Uploaded April 2021 | Updated September 2026, 2 weeks ago
A way of thinking about constructing a qualitative MO diagram for the azide anion.
#chemistry #physicalchemistry #physics #pchem #quantum #orbitals #electrons #symmetry
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When considering the molecular orbitals of a polyatomic system, it is usually easiest when there is a lot of symmetry. To illustrate these ideas, I have picked the azide anion as it only contains atoms of one element and it has a simple linear geometry. This means that there are only two types of environment that a nitrogen is in, and each one has valence s orbitals and p orbitals.
The equivalent terminal nitrogen atoms can be considered together to help simplify this problem by forming a linear combination of their atomic orbitals. This model is is often called the Linear Combination of Atomic Orbitals, or the LCAO, method. The combinations are called either symmetry orbitals, or ligand group orbitals (LGO), or symmetry-adapted linear combinations (SALCs), often just based on the context or preferences of the author or scientist. These symmetry orbitals (SALCs/LGOs) can then be used as a group to combine with the central nitrogen, and this minimises the number of possible total overlaps that need to be considered by the theoretical chemist. This is a very common technique in chemistry, and is particularly effective when considering transition metal complexes and so-called "hypervalent" structures.
Formally, symmetry orbitals (SALCs/LGOs) are the results of Group Theory, a mathematical way of formalising symmetry. A molecule is assigned to a point group, and a representation of the property being studied is determined. This representation is then "reduced" to its individual irreducible representations (irrep) of the point group which highlight the simplest way to work through a consideration of e.g. orbital overlaps or vibrational normal modes. This is very similar to the ideas of using eigenvectors in maths for simplifying algebraic problems including those involving matrix manipulation but also differential equations. The reducing of the representation can be done using a "projection operator" as an algorithm, but can frequently be done by inspection of character tables for the point group.
An alternative way of formulating this molecular orbital problem that is useful from an educational point of view is to consider all of the nitrogens as bring sp hybridised as ro quickly represent the linear structure predicted by VSEPR. This way of modelling gives the same conclusions but is hard to extrapolate to bigger molecular systems. This modelling separates this molecular orbital consideration into a different kind of simplification with a sigma system being considered first, and a pi system being layered on top. This pi system can be alternatively be considered as a particle-in-a-box model (or sometimes referred to as a "sine wave model") in one dimension. This modelling can be useful for quickly predicting the electronic properties of some simple chemical systems, but unfortunately is not based on physical evidence from, for example, photoelectron spectroscopy. It can be a useful model for educational purposes for new chemists however, and has a lot of merit in engaging students with these aspects of chemistry.
A way of thinking about constructing a qualitative MO diagram for the azide anion.
#chemistry #physicalchemistry #physics #pchem #quantum #orbitals #electrons #symmetry
----------
When considering the molecular orbitals of a polyatomic system, it is usually easiest when there is a lot of symmetry. To illustrate these ideas, I have picked the azide anion as it only contains atoms of one element and it has a simple linear geometry. This means that there are only two types of environment that a nitrogen is in, and each one has valence s orbitals and p orbitals.
The equivalent terminal nitrogen atoms can be considered together to help simplify this problem by forming a linear combination of their atomic orbitals. This model is is often called the Linear Combination of Atomic Orbitals, or the LCAO, method. The combinations are called either symmetry orbitals, or ligand group orbitals (LGO), or symmetry-adapted linear combinations (SALCs), often just based on the context or preferences of the author or scientist. These symmetry orbitals (SALCs/LGOs) can then be used as a group to combine with the central nitrogen, and this minimises the number of possible total overlaps that need to be considered by the theoretical chemist. This is a very common technique in chemistry, and is particularly effective when considering transition metal complexes and so-called "hypervalent" structures.
Formally, symmetry orbitals (SALCs/LGOs) are the results of Group Theory, a mathematical way of formalising symmetry. A molecule is assigned to a point group, and a representation of the property being studied is determined. This representation is then "reduced" to its individual irreducible representations (irrep) of the point group which highlight the simplest way to work through a consideration of e.g. orbital overlaps or vibrational normal modes. This is very similar to the ideas of using eigenvectors in maths for simplifying algebraic problems including those involving matrix manipulation but also differential equations. The reducing of the representation can be done using a "projection operator" as an algorithm, but can frequently be done by inspection of character tables for the point group.
An alternative way of formulating this molecular orbital problem that is useful from an educational point of view is to consider all of the nitrogens as bring sp hybridised as ro quickly represent the linear structure predicted by VSEPR. This way of modelling gives the same conclusions but is hard to extrapolate to bigger molecular systems. This modelling separates this molecular orbital consideration into a different kind of simplification with a sigma system being considered first, and a pi system being layered on top. This pi system can be alternatively be considered as a particle-in-a-box model (or sometimes referred to as a "sine wave model") in one dimension. This modelling can be useful for quickly predicting the electronic properties of some simple chemical systems, but unfortunately is not based on physical evidence from, for example, photoelectron spectroscopy. It can be a useful model for educational purposes for new chemists however, and has a lot of merit in engaging students with these aspects of chemistry.






![Sumatriptan Synthesis Explained - Organic Chemistry (Indoles, Diazotation)
A quick run-through of key ideas when planning on making indole ring systems in organic chemistry, showcased in the synethesis of sumatriptan.
I go over the mechanisms of the Fischer indole synthesis and a diazotation reaction.
#organicchemistry #chemistry #synthesis
Sumatriptan was released by Glaxo in the 1990s as a pharmaceutical agent for the treatment for migraines, after the standard medicinal chemistry exploration. The large-scale industrial synthesis involves a Fischer indole disconnection as its key step of making the bicyclic aromatic rings system. The mechanism involves a [3,3] sigmatropic rearrangement (a pericyclic reaction) in which a weak nitrogen-nitrogen bond is broken at the expense of big thermodynamic benefits of the generation of aromaticity. The indole system can be seen to be aromatic by counting electrons and showing that it conforms to Huckels rule.
The formation of the the N-N bond is done by a diazotation reaction, and goes through an intermediate diazonium ion. This is a common reaction for forming new bonds directly between two nitrogen atoms and uses nitrous acid (HONO) reacted with an (aryl) amine. These diazonium ions can also be used as intermediates with a really good leaving group - being nitrogen gas - in other types of substitution reactions. The diazonium ion also is prone to oxidative addition type reaction mechanisms on interaction with appropriate metals.
The starting materials for the industrial synthesis come from classic nitration conditions using nitric acid and sulfuric acid. The para selectivity of nitration can be explained mainly from the stabilisation of an intermediate carbocation.
The other aldehyde starting material is easier to handle on a large scale when masked as the dimethyl acetal - this, for example, make it less sensitive to hydrate formation with water and therefore also unintended oxidation under atmospheric conditions. The dimethyl acetal collapses under the Fischer indole reaction conditions, being aqueous acid, by the usual SN1 type process.
There are other alternative retrosynthesis ideas that can be used for this molecule, but most will involve using the central indole core as the focus. There are many alternative indole formation mechanisms and processes, that each might have their merit on occasion. The Fischer indole is probably the most archetypal disconnection, and it is certainly one of the most traditional and well-precedented. When using other carbonyl compounds in this type of mechanism, care must be taken for the regioselectivity for the enamine formation - under most circumstances this is under thermodynamic control. Disconnections therefore need to be taken carefully if the indole ring has more substitution, particularly if there are groups at the 2 and 3 positions (these are on the pyrrole type ring component of the indole). Sumatriptan Synthesis Explained - Organic Chemistry (Indoles, Diazotation)](https://i.ytimg.com/vi/v2lSd253nwU/mqdefault.jpg)



