [[File:BH3_NBOcolours_njm08.png|300px|]]
|}

The charge distribution shows that there is a build up of electron density on the hydrogens, coupled with a reduction of electron density on the boron. This reflects the Pauling electronegativities of boron and hydrogen at 2.04 and 2.20 respectively.

<references/>

===TlBr<sub>3</sub>===

A model of TlBr<sub>3</sub> was constructed in Gaussview 5.0. The trigonal planar thallium fragment was selected and each of the hydrogens were replaced by bromine atom fragments. The point group symmetry was constrained to D3h with a ''very tight'' (0.0001) tolerance. A gaussian input file was prepared, through the ''Gaussian calculation setup'' menu, to perform an optimisation, specified by: <code># opt b3lyp/lanl2dz geom=connectivity</code>. The input file was saved as TlBr3_opt.gjf and submitted to Gaussian 09<ref>https://wiki.ch.ic.ac.uk/wiki/images/7/7d/TlBr3_opt_wiki_njm08.log</ref>.

The final set of forces and displacements printed in the output final were checked to ensure the optimisation had converged. A second input file was prepared, from the output, to perform frequency analysis on the optimised geometry, specified by: <code># freq b3lyp/lanl2dz</code>. This job was submitted to Gaussian 09 on the SCAN cluster. Summaries of both calculations can be seen in '''table 6'''.

[[File:TlBr3_total_energy_graph_njm08.svg|thumb|upright=1.8|Plot of total energy]]
[[File:TlBr3_RMS_grad_graph_njm08.svg|thumb|upright=1.8|plot of RMS gradient]]
{| class="wikitable"
|+ Table 6. Calculation summaries for optimisation and frequency analysis of TlBr<sub>3</sub>
!
! Optimisation
! Frequency analysis
|-
| File Name||TLBR3_OPT||TLBR3_freq_log_57572
|-
| File Type||.log||.log
|-
| Calculation Type||FOPT||FREQ
|-
| Calculation Method||RB3LYP||RB3LYP
|-
| Basis Set||LANL2DZ||LANL2DZ
|-
| Charge||0||0
|-
| Spin||Singlet||Singlet
|-
| E(RB3LYP) (a.u.)||-91.21812851||-91.21812851
|-
| RMS Gradient Norm (a.u.)||0.0000009||0.00000088
|-
| Imaginary Freq||||0
|-
| Dipole Moment (Debye)||0.0000||0.0000
|-
| Point Group||D3H||D3H
|-
| Job cpu time (days : hours : minutes : seconds)||0 : 0 : 0 : 15.0||0 : 0 : 0 : 16.9
|}

Plots of total energy and RMS gradient show the optimisation converging in three steps. Inspection of the optimised geometry reveals Tl-Br bond lengths of 2.65Å (lit. 2.52Å in aqueous solution<ref>{{DOI|10.1021/ja00123a011}}</ref>) and Br-Tl-Br bond angles of 120.000°. The 120° bond angles and dipole moment of 0 are as expected for a tigonal planar molecule of D3h symmetry.

The low frequencies printed in the output of the frequency analysis are as follows:
<pre>Low frequencies --- -3.4213 -0.0026 -0.0004 0.0015 3.9367 3.9367
Low frequencies --- 46.4289 46.4292 52.1449</pre>
The first six frequencies correspond to the translational and rotational modes of the molecule. As the three rotational modes are often of higher frequency than the translational modes, -0.0026, -0.0004, 0.0015 are most likely translational and -3.4213, 3.9367 and 3.9367 are most likely rotational. These six frequencies are all close to zero (<10cm<sup>-1</sup>), which is good (compare to the B3LYP/3-21G opt of BH<sub>3</sub>). The other three frequencies printed in the ''Low frequencies'' section are the lowest normal vibrational modes. In this case, the lowest frequency normal vibration is 46.4289cm<sup>-1</sup>. Negative signs indicate imaginary frequencies. Optimsations that have converged to a minimum will have no imaginary frequencies (ignoring tranlational/rotational modes). A single imaginary frequency means the geometry has optimised to a transitions state.

The calculated vibrational modes can be visualised in the Jmol applet below ('''table 8'''). There are no imaginary frequencies, which confirms TlBr<sub>3</sub> has optimised to a minimum.

{| class="wikitable"
|+ Table 8. Frequencies of TlBr<sub>3</sub>
! Form of vibration
! Mode
! Description
! Frequency
! Intensity
! Symmetry (D3h point group)
|-
| rowspan="6" align="center" |<jmol>
<jmolApplet>
<name>TlBr3_vibrations</name><color>white</color><size>300</size>
<script>rotate z 160.2; rotate y 27.49; rotate z -162.14; frame 3;vectors 4;vectors scale 3;color vectors red;
</script><uploadedFileContents>TLBR3_freq_log_57572.out</uploadedFileContents>
</jmolApplet>
</jmol>
Animation: <jmol><jmolButton><script>vibration 5;</script><name>TlBr3_vibrations</name><text>ON</text></jmolButton>
<jmolButton><script>vibration OFF;</script><name>TlBr3_vibrations</name><text>OFF</text></jmolButton></jmol>
| align="center" |
<jmol><jmolButton><script>frame 3;vectors 4;vectors scale 3;color vectors red;</script><name>TlBr3_vibrations</name><text>1</text></jmolButton></jmol>
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| 46 || 3.7 || E'
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<jmol><jmolButton><script>frame 4;vectors 4;vectors scale 3;color vectors red;</script><name>TlBr3_vibrations</name><text>2</text></jmolButton></jmol>
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<jmol><jmolButton><script>frame 5;vectors 4;vectors scale 3;color vectors red;</script><name>TlBr3_vibrations</name><text>3</text></jmolButton></jmol>
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| 52 || 5.8 || A''
|-
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<jmol><jmolButton><script>frame 6;vectors 4;vectors scale 3;color vectors red;</script><name>TlBr3_vibrations</name><text>4</text></jmolButton></jmol>
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<jmol><jmolButton><script>frame 7;vectors 4;vectors scale 3;color vectors red;</script><name>TlBr3_vibrations</name><text>5</text></jmolButton></jmol>
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<jmol><jmolButton><script>frame 8;vectors 4;vectors scale 3;color vectors red;</script><name>TlBr3_vibrations</name><text>6</text></jmolButton></jmol>
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|}

What is the calculation method?

These calculations use the B3LYP hybid-DFT functional.

What is the basis set?

Why must you use the same method and basis set for both calculations?
Why do you have to carry out a frequency analysis?

In some structures gaussview does not draw in the bonds where we expect, does this mean there is no bond? Why?
What is a bond? (your reply should not be more than a paragraph in length)

==An organometallic complex: Isomers of Mo(CO)<sub>4</sub>(PPh<sub>3</sub>)<sub>2</sub>==
[[File:Cis-trans_Mo_njm08.png|thumb|upright=1.8|Fig 4. ''cis''/''trans'' isomers]]
The transition metal complex, Mo(CO)<sub>4</sub>(PPh<sub>3</sub>)<sub>2</sub>, has two possible isomers. The two triphenylphosphine ligands can either be ''cis'' or ''trans'' about the molybdenum centre ('''fig. 4'''). Which isomer is more stable depends on a number of factors, including electronic and steric effects. Density functional theory calculations shall be used to determine the relative stability and the spectral characteristics of the two isomers.

===Optimisation===

For efficiency, the computationally demanding tripheylphosphine ligands have been modeled by trichlorophosphine. PCl<sub>3</sub> is similar electronically and is also reasonably bulky. Models of ''cis''- and ''trans''- Mo(CO)<sub>4</sub>(PCl<sub>3</sub>)<sub>2</sub> were constructed in Gaussview 5.0. The computationally demanding tripheylphosphine ligands were modeled by trichlorophosphine for efficiency. As a ligand, PCl<sub>3</sub> is similar to PPh<sub>3</sub> electronically and is also reasonably bulky. The geometries of the two isomers were initially optimised at the B3LYP/LanL2MB level with loose convergence criteria. This was specified by: <code># opt=loose b3lyp/lanl2mb geom=connectivity</code>. This low level optimisation was performed to obtain an approximate geometry before optimising to more expensive, higher level of theory. The final set of forces and displacements printed in the output file were checked to ensure the jobs had converged.
{|
| [[File:Mo_trans_DZ_starting_geom.jpg|thumb|Fig 3.]] || [[File:Mo_cis_DZ_starting_geom.jpg|thumb|Fig. 4]]
|}
From the outputs of the B3LYP/LanL2MB optimisations, the dihedral angles of the PCl3 ligands were adjusted to values likely to converge to a global, rather than local, minimum. These angles (Fig. 3 and 4) were obtained from a previously run scan of the potential energy surface<ref> Scan run by Dr Patricia Hunt</ref>. These adjusted geometries were then further optimised at the B3LYP/LanL2DZ level, specified by: <code># opt b3lyp/lanl2dz int=ultrafine scf=conver=9</code>. The keyword <code>int=ultrafine</code> requests a larger grid for numerical integration. The final set of forces and displacements printed in the output file were checked to ensure the jobs had converged. Frequency analysis was run on the final optimised geometries, specified by: <code># freq b3lyp/lanl2dz int=ultrafine scf=conver=9</code>.

Calculation summaries for the B3LYP/LanL2DZ level optimisations and corresponding frequency analyses can be seen in table 5.

{| class="wikitable"
|+ Table 5. Summary of B3LYP/LanL2DZ calculations on ''cis''- and ''trans''- Mo(CO)<sub>4</sub>(PCl<sub>3</sub>)<sub>2</sub>
! rowspan="2" |
! colspan="2" | ''cis''- Mo(CO)<sub>4</sub>(PCl<sub>3</sub>)<sub>2</sub>
! colspan="2" | ''trans''- Mo(CO)<sub>4</sub>(PCl<sub>3</sub>)<sub>2</sub>
|-
! optimsation
! frequency analysis
! optimsation
! frequency analysis
|-
| File Name||Mo_cis_DZ_opt_log_57566||Mo_cis_DZ_freq_log_57568||Mo_trans_DZ_opt_log_57564||Mo_trans_DZ_freq_log_57571
|-
| File Type||.log||.log||.log||.log
|-
| Calculation Type||FOPT||FREQ||FOPT||FREQ
|-
| Calculation Method||RB3LYP||RB3LYP||RB3LYP||RB3LYP
|-
| Basis Set||LANL2DZ||LANL2DZ||LANL2DZ||LANL2DZ
|-
| Charge||0||0||0||0
|-
| Spin||Singlet||Singlet||Singlet||Singlet
|-
| E(RB3LYP) (a.u.)||-623.5770719||-623.5770719||-623.576031||-623.576031
|-
| RMS Gradient Norm (a.u.)||0.00000577||0.00000584||0.00002963||0.00002964
|-
| Imaginary Freq||||0||||0
|-
| Dipole Moment (Debye)||1.3101||1.3101||0.3049||0.3049
|-
| Point Group||C1||C1||C1||C1
|-
| Job cpu time (days : hours : minutes : seconds)||0 : 1 : 7 : 28.6 ||0 : 0 : 30 : 38.1||0 : 0 : 47 : 11.6||0 : 0 : 27 : 58.8
|}

===Extra d-functions on phosphorous===

The basis set for phosphorous implemented with LanL2DZ only has s and p functions <ref>{{DOI|10.1063/1.448800}}</ref>. This treatment neglects possible interactions involving low lying d-atomic orbitals, which may play a part in the metal-phosphine bond.
Extra basis functions can be added using the <code>extrabasis</code> keyword. Any additional functions are described in the input file, listed after the coordinates. In this case, extra d-functions can be added to phosphorus for a more complete description.

The input files used for the previously described B3lYP/LanL2DZ optimisations were modified to include an addition d- basis function on phosphorous. This was specified as follows:
<pre># opt b3lyp/lanl2dz int=ultrafine scf=conver=9 extrabasis

...(title, charge/multiplicity, coordinates)...

P 0
D 1 1.0
0.55 0.100D+01
****</pre>
The final set of forces and displacements printed in the output files were checked to ensure the jobs had converged. Frequency analysis was run of the final optimised geometries. Calculation summaries can be seen in '''table 6'''.

{| class="wikitable"
|+ Table 6. Summary of B3LYP/LanL2DZ calculations on ''cis''- and ''trans''- Mo(CO)<sub>4</sub>(PCl<sub>3</sub>)<sub>2</sub> with extra d-fuctions on phosphorous
! rowspan="2" |
! colspan="2" | ''cis''- Mo(CO)<sub>4</sub>(PCl<sub>3</sub>)<sub>2</sub>
! colspan="2" | ''trans''- Mo(CO)<sub>4</sub>(PCl<sub>3</sub>)<sub>2</sub>
|-
! optimsation
! frequency analysis
! optimsation
! frequency analysis
|-
| File Name||Mo_cis_DZ_dAO_opt_log_57567||Mo_cis_DZ_dAO_freq_log_57569||Mo_trans_DZ_dAO_opt_log_57565||Mo_trans_DZ_dAO_freq_log_57570
|-
| File Type||.log||.log||.log||.log
|-
| Calculation Type||FOPT||FREQ||FOPT||FREQ
|-
| Calculation Method||RB3LYP||RB3LYP||RB3LYP||RB3LYP
|-
| Basis Set||Gen||Gen||Gen||Gen
|-
| Charge||0||0||0||0
|-
| Spin||Singlet||Singlet||Singlet||Singlet
|-
| E(RB3LYP) (a.u.)||-623.6929123||-623.6929123||-623.6941561||-623.6941561
|-
| RMS Gradient Norm (a.u.)||0.00000947||0.00000947||0.00001184||0.00001188
|-
| Imaginary Freq||||0||||0
|-
| Dipole Moment (Debye)||0.0758||0.0758||0.2299||0.2299
|-
| Point Group||C1||C1||C1||C1
|-
| Job cpu time (days : hours : minutes : seconds)||0 : 1 : 5 : 4.0 ||0 : 0 : 35 : 34.5||0 : 0 : 58 : 57.8||0 : 0 : 35 : 31.9
|}

Discussion from 2nd year lab report:

Infrared analysis. The symmetry of the -
cis-[Mo(CO)4L2] isomer is defined by the
point group C2v. Out of the four carbonyl
stretching modes, all transform as one of the
translation vectors (Tx, Ty, Tz) and therefore
result in a change of dipole moment [5]. This
means all for carbonyl stretching modes are
IR active and one would expect to see four
peaks in the spectrum. The symmetry of the -
trans-[Mo(CO)4L2] isomer is defined by the
point group D4h. Out of the carbonyl
stretching modes, only the doubly degenerate
Eu stretch is IR active and therefore only one
peak is expected.
As you can see from the attached IR
spectra, [Mo(CO)4(pip)4] has four well
defined carbonyl stretches in the expected
region and is easily assigned as the cisisomer.
The first [Mo(CO)4(PPh3)2] has one
sharp absorption at 2013cm-1 and an intense
series of overlapping peaks around 1900cm-1. It is difficult to determine the precise number of peaks in this
region. However, the absorption at 2013.59cm-1 is characteristic of the A1
(1) mode of the cis- isomer.
The thermal isomer shows a single strong absorption at 1891.19cm-1. This can be assigned to the Eu
mode of the trans- isomer, with only one IR active carbonyl stretch. There is a small peak at 2025cm-1. This
may either indicate a small amount of cis- impurity, which may explain the low decomposition point, or it
may be the A1g stretching mode of the trans- isomer. Although this mode is theoretically IR inactive, the
influence of the bulky PPh3 ligands can distort the geometry away from ideal D4h symmetry allowing the
inactive mode to be weakly observed.

...

Computational analysis. Density function theory B3YLP calculations using the LANL2DZ basis set
with extra d functions were carried out on a model system to find the relative energies and calculate the
theoretical IR stretching frequencies using Gaussian 09. Trichlorophosphine was used as an approximation to
the computationally demanding triphenylphosphine groups. Both geometries optimized with the transisomer
coming out at 1.2432×10-3 Hartrees lower in energy (3.26 kJ mol-1). This is quite a small difference
in energy, but considering that the phenyl ring is larger that the chlorine atom (PCl3 cone angle = 124° [10]),
the true difference is most likely even greater. The computed IR spectrum of the cis- isomer predicts a
overlap of peaks for the A1
(2), B1 and B2 modes at 1952, 1941 and 1938cm-1 respectively with the A1
(1) peak
at 2019cm-1 which agrees well with the experimental spectra given the approximations of the model. The
trans- spectrum predicts a strong absorption at 1938cm-1 for the Eu mode, with trace absorptions for the A1g
and B2g modes at 2024 and 1966cm-1 respectively caused by minor distortions to the D4h symmetry from the
phosphine ligands. Again, this supports the experimental results.

<references/>

==Mini Project: The structure, bonding and coordination chemistry of [Pd<sub>4</sub>(C<sub>8</sub>H<sub>8</sub>)(C<sub>9</sub>H<sub>9</sub>)][BAr<sup>f</sup><sub>4</sub>]==

===Introduction===

A recent development in organometallic chemistry has been the isolation of "sheet" sandwich complexes consisting of mono-layer metal clusters, typically of palladium, coordinated between planar aromatic hydrocarbons. A few selected examples of sheet sandwich complexes that have been synthesized so far can be be seen in '''Fig. 1'''.
[[file:Sheet_sandwich_examples_njm08.png|thumb|upright=2.5|Fig. 1. Examples of sheet sandwich complexes]]
Complex '''1''', a trinulear Pd<sub>3</sub>Cl<sub>3</sub> cluster capped by two tropylium ligands, was reported by Murahashi ''et al'' in 2006<ref name="science">{{DOI|10.1126/science.1125245}}</ref>, along with a Pd<sub>5</sub> complex with polycyclic capping ligands. These two compounds were the first "sheet" sandwich complexes to be characterized; a sheet being defined as a monolayer cluster consisting of three or more metal centers. The tetranuclear sheet sandwich complex, '''2''', was reported by Murahashi ''et al'' <ref name="Pd4">{{DOI|10.1021/ja903679f}}</ref> in 2009 and has several interesting features. X-ray crystallography shows that the Pd<sub>4</sub> cluster is almost perfectly square and planar and, unlike '''3''' and its synthetic precursor, is uncoordinated by acetonitrile. This has prompted theoretical studies into whether '''2''' is an example of transition metal aromaticity<ref name="arom1">{{DOI|10.1063/1.3382340}}</ref><ref name="arom2">{{DOI|10.1039/c0cp00475h}}</ref>. The complex is also a rare example of coordination to the cyclononatetraenyl anion. This ten electron Hückel aromatic species is simliar to the more common cyclopentadienyl anion, but is usually susceptible to skeletal rearrangement. A theoretical study has been carried out to assess the feasibility of using '''2''' to isolate planar tetra-coordinate carbon<ref name="tetracarbon">{{DOI|10.1002/ejic.201000620}}</ref>. '''3''' is the first example of a sheet sandwich complex to contain a metal other than palladium and was reported by Murahashi ''et al'' in 2011<ref name="Pt3">{{DOI|10.1039/c0sc00269k}}</ref>. This complex has a similar structure to '''1''', and was found to complex to various L-type ligands. '''1''', '''2''' and '''3''' are each reminiscent of the archetypal metallocene structure of ferrocene.

This project will focus on the Pd<sub>4</sub> sheet sandwich complex, '''2'''. Experimentally, the structure of '''2''' is well characterised through NMR and x-ray crystallography. The structure and bonding has also been investigated further through inital and subsequent computational DFT studies. However, one aspect that hasn't been so thoroughly investigated is the coordination chemistry of '''2'''. Trinuclear sheet sandwich complexes, such as '''3''', are typically stabilized upon synthesis by coordination to acetonitrile, acting as an L-type ligand. '''2''' is uncoordinated in this respect, even in solutions with a large excess of acetonitrile. On the other hand, titration studies have shown that it will coordinate with phosphine ligands, forming ''mono''- and ''bis''- PR<sub>3</sub> adducts, with possible evidence for ''tris''- coordination. The ''cis''/''trans'' stereochemistry of the ''bis''- PR<sub>3</sub> adducts has not been established.

This project will aim to compare the binding of ''2'' to a variety of L-type ligands and investigate how coordination effects the aromatic character of the Pd<sub>4</sub> cluster. The preference of bis-adducts to form ''cis'' or ''tans'' isomers will also be determined.

===Optimisation===

====From the x-ray coordinates====

The geometry of '''2''' was initially optimised at the B3LYP/lanL2DZ level. The x-ray crystallographic coordinates were used to specify the starting geometry. These were obtained from the .cif file, downloaded from the Cambridge Crystallographic Database. The output was then further optimised using the PBE1 hybrid DFT fuctional, with the Stuttgart/Dresden pseudopotential on palladium and the 6-31G(d) basis set on carbon and hydrogen. This was specified by:
<pre># opt pbe1pbe/gen pseudo=read

... (title, charge/multiplicity, coordinates) ...

Pd 0
SDD
****
C H 0
6-31G*
****

Pd 0
SDD

</pre>
In addition to the above, a 50 cycle limit was imposed (<code>opt(maxcycles=50)</code>) for this first calculation with the new method. PBE1 was chosen, as a comparison of density functional methods found it to be superior to the more popular B3LYP in calculating the geometries of transition metal complexes <ref name="PBE1-1">{{DOI|10.1021/ct700178y}}</ref><ref name="PBE1-2">{{DOI|10.1021/ct800172j}}</ref>. The Stuttgart/Dresden ECPs were also found to significantly outperform the Los Alamos ECPs that are implemented with LanL2DZ. After each optimisation, the final set of forces and displacements printed in the output file were checked to ensure the job had converged. Frequency analysis was carried out on the final geometry to ensure the optimisation had converged to a minimum. All calculations were carried out through Gaussian 09 on the SCAN cluster and a summary of each can be seen in '''Table 6'''.

{|class="wikitable"
|+ Table 6. Summary of optimisation of 2 from .cif coordinates
!
!B3LYP/LanL2DZ
!PBE1/SDD(Pd), 6-31G*(C, H)
!Frequency analysis
|-
| File Name||Pd_4_opt_log_57578||Pd_4_opt_PBE1_SDD_log_57726||Pd_4_opt_PBE1_SDD_freq_log_57754
|-
| File Type||.log||.log||.log
|-
| Calculation Type||FOPT||FOPT||FREQ
|-
| Calculation Method||RB3LYP||RPBE1PBE||RPBE1PBE
|-
| Basis Set||LANL2DZ||Gen||Gen
|-
| Charge||1||1||1
|-
| Spin||Singlet||Singlet||Singlet
|-
| E(RB3LYP) (a.u.)||-1164.730964||-1168.613774||-1168.613774
|-
| RMS Gradient Norm (a.u.)||0.00002185||0.00005655||0.00005654
|-
| Imaginary Freq||||||'''1'''
|-
| Dipole Moment (Debye)||0.4685||0.1821||0.1821
|-
| Point Group||C1||C1||C1
|-
| Job cpu time (days : hours : minutes : seconds)||0 : 6 : 41 : 22.7 ||0 : 11 : 28 : 11.5||0 : 7 : 52 : 57.0
|}
[[File:57754_imaginary_freq_njm08.gif|thumb|Imaginary frequency]]
Unfortunately, the frequency analysis revealed one imaginary frequency corresponding to rotation of the cyclononatetraenyl (CNT) ring. This indicates that the geometry has optimised to a saddle point on the potential energy surface, which corresponds to a transition state connecting two local minima.

The output file was opened in Gausview 5.0 with the ''read intermediate geometries'' checkbox ticked. The plots of energy and RMS gradient against optimisation step show a decrease in energy, followed by an increase in energy. It seems the optimisation "passed through" a minimum but wouldn't converge under the set criteria. Therefore, a new molecule group was created from the structure at step 7, which was the lowest in energy, and the optimisation repeated from this point specified by: <code># opt freq pbe1pbe/gen pseudo=read int=ultrafine. The additional <code>int=ultrafine</code> keyword requests a larger grid for numerical integration, although it also increases the job time. Unfortunately, this calculation converged in eight steps to a structure that also had an imaginary frequency.

====From an "ideal" model====

To try and find the elusive minimum, another starting structure was constructed in Gaussview 5.0. Unlike the first attempt based on crystallographic coordinates, this model was made entirely from scratch using the Gaussview builder tools. It had idealised bond lengths, angles and dihedrals, the values of which were informed by the x-ray structure, and the cyclononatetraenyl ring was orientated as to give the molecule a Cs plane of symmetry. The structure was initially optimised by PBE1/LanL2DZ (<code># opt pbe1pbe/lanl2dz</code>) and then subsequently by PBE1/SDD(Pd), 6-31G*(C, H) (<code># opt pbe1pbe/gen pseudo=read int=ultrafine</code>). Unfortunately, the frequency analysis carried out on the final optimised structure had a single imaginary frequency, again corresponding to rotation of the CNT ring.

If the structure has converged to a transition state, then one would expect displacement along the imaginary frequency to lower the energy. To test this, a series of new input files were saved from various manual displacements along the imaginary frequency (0.2, 0.4, 0.6, 0.8, 1.0). Single point energy calculations (<code># pbe1pbe/gen pseudo=read int=ultrafine</code>) were performed on each structure. Each of the energies were higher than the original suggesting that the imaginary frequency may be product of noise. However, the displacements may have been too large and it doesn't take into account the other degrees of freedom so the results are inconclusive. An IRC calculation was also attempted, but this failed to converge.

In hindsight, it may have been worth performing the initial optimisation with the <code>nosymm</code> keyword.

====From previously optimised coordinates====

It was decided to check whether the problem of not being able to converge to a minimum was to do with the method. The theoretical study on whether compounds such as '''2''' could be used to isolate planar tetra-coordinate carbon had successfully optimised '''2''' to a minimum with no imaginary frequencies. Their calculations were performed using the B3LYP functional with 6-311+G(3df,p) on carbon and hydrogen and SDD with extra 2f and 1g functions on palladium. The Cartesian coordinates as provided in the supplementary information were optimised using PBE1/SDD(Pd), 6-31G*(C, H) (<code># opt freq pbe1pbe/gen int=ultrafine pseudo=read pop=(full,nbo)</code>). A summary of this calculation can be seen in '''table 11'''.

The optimisation converged to a minimum with no imaginary frequencies. This shows that optimising to a stationary point with no imaginary frequencies is at least possible with the current method, given a good enough starting point. The difficulty seems to be in converging with several of the failed optimisations "passing through" energy minima. 6-31G(d) and the SDD double zeta basis set should be adequate for most applications in transition metal organometallic chemistry. However, it seems that they are unable to describe the

===Coordination of 2 to L-type ligands===

[[File:Synthesis_of_2_njm08.png|thumb|upright=2|Scheme 1. Synthesis of '''2''']]
An interesting observation is that '''2''' is uncoordinated with respect to acetonitrile acting as a L-type donor ligand. This is on the basis of <sup>1</sup>H-NMR analysis in CDCl<sub>3</sub>, which found no evidence of coordination to acetonitrile or pyridine, even with excess present in solution. This is unlike its synthetic precursor ('''Scheme 1.''') or trinuclear sheet sandwich complexes, such as '''3''', that have so far been reported. However, evidence was found for coordination of '''2''' to phosphine ligands, with mono- and bis- triphenylphosphine adducts observed at equilibrium.

To explore its coordination chemistry, '''2''' will be modeled as a mono-coordinated adduct with acetonitrile, PCl<sub>3</sub> and ethene. PCl<sub>3</sub> will be used instead of PPh<sub>3</sub> for computational efficiency. These three represent different classes of L-type ligand that have all be shown to bind to the trinuclear platinum complex, '''3'''.

====Qualatative assesment with electron counting====

One guide as to whether a metal center has "room" to accommodate extra ligands is the 18 electron rule.
{|
| Pd = 10 e<sup>-</sup>
|-
| CNT = 2 1/4 e<sup>-</sup>
|-
| COT = 2 e<sup>-</sup>
|-
| 2x Pd-Pd bond = 2 e<sup>-</sup>
|-
| +1 charge = - 1/4 e<sup>-</sup>
|-
|
|-
| total = 16 VE
|}
This quick analysis, as outlined above, suggests that each palladium has 16VE. This potentially allows for coordination with a 2e- donor into an unoccupied d-orbital.

====Calculations====

[[File:Adducts_njm08.png|thumb|upright=1.5|Fig. 2. Adducts]]

Models of adducts of '''2''' to acetonitrile ('''2A'''), ethene ('''2E''') and trichlorophosphine ('''2P''') ('''Fig. 2''') were constructed in Gaussview 5.0 from the optimised structure of '''2'''. The geometries were initially optimised, with frequency analysis, at the PBE1/LanL2DZ level, specified by: <code># opt freq pbe1pbe/lanl2dz</code>. The outputs were then further optimised to the PBE1/SDD(Pd), 6-31G*(C, H, N/P/Cl) level specified by: <code># opt pbe1pbe/gen pseudo=read</code>. Subsequent frequency analysis was run on the final optimised geometries. Optimisations were carried out on acetonitrile, ethene and PCl<sub>3</sub>, along with frequency analysis, at the pbe1pbe/6-31G* level. A summary of these calculations can be seen in '''table 8''' and '''table 9'''.

In order to calculate the equilibrium constant, 2, 2A, 2E, 2P, acetonitrile, ethene and PCl3 were optimised from the outputs of the gas phase optimizations with PCM solvent model (<code>SCRF=(Solvent=Chloroform</code>) and frequency analysis (<code> opt freq </code>). These calculations were also performed using the M06L pure DFT meta-GGA functional.

To estimate effect of coordination upon ring currents, nuclear independent chemical shift was calculated at the centre of the CNT, Pd4 and COT rings. This was done by placing a ghost atom (Bq) in the centre of rings using the ''place fragment at centroid of selected atoms'' tool in Gaussview and NMR calculation performed with the GIAO method. Signs reversed according to ppm convention.

{| class="wikitable"
|+ Table 8. Summary of PBE1/SDD(Pd), 6-31G*(C, H, N/P/Cl) optimisations of 2A, 2E and 2P
!
! 2A
! 2E
! 2P
|-
| File Name||p4_opt_1acetonitrile_SDD_log_58431||p4_opt_1ethene_SDD_log_58473||p4_opt_1PCl3_SDD_log_58432
|-
| File Type||.log||.log||.log
|-
| Calculation Type||FOPT||FOPT||FOPT
|-
| Calculation Method||RPBE1PBE||RPBE1PBE||RPBE1PBE
|-
| Basis Set||Gen||Gen||Gen
|-
| Charge||1||1||1
|-
| Spin||Singlet||Singlet||Singlet
|-
| E(RB3LYP) (a.u.)||-1301.229478||-1247.115718||-2889.992278
|-
| RMS Gradient Norm (a.u.)||0.00001596||0.00001105||0.00000973
|-
| Imaginary Freq||||||
|-
| Dipole Moment (Debye)||6.5467||1.2824||3.9535
|-
| Point Group||C1||C1||C1
|-
| Job cpu time (days : hours : minutes : seconds)||0 : 12 : 35 : 56.4 ||1 : 1 : 38 : 31.9 ||1 : 5 : 0 : 4.3
|}

{| class="wikitable"
|+ Table 9. Summary of PBE1/6-31G* optimisations of acetonitrile, ethene and PCl<sub>3</sub>
!
!Acetonitrile
!Ethene
!PCl3
|-
| File Name||acetonitrile_opt_log_58474||ethene_opt_log_58476||PCl3_opt_log_58477
|-
| File Type||.log||.log||.log
|-
| Calculation Type||FOPT||FOPT||FOPT
|-
| Calculation Method||RPBE1PBE||RPBE1PBE||RPBE1PBE
|-
| Basis Set||6-31G(d)||6-31G(d)||6-31G(d)
|-
| Charge||0||0||0
|-
| Spin||Singlet||Singlet||Singlet
|-
| E(RB3LYP) (a.u.)||-132.5907247||-78.47954389||-1721.361269
|-
| RMS Gradient Norm (a.u.)||0.0000393||0.00006914||0.00028755
|-
| Imaginary Freq||||||
|-
| Dipole Moment (Debye)||3.8576||0||0.8464
|-
| Point Group||C3V||C2H||C3V
|-
| Job cpu time (days : hours : minutes : seconds)||0 : 0 : 0 : 25.5 ||0 : 0 : 0 : 23.0 ||0 : 0 : 0 : 36.2
|}
All optimisations described above, including PBE1/LanL2DZ, converged to minima without any imaginary frequencies.

{| class="wikitable"
|+ Optimised geometries of 2A, 2E and 2P
!2A
!2E
!2P
|-
|
<jmol>
<jmolApplet>
<name>acetonitrile</name><color>white</color><size>300</size>
<script>rotate z -80.89; rotate y 120.84; rotate z -95.89; zoom 110.41;
</script><uploadedFileContents>P4_opt_1acetonitrile_SDD.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<name>ethene</name><color>white</color><size>300</size>
<script> rotate z -105.77; rotate y 55.08; rotate z 87.91; zoom 100.0;
</script><uploadedFileContents>P4_opt_1ethene_SDD.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<name>PCl3</name><color>white</color><size>300</size>
<script>rotate z -107.47; rotate y 51.26; rotate z 89.06; zoom 110.41;
</script><uploadedFileContents>P4_opt_1PCl3_SDD.mol</uploadedFileContents>
</jmolApplet>
</jmol>
|- valign="top"
|
Selected bond lengths (nm):
<jmol>
<jmolRadioGroup>
<item>
<script>measure OFF; measure 1 4;</script>
<text>Pd1-Pd4 = 0.402</text>
</item>
<item>
<script>measure OFF; measure 2 3;</script>
<text>Pd2-Pd3 = 0.378</text>
</item>
<item>
<script>measure OFF; measure 4 39;</script>
<text>Pd4-N39 = 0.226</text>
</item>
<item>
<script>measure OFF; measure 39 40;</script>
<text>N39-C40 = 0.116</text>
</item>
<target>acetonitrile</target>
<vertical>true</vertical>
</jmolRadioGroup>
</jmol>
|
Selected bond lengths (nm):
<jmol>
<jmolRadioGroup>
<item>
<script>measure OFF; measure 1 4;</script>
<text>Pd1-Pd4 = 0.415</text>
</item>
<item>
<script>measure OFF; measure 2 3;</script>
<text>Pd2-Pd3 = 0.368</text>
</item>
<item>
<script>measure OFF; measure 39 40;</script>
<text>C39-C40 = 0.137</text>
</item>
<target>ethene</target>
<vertical>true</vertical>
</jmolRadioGroup>
</jmol>
| align="top" |
Selected bond lengths (nm):
<jmol>
<jmolRadioGroup>
<item>
<script>measure OFF; measure 1 4;</script>
<text>Pd1-Pd4 = 0.411</text>
</item>
<item>
<script>measure OFF; measure 2 3;</script>
<text>Pd2-Pd3 = 0.372</text>
</item>
<target>PCl3</target>
<vertical>true</vertical>
</jmolRadioGroup>
</jmol>
|-
| Distortion factor = 1.06 || Distortion factor = 1.13 || Distortion factor = 1.11
|}

Optimised geometries of '''2''', '''2A''', '''2E''' and '''2P''' can be seen in the Jmol applets above. Coordination appears to cause a distortion in the tetra-palladium ring from a square to a rhombus. The Pd-Pd distance in line with the coordinating ligand increases and the Pd-Pd distance perpendicular to the coordinating ligand decreases. This is in comparison with uncoordinated '''2''', where the Pd-Pd distances across the ring are 0.389nm and 0.386nm. This has been quantified by a "distortion factor", which is the Pd1-Pd4 bond distance divided by the Pd2-Pd3 bond distance and can be thought of as the ratio between the distances across the palladium ring. Uncoordinated '''2''' has a distortion factor of 1.01. Interestingly, ethene and trichlorophosphine have much larger distortion factors than acetonitrile, with ethene having the largest.

====Binding energies====

An estimation of the binding energy for each of the three ligands was made by comparing the energy of the adducts to the sum of the energy of '''2''' and the coordinating species ('''Table 10.''').
{| class="wikitable"
|+ Table 10. PBE1 binding energies of acetonitrile, ethene and PCl<sub>3</sub>
! rowspan="2" |
! rowspan="2" | energy of adduct (a.u.)
! rowspan="2" | sum of energy of fragments (a.u.)
! colspan="2" | difference
|-
! a.u.
! kJ/mol
|-
| acetonitrile||-1301.229478||-1301.204672||0.02480599||65
|-
| ethene||-1247.115718||-1247.093491||0.02222682||58
|-
| PCl3||-2889.992278||-2889.975216||0.01706187||45
|}

The calculations above suggest that the electronic stabilization upon coordination to acetonitrile is around 20kJ/mol greater than for PCl'''3'''. Clearly this does not tell the whole story since experimentally, coordination to PPh<sub>3</sub> was found to be favorable whereas coordination to acetonitrile was not observed. However, it does show that electronically, there is a stabilization associated with coordination to each of the L-type ligands.

To find of whether coordination is favourable requires calculation of the equilibrium constant. This is related to the change in Gibbs free energy, which is in turn related to the change in enthalpy and entropy. The entropic penalty upon binding may play a significant role. Thermochemical corrections can be obtained through frequency calculations.

The optimisations and frequency analyses were repeated with chloroform solvent model

It has been found that one of the shortfalls of DFT is its ability to correctly predict the energy of metal-phosphine bonds. Popular DFT and hybrid-DFT functionals widely used with organic molecules, are seen to significantly underestimate the M-P bond strength.
Given this, PBE1 may be underestimating the Pd-P bond strength in '''2'''. To test this, single point energy calculation were performed on the optimised structures of '''2''', '''2A''', '''2P''', acetonitrile and PCl<sub>3</sub> with the M06L functional. M06L is a fairly recent meta-GGA pure DFT functional, developed by . It has been shown predict metal-phosphine bond energies in line with experiment, where popular DFT and hybrid DFT methods have fallen short, and will provide a useful test as to the reliability of the PBE1 energies is '''table 10'''.

{| class="wikitable"
|+ Table 10. M06L binding energies of acetonitrile, ethene and PCl<sub>3</sub>
! rowspan="2" |
! rowspan="2" | energy of adduct (a.u.)
! rowspan="2" | sum of energy of fragments (a.u.)
! colspan="2" | difference
|-
! a.u.
! kJ/mol
|-
| acetonitrile||-1302.523137||-1302.507578||0.01555946||41
|-
| PCl3||-2891.709088||-2891.692805||0.01628295||43
|}

Interestingly, M06L functional predicts that the binding energy acetonitrile is <u>less</u> than that of PCl<sub>3</sub>.

====Effect of coordination upon NICS====

{| class="wikitable"
|+ Table 11. NICS
!
! 2A
! 2E
! 2P
! 2
|-
| COT|| -4.912|| -4.3476|| -4.2429|| -4.1943
|-
| CNT|| -10.1471|| -9.8919|| -9.6969|| -9.5392
|-
| Pd4|| -32.3052|| -31.3771|| -31.3401|| -29.9051
|}

===''cis''/''trans'' sterochemistry of the ''bis''-PPh<sub>3</sub> adduct===

The ''cis''/''trans'' sterochemistry of the ''bis''-PPh<sub>3</sub> adduct was not established by experiment.

====Optimisation====

===Conclusions===

<references/>

[[Category:Njm08]]

Rep:Mod:8039662

2012-10-10T22:22:49Z

Njm08: