Help and explanations of these lecture notes

3D [JSmol(def)♦Jmol(Java)]: Show♦Hide. . 2D: Show♦Hide. Print♦Help

Help and explanations of these lecture notes.

These notes are what is called streamed; this means you have to be online to use them (streamed means repeated viewings require repeated downloads) There are alternative presentations, which include
1. Panopto materials (audio + non-interactive visual capture of these notes). This is also streamed using the Panopto app (on tablets)
2. Audio + non-interactive visual capture of these notes, in a non-streamed download-n-go format using the iTunesU app (on tablets). Once on the tablet, the notes can be used with no online access.
3. A non-interactive eBook presentation, again a non-streamed download-n-go format using a variety of epub-compatible tablet apps (for example on an iPad, iBooks, Kindle, Nook, Kobo etc). Some of these apps will display the animated diagrams (but some do not). The challenge of creating a fully interactive download-n-go version using e.g. the epub3 standard will be fulfilled at some stage in the future.
Layout. The navigation toolbar along the top allows access to the notes for any individual lecture, along with problem examples. The notes are presented in continuous galley-form, to allow facile scrolling if e.g. using a tablet. Below that is a Google search box, where only the contents of the lectures have been indexed. The third row allows control of the interactive aspects of the notes (see below).
Why interactive? Pericyclic processes show a wide diversity of factors which control their outcome. The symmetry characteristics of the wavefunctions, and the aromaticity that may or may not ensue, have been dealt with in the main section of this lecture course. But electronic symmetry does not always allow a single reaction path to be predicted; often two or more "allowed" pericyclic processes can be identified, and to further distinguish them, other factors such as steric effects, hydrogen bonding, etc must be taken into account. It is important to evaluate each effect quantitatively, since sometimes they might act in the same direction, sometimes in the opposite, and it is only by adding all the effects together that the final outcome can be predicted. The technique that allows this to be done is called molecular modelling, and in this particular context, since electrons are involved, it is often referred to as quantum molecular modelling. In the examples scattered throughout this lecture course, modelling was done at the DFT ωB97XD/6-311G(d,p) level, using the Gaussian 09 program. This technique is illustrated in the third year Computational modelling laboratory course. The models built using these techniques are incorporated into these lecture notes.
- Sometimes more information regarding the visual model shown here may be needed. To facilitate this, most of the models are linked to a digital repository entry for the calculation that generated them. There you can retrieve the original input for the calculation, along with a selection of output files. These can be used to re-generate the model, either exactly as previously computed or with variations of your own choosing.
Jmol vs JSmol.The course notes contain interactive elements rendered using the Jmol/JSmol environment, which allows these components to be viewed on a wide range of devices, including most Tablets.
1. JSmol. This is the default environment for a window that appears when show is toggled. It uses Javascript to produce 3D models of molecules and their properties. This should display in most browsers and devices.
2. Jmol. This can be toggled on if your device supports Java. Whilst most desktop computers can support Java, it may not necessarily be installed. The advantage of using this option is that the rendering of the 3D models is much faster (from 5-fold to up to 20-fold) than Javascript. Jmol is not available for the iPad.
3. Show/Hide. This produces a fixed window in the bottom right of the screen. It stays in place even if the page itself is scrolled. By default it is hidden, and if you do want to see any models, you should first show it.
4. Spin. This rotates the model about the Y-axis.
5. Vibrate. If the model is a transition state, the imaginary normal mode will be displayed as green vectors and the model will animate.
6. Anti-alias. This will sharpen up the bonds and atoms in the model, at the expense of slower rotation of that model.
7. Saving model data. From the interactive window, right-click and scroll down to the file option. Select save a copy of XXX (where XXX is the name of the file loaded, normally a calculation log file) and you will have an opportunity to save the file to your file system (desktop computers only).
Images. To allow most images to scale without loss of resolution on devices such as tablet computers, a scaleable vector format has been adopted here called SVG (a format written directly by ChemDoodle, and indirectly via EPS by ChemDraw). Whilst most browsers nowadays support this format, there is one exception; Microsoft's Internet Explorer browser series. If you want to see these diagrams, do not use this browser. Some animations (which are too slow to compose using e.g. Jmol) are pre-rendered into a GIF animation.
2D Printing. The notes are designed to be interactive. This means displaying some elements only on demand, and including both animations and rotatable models. The notes have been optimised for these tasks. However, the print functionality of the browser is available for anyone who wishes a printed copy. The print copy will probably not faithfully reproduce the interactive elements, but the text and images should be captured. Different browsers may respond differently in the way they try to handle these components, and you have to test the browser to see if it achieves the result you desire. The safest option is to use the link provided to print, since this automatically hides the toolbar and the interactivity window before printing.
3D Printing. Sometimes a tactile inspection of a 3D model can carry additional insight. 3D printing also allows one to go beyond the traditional ball&stick model to representation of more complex surfaces, such as molecular orbitals and such models can be accurately quantitative, representing e.g. transition states and other computable objects. A small library of such objects is held here and will be added to over time.
Tablet devices. These notes have been tested on the following types of tablet:
1. Apple iPad (IOS 7).
2. Hudl (Android 4.2)
3. Samsung (Android 4.2)
If you have a tablet not listed here please let me know, both if it works and especially if it does not (although a fix may not necessarily be possible). A pilot project for the evaluation of the use of tablets for lecture notes is documented here. All Imperial College students have read/write access to this project page, and constructive comments there are warmly welcomed.
Tablet annotation and note taking.. One of the advantages of these devices is that one can annotate/take notes. There are many ways of doing this, but these two are relevant to chemistry:
1. Annotation using Diigo. This allows sticky notes to be attached to any Web-page (including this one) or selections of text to be highlighted. You will have access to the notes every time you re-open the page. The notes are stored in a specified account, which can be either Diigo themselves, or Google/Facebook etc.
  - On a desktop browser, you will need to install the Diigo extension into the browser (e.g. Firefox, Chrome). In the Imperial environment, this will need to be done only once (on conventional desktop computers or laptops).
  - On a tablet, you can use a native Diigo browser to browse Web pages and append notes.
2. Annotation by sketching chemical diagrams. A typical use is JSME (for which separate help is available). Watch this space.
3. Voice and text-based notes. For example, Siri-to-chemical structure conversion.
Help with the chemistry. Please consult your tutor in the first instance, or ask after the lecture.

The HTML/CSS/JS source code for these notes has been Tidied/Beautified using this site. See also here. If you are interested in how the effects in these notes were achieved, please contact me.