Congeneric behaviour – linear or predictable structure and reactivity traits, an extension of the well known idea of periodicity – is explored amongst the products of the hydrogen probe experiments, as discussed on the previous page. Sets of chemical species with similar structure and/or behaviour are identified.

 

Congeneric Behaviour Amongst Simple Species

The main group elemental hydrides and the products of the hydrogen probe experiments can be explored for congeneric dots, series and planars, for types of reactivity behaviour and for regions linear reactivity:

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Onium Ions, Hydrides, Conjugate Bases, Enium Ions, Radicals and their Congeneric Series

The hydrogen probe experiments generate several, general types of reactive species and associated reaction behaviour: onium Ions, anionic conjugate bases, enium Ions, radicals, metals and metal cations. A word about onium ions and enium ions:

Onium Ions are hypervalent cations: the ammonium ion, [NH4]+, and protonated water, [OH3]+, also called the oxonium ion. All the onium ions produced by the hydrogen probe experiments are, themselves, proton donating Brønsted acids. As cations, onium ions require anionic counter ions and the products are invariably ionic salts.

As part of the unfolding chemogenesis story, ionic salts – like ammonium chloride – are considered to be one of several types of Lewis acid/base complex. It follows from that onium ions are Lewis acids. Indeed, all positively charged species are Lewis acids.

Enium Ions are hypovalent cations. They are obtained by removing a negative ligand from a neutral species. Enium ion species are classic Lewis acids; like the isostructural Lewis acid borane, BH3, enium ions "only have six electrons in their valence shell", to use the arguments of Lewis octet theory.

The name "enium" comes from the George Olah who identified two types of "carbocation":

  • [CH5]+ is the carbonium ion

  • [CH3]+ is the carbenium ion

We follow the Olah system. All hypervalent cations are called onium ions and hypovalent cations are called enium ions. Cl+ is the chlorenium ion. [But, we do not go so far as to rename the proton, H+, the hydrenium ion.]

Collections of congeneric series from the periodic table groups show how onium ion, anionic conjugate base, enium ion and radical characteristics have common features. These collections of congeneric species show the rich patterns of behaviour that can be found within reaction chemistry space.

 

The Congeneric Array Database

Search for congeneric arrays using the database page, here. For example:

The Hydrogen Series, including Deuterium & Tritium, here:

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The Group 14 Series, here:

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Linear Alkene Series, Methane (for comparison), Ethene, Propene & Butadiene, here:

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Cyclic π-System Series: Cyclopentadiene, Benzene & the Benzyl System, here:

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Grouping Congeneric Series by Geometry

Valence shell electron pair repulsion (VSEPR) theory recognises that the spatial arrangement of bonds around an atomic centre is correlated with the number of ligands and electron lone pairs, and that these are to be found at or near the vertices of regular polyhedra.

Ligand-electron pair configurations can be represented with the AXE system. Several geometries are commonly found:

  • AX5 trigonal bipyramidal
  • AX4 tetrahedral
  • AX3 trigonal planar
  • AX3E trigonal pyramidal
  • AX2E2 angular
  • AXE3 (only one ligand)

Examples of these sets are shown below:

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Search for congeneric arrays, here.

 

Quantifying Congeneric Behaviour

Arrays can be checked for linear structure and linear behaviour traits using:

Atomic radius, well known data
Ionic radius, well known data
Ionisation energy, well known data
Bond length, calculated at the HF 3-21G* level or better
Electronegativity, Revised Pauling, well known data
% Ionic-covalent character, calculated using the Pauling eqn.
pKa, well known data

We shall be looking for linear data, across series and over planars:

 Note: 'curve' is considered to be linear, or more strictly  linearizable , when it can be transformed into a straight line by the application of a simple function: 1/X, log(X), ex, COS(X), etc.

Note: 'curve' is considered to be linear, or more strictly linearizable, when it can be transformed into a straight line by the application of a simple function: 1/X, log(X), ex, COS(X), etc.

We will find that, yes, linear relationships are common within the congeneric array data sets, both when parameters are plotted singly and when pairs of parameters are plotted against each other. The two dimensional plots can be most revealing.

We find that within a particular congeneric series it is quite reasonable to decide that one end is [Pearson] harder and the other is [Pearson] softer. We are able to do this is because the terms "hardness/softness" are actually being used as a proxy for a physical parameter. Bond length is a good example, we find that:

  • Short "to–hydrogen" bond length equates with a harder conjugate centre
  • Long "to–hydrogen" bond length equates with a softer conjugate centre

 

p-Block Anions and Conjugate Brønsted Acids

Of all the congeneric planars, the p-block anions and their conjugate acids, related as they are by protonation, are the most interesting. We shall study these planars by examining the pKa of the conjugate acids and the "to–hydrogen" bond lengths.

pKa data is linear over the planar. Proton donating power ranges from the strong Brønsted acid hydrogen iodide, to methane, CH4, a species that many would not consider to be a Brønsted acid at all. But the conjugate base to methane is the super base methyl lithium. Alkyl lithium reagents (of which methyl lithium is a member) are extraordinarily powerful proton abstractors.

"To-hydrogen" bond length is linear over the planar. The shortest bond length is seen with HF, and the longest with SnH4.

Observe: the two data sets are orthogonal (at 90°) to each other:

  • Brønsted proton donation-abstraction behaviour runs from top-left-to-bottom-right
  • "To-hydrogen" bond length runs from bottom-right-to-top left

This is one of the keys to unlocking the chemogenesis story.

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The above examples show that, yes, the congeneric series and planars generated from the five hydrogen probe experiments do exhibit linear or distorted linear structure and reaction behaviour traits. And so yes, the series and planars discussed are congeneric.

There is actually one place where the data does show a slight anomaly. Electronegativity data shows that the period 2 elements: Si, P, S, Cl are slightly less electronegative than expected. This is reflected in the corresponding distortion in the elemental hydride bond length data.

 

The Hard Soft [Lewis] Acid Base Principle

In the 1960s, Ralph Pearson introduced his hard soft [Lewis] acid base (HSAB) principle, here. As part of his analysis, Pearson suggested that hard-to-soft trends could be found amongst groups 15, 16 and 17 of the periodic table. The idea was extended by Tse Lok Ho who used realistic chemical species and coined the term congeneric.

 Pearson, R.G., Hard and Soft Acids and Bases,  JACS   85 , 3533-3539 (1963) and Ho, T.-L., The Hard Soft Acids Bases (HSAB) Principle and Organic Chemistry  Chemistry Reviews   75 , 1-20 (1975)

Pearson, R.G., Hard and Soft Acids and Bases, JACS 85, 3533-3539 (1963) and Ho, T.-L., The Hard Soft Acids Bases (HSAB) Principle and Organic Chemistry Chemistry Reviews 75, 1-20 (1975)

Neither Pearson or Ho used quantitative data to back up their ideas, and with good reason!

As is discussed elsewhere in this web book, Pearson classified some 90 species as hard, borderline & soft Lewis acids and bases, here. But, no physical parameter correlates with behaviour over Pearson's sets. And this is the problem with the Pearson hard soft [Lewis] acid base (HSAB) classification system: the set of species is simply too large and diverse.

However, the chemogenesis approach starts with the isoelectronic series and planars (arrays) derived from the five hydrogen probe experiments and asks whether linear structural and reaction behaviour trends can be found in the isolated arrays.

 

Ligand Replacement Congeneric Series

Congeneric arrays of chemical species can be produced by changing the ligands about an atomic centre in a regular way. There are several approaches: ligands can be exchanged en masse or one-at-a-time. Carbon, with its propensity to form chains, gives rise to numerous homologous series.

Inorganic Congeneric arrays

Congeneric series can occur when a multivalent atomic centre, such as boron or aluminium, has its ligands exchanged in a regular manner. This can occur in two ways:

Firstly, an atomic centre can have a congeneric series of ligands changed en masse:

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The symbiosis logic of C.K. Jørgensen suggests that Lewis acid and Lewis base atomic centres are symbiotically hardened by hard ligands and softened by soft ligands. The chemogenesis analysis fully supports this view, with the proviso that quantitative structure-reactivity behaviour will only be found when the ligands are congeneric:

  • Fluoride ion, F, ligands are harder than bromide ion, Br, ligands and therefore the Lewis acid centre of BF3 is symbiotically harder than the Lewis acid centre of BCl3 < BBr3 < BI3.

  • Certainly, boron trifluoride has a high differential affinity for hard F, to generate the spherically symmetric [BF4] ion.

  • Likewise, BBr3 has a high affinity for the softer Br Lewis base to yield the tetrahedral and spherically symmetric [BBr4] species.

The ligand replacement is also seen amongst transition metals. Copper(I) & copper(II) both form halides, and according to web elements, these copper halides are known:

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Pearson suggested that higher oxidation states are harder than lower oxidation states. As predicted, copper(II) iodide – the hardest cation with the softest anion – is the unknown copper halide.

Secondly, ligands can also be changed one-at-a-time:

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Notice, when the ligands are changed one-at-a-time, the termini (ends) of the series end up being unrelated in a chemical reactivity sense, even though they remain isoelectronic:

  • Methane is a hydrocarbon but not a haloalkane. Carbon tetrachloride is a haloalkane but not a hydrocarbon.
  • The ammonium ion is a Brønsted acid but the tetraalkyl ammonium ion is not.

Hydride Donor Complex Anions

This combinatorial approach has been exploited in the development of specialised and selective hydride donor reagents with anions of:

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The counter ion cations can be: Li+, Na+, K+, Rb+ or Cs+. However, lithium salts are generally preferred because they are more soluble in diethyl ether, the usual solvent of choice for these aggressive and reactive reagents which must be used in an anhydrous environment.

The following is a selection of the hydride donor reagents are available from the Aldrich Chemical Company:

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Organic Ligand Exchange Congeneric Series

Tse-Loc Ho, an organic chemist, argued that hydride ligands, H, are soft compared with alkyl ligands, R, so the carbenium ion, H3C+, is symbiotically softer than a trialkyl (tertiary) carbenium ion, R3C+. Likewise, the methyl carbanion, H3C, is symbiotically softer than a tertiary alkyl carbanion, R3C.

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This argument is born out: Methyl reactive intermediates: H3C, H3C or H3C+, are more polarisable and "forgiving" moieties than the trialkyl equivalents: R3C, R3C or R3C+ which implies that they are softer.

Tertiary alkyl bromides will readily dissociate in polar solvents and undergo first order SN1 nucleophilic substitution, whereas methyl bromide will only undergo concerted, second order SN2 nucleophilic substitution. The alkyl ligands appear to have hardened the carbon centre making the C-Br bond labile with respect to the hydrogen ligated methyl function.

Tertiary butyl lithium, tBuLi, is a stronger base and is less nucleophilic than methyl lithium, MeLi.

However, symbiotic hardening and softening effects are obscured by other factors such as the substantial steric hindrance which occurs about bulky tertiary alkyl carbon centres and the fact that alkyl functions strongly stabilise carbenium ion, R3C+, centres and strongly destabilise carbanion centres, R3C, compared with H3C+ and H3C.

It is simply not possible to disentangle symbiosis from steric hindrance and charge stabilisation. We just note that the H3C > RH2C > R2HC > R3C series – whether cationic, anionic or radical – show regular structural and reactivity trends and so are congeneric.

The author has performed numerous ab initio calculations to try and find some structural parameter such as bond length which quantifies the assertion that methyl anions, radicals and enium ions are softer that the alkylated analogues. However, it does not seem to be possible to disentangle bonding preference from steric and charge stabilisation effects. While the author agrees with the Ho analysis, he argues that it is not possible in principle to provide quantitative proof.

This point is stressed because we will be returning to the methyl, 1°, 2° & 3° carbenium, radical and carbanion congeneric series which are so important to organic chemistry.

There are many examples of ligand exchange congeneric series in organic chemistry, often based on exchanging hydrogen and alkyl ligands around carbon, nitrogen, oxygen, silicon, phosphorus, sulfur, etc. centres. These are all listed in Congeneric Array Database.

Chloroacetic Acids

The chloroacetic acids are congeneric with electronegative chlorine atoms rendering the carboxylic acid function a stronger Brønsted acid. pKa data shows the species to be congeneric.

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Alkanes: Melting Points & Boiling Points

The linear alkanes and cycloalkanes can be considered ligand replacement congeneric series. Boiling point data show these series to be congeneric.

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Notice, that with both the linear and cyclic alkanes, the boiling points (liquid to gas phase change) are linear with respect to carbon number, but melting points (solid to liquid phase change) are not. The reason is due to packing and crystallinity effects which are important in the ordered solid phase, but which not found in the disordered liquid or gas phases.

So, ordered to disordered phase changes likely to exhibit non-linear effects whereas disordered to disordered phase changes are not.

Now, some readers may be surprised that we are using melting point and boiling point examples while discussing chemical reactions.

The reason is that while some authors like to differentiate between physical processes, such as phase change, and chemical reaction processes, there is no real difference. When a water molecule moves from the liquid phase to the gas phase it [the defined water molecule] is transferring from one chemical environment to another, in other words it is undergoing a chemical reaction.

Throughout the Chemogenesis web book and The Chemical Thesaurus reaction chemistry database, we use a very broad definition of what it is that constitutes a chemical reaction. In essence, it comes down to whether the process can be described in the form or a chemical reaction equation with an arrow:

X    +     Y    →    Z              or               Y    →    Z

Using a broad definition of what it is that constitutes a chemical reaction solves many problems, and causes few.

 

Congeneric Array Interaction Algebra

Congeneric interactions follow the usual rules of array algebra:

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For example, the proton x hydride ion (a dot x dot interaction) gives H2, a congeneric dot. Here is no other chemical species at all like H2 [other than its isotopic homologs D2, T2, HD, etc.]:

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Likewise, the Group 1 cations vs. the hydride ion (a series x dot interaction) gives rise to the Group 1 saline hydrides (a series):

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We have already seen these interactions with the hydrogen probe experiments, but the logic can be continued to generate a range of ionic and polar covalent materials.

We shall explore three (series x series) interactions to generate corresponding congeneric planars:

  • Group 1 cations (Li+ to Cs+) vs. the Period 2 anions (H3C to F)
  • Group 1 cations (Li+ to Cs+) vs. the Group 17 anions (F to I)
  • Group 1 cations (Li+ to Cs+) vs. the methyl to tertiary butyl carbanions
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The (5 x 1) x (4 x 4) Congeneric Array Interaction: A Congeneric Volume

The logic of congeneric array interaction can be continued to produce a congeneric volume:

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One such congeneric volume is discovered when the Group 1 cations, Li+ to Cs+, are arranged against the anionic Lewis bases of the type H3C, F and I.

The resulting congeneric volume has regular changing bond polarisation properties over the volume:

  • Over the set of compounds, the least [Brønsted] basic compound is lithium iodide, LiI. (The iodide ion is the weakest proton abstractor because its conjugate Brønsted acid is hydrogen iodide and that is the strongest Brønsted acid.) Proton abstracting ability increases to lithium fluoride, to methyl lithium and to methyl cesium. Thus, Brønsted base strength increases over three connected vertices of the congeneric volume.
  • The Li-Sn bond of LiSnH3 will be the most covalent (21% ionic) and the cesium fluoride bond will be the most ionic (89% ionic). These species are found at opposite corners of the congeneric volume.
  • All the Group 1 (and Group 2) halides have excellent optical properties and can be used as lenses and prisms from the UV to infrared. Of these, cesium iodide is often the optimum material because it is able to pass infrared light of the longest wavelengths, to 70 microns.
  • The density of aqueous solutions can be increased by dissolving salts, particularly the Group 1 halides. The aqueous solutions with the highest specific gravity are prepared by saturating water with cesium iodide.
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The Emergence of Organic Chemistry

A Bit of Personal History...

"In January 2000, I was in my office playing with the congeneric array interactions discussed over the previous few pages. I was using my all time favourite graphics package – Macromedia Freehand – to cut-n-paste, when I built the following array interaction:
[methyl anion to fluoride ion] x [alkyl substituted carbenium ions]
"I started to write how this was yet another congeneric planar with regularly changing properties of bond length (true), % ionic bond character (true) and reaction chemistry behaviour... when I suddenly realised that this was not the case at all. The species were simply NOT congeneric. Instead, some of the most common and distinct functional groups of organic chemistry emerged: alkanes, amines, alkanols and alkyl fluorides. These are chemicals known to every chemistry student, and as a set they are not congeneric.
"I spent several minutes staring at the screen in amazement. I had travelled from the main group elemental hydrides and the five hydrogen probe experiments to congeneric array interactions, where I had found a volume consisting of 80 congeneric species. Extending this array interaction logic, the 'complexity' and richness of organic chemistry had simply appeared!"
Mark Leach
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The products of the carbenium ion/period 2 anion interaction are alkanes, amines, alkanols and alkyl fluorides and the formation of these chemically distinct species marks the place in reaction chemistry space where organic chemistry breaks away from main group chemistry and assumes its own distinct identity.

The reason why this particular planar bifurcates - forks - is twofold:

Firstly, the alkanes are not isoelectronic with respect to the corresponding amines and alkanols because the alkanes do not possess a functional group with a lone pair of electrons.The two relevant series of congeneric Lewis bases run:

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Notice that there is a "frame shift" between the two series, C to F and N: to Ne:. The effect is that while carbanions are congeneric with nitranions (also called amide ions), alkanes are not congeneric with amines. This is an inevitable property of congeneric array interaction logic.

Secondly, we know the chemistry of alkanes, amines, etc., by their common chemistry: aqueous solubility, chemical reactivity, etc. The crucial point is that many reaction pathways that become available over the pH range from: concentrated acid (<0) through water (7) to strong alkali solutions (>14), and this experience dominates our understanding of the materials produced by congeneric array interactions.

  • Alkanes are insoluble in acid, neutral water and alkali. Alkanes are chemically inert with respect to these environments.
     
  • Amines are very soluble in aqueous mineral acids where they form the corresponding ammonium salt. Amines are much less soluble in neutral water or alkaline solutions. Indeed, amines are commonly separated from other organic functions by extracting with aqueous acid, changing the pH to alkaline (basic), and extracting into a non-polar solvent.
     
  • Alkanols (of lower molecular weight) are fully miscible with water which they hydrogen bond.
     
  • Alkyl fluorides are chemically inert, they are not soluble in aqueous acid or alkali.

Very interestingly, if instead of using aqueous Brønsted acids and bases we move to aprotic solvent systems the distinction between the functional groups is much less clear. (Recall that in water, the strongest acid that can exist is [H3O]+ and the strongest base is HO.

Under George Olah "super [Brønsted] acid" conditions, H+/[SbF6] in liquid SO2, alkanes, amines, alkanols and alkyl fluorides are all protonated and dissolve.