Web Pages for Teaching and Learning Chemistry

by Dr. Bruce W. Tattershall, Chemistry, Newcastle University, England

This is a list of web pages designed for undergraduate students of Inorganic or Structural Chemistry

• They provide interactive computer models of orbitals, molecules, or reaction paths

Note about Popups

• Most of the pages in this list show calculated models in popup browser windows or tabs, so that the user can compare two models
• Most browsers block popups, so when you click on a chart or button to select a model, you will see a warning box rather than the desired model
• There is no need to reduce the security of your browser, because a green Continue button will also appear on the web page, near to the chart or button which you clicked
• If you are working in a small window, you may need to scroll a bit to find this green button
• Click the green Continue button.   This should satisfy the browser that you are not malware, and the popup should open, showing the desired model

Molecular Orbitals

• All of these pages work in the same way, using the same or similar web application software
• Each has a schematic molecular orbital energy level correlation diagram, and when the student clicks on a MO, a new window pops up to show a JSmol/Jmol model of a surface of the selected orbital
• The models come up as a ball and stick model of the geometry, with a surface at ψ = ±0.04 for the selected orbital, coloured blue and red to show relative signs of the wavefunction
• A radio button is provided to switch on a contour plot in the plane of the screen in the initial view.   For each orbital the direction of view is selected so that some useful contour plot is visible if the contours are switched on
• What is different between these pages are the notes provided, which point up the principles illustrated by the particular species

• From a Natural Bond Orbital analysis of the calculated MOs, tables of LCAO coefficients of natural atomic orbitals in the MOs, and of contributions of their overlaps to bonding, are provided and discussed
• Orthogonality of the σ and π systems with each other, and between the π orbitals, is introduced
• sp mixing in the σ system of peroxide is compared with the N₂ case, where it is much more important and, in contrast to peroxide, it results in crossover in energy of the σN(2p)N(2p) and the bonding π levels
• For peroxide it is pointed out that although the σO(2s)O(2s) MO contains only 5.6% p character, 2s — 2p_z overlaps in it still provide 30.3% of the total bonding
• The unusual situation that the HOMOs are antibonding, and that their negative contribution to bonding exactly cancels the positive contribution of the π-bonding orbitals, is dealt with

• The ab initio calculations were done at the same level as for peroxide ion or for CO (see below), so the tables of LCAO coefficients etc. may be compared directly, between these web pages for diatomic species
• A button is provided to switch on an additional explanation of sp mixing in terms of stepwise LCAO to make σ_g(s) and σ_u(s), etc., followed by mixing of σ_g(s) with σ_g(p) to produce the calculated overall coefficients.   This follows the approach in some introductory textbooks
• The competing requirements of different natural atomic orbitals, in determining the equilibrium bond length, is discussed.   The dominant π bonding in N₂ needs a shorter bond length, so it is too short for optimum N(2_pz) - N(2_pz) overlap

Polarisation of molecular orbitals is the chief new topic for this heteronuclear molecule

• The percentage compositions of most MOs, in terms of the contributions of natural atomic orbitals, are shown against the correlation lines of the energy level diagram
• All of the valence shell NAO contributions to the σ MOs are shown in the Table of Coefficients, so the student can assess the effect of polarisation, particularly in comparison with the isoelectronic N₂
• Although the MO names are retained from the N₂ case for the sake of comparison, the HOMO σC(2p)O(2p), illustrated here, has 56% s character, and is 90% composed of carbon NAOs
• The LUMO π^* orbitals are seen to be polarised towards carbon, with 71% C_2p character, and the concept of synergic bonding as a π-acceptor ligand to a transition metal is mentioned
• A switch is provided to select either a high level of calculation for comparison with N₂, or a lower level of calculation for comparison with CO₂ (see below).   Both the JSmol/Jmol models available, and the tables and notes, change appropriately on clicking this switch, but the student may see relatively little difference in either

• Both σ and π MOs are each delocalised over all three atoms
• s and p orbitals on the central atom do not mix with each other, because they require different combinations of signs of coefficients of the ligand orbitals.   Correlation lines and orbital symbols on the energy level correlation diagram are colour coded accordingly
• There are delocalised π MOs which are neither bonding nor antibonding, but are non-bonding by symmetry
• The LUMO π^* orbitals are strongly polarised towards carbon, corresponding to the Lewis acidity which is an essential property of CO₂

• These may be turned off using a provided switch, if a suitable group theory course has not yet been taken
• As in the CO₂ case, the 2s orbital on the central atom does not mix with any of its 2p orbitals, because they have different symmetries relative to the molecular symmetry
• There are five delocalised MOs which are fluorine 2p combinations that are non-bonding by symmetry
• The LUMO π^* orbital is even more strongly polarised towards boron than the antibonding LUMOs are towards carbon in CO₂, and BF₃ is a strong Lewis acid

Learning about LCAO MO theory is usually done in the context of small molecules, e.g. N₂, CO or CO₂.   People doing wavemechanical calculations on larger molecules most often seek molecular geometries or energies of reaction or of activation, or perhaps other observables such as NMR shieldings.   They are comparatively unlikely to look at details of the delocalised molecular orbitals involved in these calculations

So what is the biggest molecule in which it is worthwhile to learn in depth about the makeup of its MOs, as an aid to understanding MO theory?

• I should say it is B₂H₆, with 14 valence shell atomic orbitals and hence 14 valence shell MOs
• This is because it is a beautiful example of the application of group theory to the understanding of orbitals:   many of the nodal surfaces of the MOs are planes of asymmetry in their group theory representation
• To make most use of this web page, a student should have a working ability to set up a representation of a set of atomic orbitals in the molecule, given the character table for the point group, and to reduce this representation, at least using a publicly-available web page to do the reduction arithmetic
• The discussion provided does use symmetry representation labelling, on the assumption that this will be familiar to the student

Interesting Molecules

The point of providing JSmol/Jmol rotatable models of molecular structure for teaching and learning inorganic or organic chemistry is usually so that the student may explore molecular shape, conformation, chirality, or symmetry.   Physical ball and stick models, which the student may hold and manipulate, are possibly best, but ready-made computer graphics models have the advantage of speed and ease

Main Groups Inorganic Ring and Cage Molecules

This web page was developed to support a course which taught about synthesis, structure and bonding, symmetry and chirality in non-metal ring and cage chemistry, particularly that of sulfur and of phosphorus, where it is quite a dominant feature

• The course was a vehicle for teaching principles of bonding and electron counting, aromaticity, and exercising the students' ability to spot symmetry elements and hence assign point groups
• It introduced the idea of molecular chirality and its connection with symmetry operations, beyond the introductory organic chemistry idea of chiral centres
• Most of the examples are of academic interest only, though some have a long history

• The web page takes the form of a table with a line for each example
• Most lines contain one or two questions, telling the student what to look for, and providing reinforcement of points made in the lecture course
• Each line has a Model button, which replaces the table page with a page showing the JSmol/Jmol model.   The student uses the back button to return to the table
• All model pages have buttons to control the appearance of the model, and some have extra, customised controls, e.g. to set particular viewpoints helpful to the student in their exploration
• Each model page has an Answers or Comments button which produces a half-width popup page, usually answering the original questions and often giving further guidance about looking at the model.   Where the model might provide a useful example for assigning the point group symmetry, this answer is usually given, so as to provide a self-study tool for the student

Reaction Pathways

This is probably one of the first fluxional molecules that chemistry undergraduates meet, as well as being an historical starting place for conformational analysis

• The default JSmol mode works adequately in a fast browser such as Chrome in a PC or in Safari, but students with a Java-enabled browser may select the Java_Jmol mode to obtain faster animations and response to mouse rotations etc.
• Like the MO web pages above, this Cyclohexane web page has a clickable schematic energy level diagram, but this time showing the end conformations, intermediates, and transition states in the inversion of the cyclohexane ring

• Clicking on any of these structures produces a JSmol/Jmol rotatable model in a popup window
• Up to two such windows are allowed, so that two different structures may be compared
• The models come up as stick models and in profile so that e.g. the chair shape of the end conformations may be seen
• The student may turn them around or select the more exciting representations Ball and Stick or Spacefill
• Axial and equatorial hydrogen atoms are colour-coded so that the student may follow them during the animation
• When all is ready, radio buttons allow the animation to be switched on or off, and further buttons allow a quick move to the beginning or end of the reaction pathway, or to nudge backwards or forwards
• A frame counter allows the student to keep track of where the animation has got to, and this shows also the name of each of the clickable structures if and as they are passed
• Quite a lot of notes are given on the calling web page, suggesting experiments for the student to do and explaining how to find the symmetry elements


• Besides the simple reaction path via a Twist-Boat intermediate, given in most introductory textbooks, this web page shows also a 'Route B', going from one Twist-Boat intermediate to its enantiomer, via an untwisted boat transition state


• The clickable models came from ab initio optimisations, and many of the intermediate frames from ab initio IRC calculations.   A few were interpolated by hand