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Molecules and 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 diagrams or VSEPR theory . 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.

Seeds are not enough, so Mr. Quirky is here to remind us about other sensations.
Don’t forget about other sensations. Click 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 EthnoPhysics, 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 by earlier hypotheses. So instead, we differentiate them by association with different taste sensations. To satisfy Pauli’s exclusion principle, electrons  \mathsf{e^{-}} are distinguished from each other by their union with various chemical quarks such as or . We use the letter  \mathbb{B} to identify specific bonds in the following discussion. Each bond is characterized by D_{ \mathsf{o}} a bond dissociation energy that depends on the enthalpy H and internal energy  U as

\displaystyle D^{\mathbb{B}}_{\mathsf{o}} \equiv H \! (\mathbb{B}) - N_{\mathsf{e}} H \! (\mathsf{e^{-}}) = \sum_{\mathsf{q} \in \mathbb{B}} \Delta n^{\mathsf{q}} U^{\mathsf{q}}

where   \Delta n notes the coefficients of quark  \mathsf{q}, and  N_{\mathsf{e}} is the number of electrons in the bond. Experimental observations1Bond Dissociation Energies in Simple Molecules , National Standard Reference Data Series Number 31, B. deB. Darwent, U.S. National Bureau of Standards, 1970., 2Bond Dissociation Energies of Organic Molecules , Stephen J. Blanksby and G. Barney Ellison, Accounts of Chemical Research 36 (4), 2003., 3Bond Dissociation Energies , Armen Zakarian, University of California Santa Barbara., 4Strengths of Chemical Bonds , J. Alistair Kerr and David W. Stocker, CRC Handbook of Chemistry and Physics 81st Edition, Lide, D.R. (Editor), Boca Raton, Florida, 2000. report D_{ \mathsf{o}} for the gaseous state.

Archetypical 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{\mathsf{(semi \ acidic) }}. It is the first example of a bond formed predominantly from acidic quarks.

\mathbb{B} \mathsf{(semi \ acidic)} \equiv { { \mathsf{e^{-}}, }, \mathsf{e^{-}} }

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

\mathbb{B} \mathsf{(acidic)} \equiv { { \mathsf{e^{-}}, }, \mathsf{e^{-}}, }

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

\mathbb{B} \mathsf{(basic)} \equiv { { \mathsf{e^{-}}, }, \mathsf{e^{-}}, }

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.

Double 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

\mathbb{B} \mathsf{(double \ acidic)} \equiv { { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, , } }

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

\mathbb{B} \mathsf{(double \ basic)} \equiv { { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, , }, { \mathsf{e^{-}}, , }, { \mathsf{e^{-}}, } }

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

\mathbb{B} \mathsf{(double \ aqueous)} \equiv { { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, , }, { \mathsf{e^{-}}, }, \mathsf{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 bond

\mathbb{B} \mathsf{(double \ wet)} \equiv { { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, } }

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

\mathbb{B} \mathsf{(double \ wet \ type1)} \equiv { { { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, } }, { { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, } } }

\mathbb{B} \mathsf{(double \ wet \ type2)} \equiv { { { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, } }, { { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, } } }

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

cis-diazene
and

trans-diazene

The distribution of stereochemical quarks is thus associated with geometric isomerism.

Triple Bonds

The forgoing double-bonds all contain just four electrons, but we may also include another pair of electrons to define triple bonds such as

\mathbb{B} \mathsf{(triple \ wet \ acidic)} \equiv { { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, , }, { \mathsf{e^{-}}, , }, { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, }, \mathsf{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

\mathbb{B} \mathsf{(triple \ aqueous)} \equiv { { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, , }, { \mathsf{e^{-}}, , }, { \mathsf{e^{-}}, }, { \mathsf{e^{-}}, }, \mathsf{e^{-}}, }

And here are some other double and triple bonds

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}_{\mathsf{2}}, a diatomic molecule of hydrogen gas

\mathbb{B} \mathsf{(1)} \equiv { { \mathsf{e^{-}}, , }, { \mathsf{e^{-}}, , }, }

The following models give results that are within experimental uncertainty even though observations of the hydrides are so precise that ten quarks are required to include hydrogen deuteride.

Salts and Halogens

It is possible to construct models of salt molecules and halogen gases that make extensive use of ionic quarks.

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 forces may be more relevant, especially for weak bonds. Nonetheless, we have working models for the bonding in a variety of other dimers.5For details about calculating bond strengths, please see the spreadsheet titled Bonds & Photons. Experimental observations are reported at various temperatures, and in diverse measurement units. Details for each molecule about reference sources, and conversion factors, are shown in a spreadsheet called Observed Bonds.

Sensory Interpretation

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.

References
1Bond Dissociation Energies in Simple Molecules , National Standard Reference Data Series Number 31, B. deB. Darwent, U.S. National Bureau of Standards, 1970.
2Bond Dissociation Energies of Organic Molecules , Stephen J. Blanksby and G. Barney Ellison, Accounts of Chemical Research 36 (4), 2003.
3Bond Dissociation Energies , Armen Zakarian, University of California Santa Barbara.
4Strengths of Chemical Bonds , J. Alistair Kerr and David W. Stocker, CRC Handbook of Chemistry and Physics 81st Edition, Lide, D.R. (Editor), Boca Raton, Florida, 2000.
5For details about calculating bond strengths, please see the spreadsheet titled Bonds & Photons. Experimental observations are reported at various temperatures, and in diverse measurement units. Details for each molecule about reference sources, and conversion factors, are shown in a spreadsheet called Observed Bonds.