Molecules and Chemical Bonds
WikiMechanics portrays molecules as compound atoms that are held together by chemical bonds. The bonds that we consider here are defined from pairs of electrons. We intend to treat these bonds as countable entities, as for example in Lewis dot diagramsXlink.png or VSEPR theoryXlink.png. So we need to follow some rules of logic and mathematics. Specifically, by Pauli's exclusion principle we cannot have two identical electrons in the same set. So we need to distinguish electrons from each other. And, in molecules with more than one bond, we need to distinguish bonds from each other too.
Don't forget about other sensations. Click [http://wikimechanics.org/seeds here] for more ...
Don't forget about other sensations. Click here for more …

Traditionally, we meet this requirement by saying that different bonds and electrons are distinct from each other because they are in different places. But, by the premise of WikiMechanics, we cannot satisfy Pauli's exclusion principle by resorting to a spatial explanation. And also we cannot use any visual sensation to make the distinction either, because the visual sensations used to define dynamic seeds have already been constrained, and obviated, by earlier hypotheses. So instead, we differentiate them by association with different taste sensations. To satisfy Pauli's exclusion principle, electrons $\, \sf{e^{–}}$ are distinguished from each other by their union with various chemical quarks such as acidic-quark.png, ionic-quark.png or dextro-quark.png. We use the letter $\mathbb{B}$ to identify specific bonds in the following discussion. Each bond is characterized by $D_{ \large{\circ}}$ a bond dissociation energy that depends on the enthalpy $H$ and internal energy $U$ as

$\begin{align} D^{ \mathbb{B} }_{ \large{\circ}} \equiv H^{ \mathbb{B} } -N H^{ \sf{e^{–}} } = \sum_{ \sf{q} \in \mathbb{B}} \Delta n^{\sf{q}} U^{\sf{q}} \end{align}$

where $n$ is the coefficient of quark $\sf{q}$, and $N$ is the number of electrons in the bond. Experimental observations1,2,3,4 report $D_{ \large{\circ}}$ for the gaseous state, and are given5 at 0 (K).

Typical Single Bonds

Let us start by associating an acidic quark with one of the electrons in a covalent bonding pair. This simple arrangement is called $\mathbb{B}\small{\sf{(semi \ acidic) }}$. It is the first example of a bond formed predominantly from acidic quarks.

$\large{\mathbb{B}}\small{ \sf{(semi \ acidic) }} \equiv \, \,${ {e, acidic-quark.png}, e }

Single bonds are often indicated using a short line segment. For example, in the chemical structure diagram for $\mathrm{Au}_{\sf{2}} \,$, a diatomic gold molecule, the bond is represented as Au–Au. This is the only ligature defined from just one quark. The archetypal acidic bond involves two acidic quarks like this

$\large{\mathbb{B}}\small{ \sf{( acidic) }} \equiv \, \,${ {e, acidic-quark.png}, e , acidic-quark.png }

This arrangement accurately represents the bond in H–Cl, a strong acid. No more acidic quarks can be added to a pair of electrons without violating Pauli's exclusion principle. So next we consider distinguishing electrons by association with basic quarks

$\large{\mathbb{B}}\small{ \sf{( basic) }} \equiv \, \,${ {e, basic-quark.png}, e , basic-quark.png }

This set of quarks and electrons accurately represents the bond in sodium hydroxide, Na–OH, also known as lye. Similar bonds can be defined using ionic and aqueous quarks for molecules of table salt, and water. These bonds are made from groups of quarks that are all the same quark-type. They are very homogeneous, so quark character may extend to molecular character. And here is a list of some other typical single bonds.

typical.png

Double and Triple Bonds

The single bonds discussed above all involve one pair of electrons. But we may also include more electrons to define double bonds which are made from four electrons. For example, here is a double acidic bond

$\large{\mathbb{B}}\small{ \sf{( double \ acidic) }} \equiv \, \,${ {e, acidic-quark.png}, {e, dextro-anti-quark.png} , {e, levo-quark.png}, {e, acidic-quark.png, levo-anti-quark.png } }

This set correctly describes the bond strength in sulfur dimers, S=S. Here is a double basic bond

$\large{\mathbb{B}}\small{ \sf{( double \ basic) }} \equiv \, \,${ {e, basic-quark.png}, {e, basic-quark.png, dextro-quark.png} , {e, basic-quark.png, dextro-anti-quark.png}, {e, levo-quark.png} }

The strength of the double-bond in carbon dioxide, O=CO, is correctly represented by this arrangement. And here is a double aqueous bond

$\large{\mathbb{B}}\small{ \sf{( double \ aqueous) }} \equiv \, \,${ {e, aqueous-quark.png}, {e, aqueous-quark.png, levo-quark.png} , {e, dextro-anti-quark.png}, e }

This bond accurately represents the link between oxygen atoms in the important diatomic gas molecule $\mathrm{O}_{\sf{2}} \,$. Stereochemical quarks have about 1% of the internal-energy of other chemical quarks, but nonetheless, they still play an important logical role by distinguishing between similar bonds. For example consider this double bond

$\large{\mathbb{B}}\small{ \sf{(double \ wet ) }} \equiv \, \,${ {e, aqueous-quark.png}, {e, dextro-anti-quark.png} , {e, ionic-quark.png}, {e, levo-quark.png} }

which accurately describes the strength of the double-bond in diazine, HN=NH. If we imagine that each single-bond of the pair is formed from one wet-quark and one stereochemical-quark, then there are two distinct possibilities. They can be written as

$\large{\mathbb{B}}\small{ \sf{(double \ wet \ type1) }} \equiv \, \,${ {{e, aqueous-quark.png}, {e, dextro-anti-quark.png}} , {{e, ionic-quark.png} , {e, levo-quark.png}} }

$\large{\mathbb{B}}\small{ \sf{(double \ wet \ type2) }} \equiv \, \,${ {{e, aqueous-quark.png}, {e, levo-quark.png}} , {{e, ionic-quark.png} , {e, dextro-anti-quark.png}} }

Both of these bonds contain the same quarks, but they are still logically different from each other. And in the laboratory, chemists do indeed find two different forms of diazine

cisdiazene.png and transdiazene.png
cis-diazene trans-diazene

The distribution of stereochemical quarks is thus associated with geometric isomerism. This points again, to the relationship between chemical-bonds and space, that was mentioned at the top of the page. The forgoing double-bonds all contain just four electrons, but we may also include another pair of electrons to define triple bonds such as

$\large{\mathbb{B}}\small{ \sf{( triple \ wet \ acidic ) }} \equiv \, \,${ {e, ionic-quark.png}, {e, ionic-quark.png, dextro-quark.png} , {e, ionic-quark.png, dextro-anti-quark.png}, {e, acidic-quark.png}, {e, aqueous-quark.png}, e }

The very strong triple-bond in carbon monoxide, C≡O, is correctly represented by this arrangement. And here is another triple-bond that accurately models the link in N≡N, a molecule of nitrogen gas

$\large{\mathbb{B}}\small{ \sf{( triple \ aqueous) }} \equiv \, \,${ {e, aqueous-quark.png}, {e, aqueous-quark.png, ionic-quark.png} , {e, aqueous-quark.png, dextro-quark.png}, {e, dextro-anti-quark.png}, {e, levo-quark.png}, e, levo-anti-quark.png} }

And some other double and triple bonds

multi.png

Hydrides

Acidic quarks are featured prominently in models of binary hydrogen compounds. For example, this bond accurately represents the link between hydrogen atoms in $\mathrm{H}_{\sf{2}} \,$, a diatomic molecule of hydrogen gas

$\large{\mathbb{B}}\small{ \sf{( 1) }} \equiv \, \,${ {e, ionic-quark.png, levo-quark.png} , {e, acidic-quark.png, levo-quark.png}, levo-quark.png}

Experimental observations of the hydrides are remarkably precise, these molecules stress the theory. However the following models for their bonds all give results that fall within experimental uncertainty.
hydrides.png

Salts and Halogens

It is possible to construct models of salt molecules and halogen gases that make extensive use of ionic quarks.
salts.png
But laboratory observations that report only two or three significant figures do not constrain the theory very much. So models that do not include ionic quarks are also possible. And more generally, the chemical characteristics of molecules are only weakly related to the quarks in their bonds. It is not even clear that the notion of an electron-pair bond is always a good idea. Van der Waals forcesXlink.png may be more relevant, especially for weak bonds. Nonetheless, we have working models for the bonding in a variety of other dimers. See the wiki-files at the bottom of this page for details.

All of the bonds discussed here are defined from three distinct classes of sensation; sour, salty and sweet tastes. They may vary independently from each other. So, in an upcoming article, we use these bonds to define a three-dimensional Cartesian coordinate system for making space-time descriptions of molecules. And after that, we stop worrying about Pauli's principle.

Right.png Next step: hydrogen.
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