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The rules stated in the previous chapter also apply to this chapter. To build 3D atoms we will need two basic building units. The first of them is the nucleus of the 4He atom, referred to in the text as the 4He plateau. We can figuratively imagine this as a strong rubber ring, into the central opening of which we will gradually insert the second building unit, which is actually deuterium. So the neutron-proton-electron system as shown below. Neutron-proton binding passes right through the hole in the 4He plateau. The binding neutron, located on the other side of the 4He plateau, will be called the paired neutron. A possible additional binding neutron in some isotopes will be called supplementary. As the deuterium building units are gradually inserted, the hole in the 4He plateau gradually expands and deforms. In this way, we get atoms from Lithium to Calcium and then those whose valence electron shells, according to the current classification, are made up of s and p orbitals.
Another important feature of the 4He plateau is that it separates the spaces on its two sides. The pulsation of nucleons on the one hand is thus restricted from entering space on the other hand. This effect then significantly affects the properties of the entire atom.
To study the 3D model of the atom, it is advisable to first find the position of the 4He plateau and then compare it with the position of the other nucleons. The configuration of 4He plateau is unique and will never be repeated, as will be explained using the example of the non-existent Beryllium isotope 8Be.
Building deuterium unit
Lithium 6Li
The 6Li isotope is the simplest 3D atom. It is stable with a minority natural abundance, approx. 5% (https://en.wikipedia.org/wiki/Lithium). The reason for such a low natural abundance is that the essentially lone proton is clearly offering itself to combine with a supplementary neutron, as will be shown below. It contains one deuterium building block as shown in the following 3D model.
3D model of 6Li atom
Lithium 7Li
The 7Li most widespread isotope of lithium, with a natural abundance of about 95%, as explained in the previous chapter. Since the interaction of the supplementary neutron and the pair neutron is significantly weaker than the interaction between the proton and its pair neutron, it can be expected that due to the limited permeability of the hole in the 4He plate, the additional neutron will be pushed to the side and the proton will be pushed slightly off-center. Both neutrons in 7Li are separated by the 4He plateau and are not in direct contact as in the case of tritium 3H. This is reason why is 7Li unlike tritium stable and non-radioactive. The deuterium building unit with an supplementary neutron forms a plane perpendicular to the 4He plateau surface. This is the reason for its cubic crystal structure. As you can see in the following link, the point in the middle has two perpendicular planes.
https://en.wikipedia.org/wiki/Lithium#/media/File:Cubic-body-centered.svg
Another important feature of the 7Li structure is that the proton is limited to its pulsation by interacting with both neutrons from two sides, which means that its pulsation on the free side is all the stronger. According to the theory described above, this means that the electron is pushed further away from the nucleus. This is reflected in the value of its covalent radius (approx. 128 pm) and in the electronegativity, which with a value of 1.5 is smaller than in the case of hydrogen (2.2).
3D model of 7Li atom
The lithium atom was chosen for further study of the configuration of the nucleus and the distribution of the “charge” of its ion into both electron orbitals. Lithium has 3 protons in its nucleus and two stable isotopes. 6Li with 3 neutrons and the most common 7Li with four neutrons. It can be assumed that the core of Lithium is built on the core of 4He, which forms a plateau for s1 orbital. The following figure shows a probable variant of the 7Li ion.
Beryllium 7Be
7Be is only a trace, moreover unstable isotope of beryllium (https://en.wikipedia.org/wiki/Beryllium). It is rather interesting for study reasons. It is possibly the only isotope that has one paired neutron in common with two protons. In a way, it is a combination of 3He and 4He.
3D model of 7Be atom
Beryllium 8Be
8Be is practically nonexistent isotope of beryllium (https://en.wikipedia.org/wiki/Beryllium-8). What makes it interesting is precisely its incredibly high instability. We will study its most probable variant, i.e. that it is a pair of two deuterium units as shown in the following figure.
3D model of 8Be atom
The probable mechanism of decay is shown in the following scheme. Red arrows showing the direction of action of the strong nuclear interaction of the proton with its paired neutron. Blue arrows showing the direction of action of the strong nuclear interaction of a neutron with its paired proton. The system of both deuterium building blocks is in dynamic equilibrium. Once one of the protons is captured by interaction with a neutron from the second deuterium unit, it is pulled across the 4He plateau by the combined force of the interaction with both neutrons. Subsequently, the second proton is extracted by the same mechanism, forming a 4He nucleus. The rapid decay of 8Be is made possible due to the lack of a sufficiently large energy barrier during the process.
Probable decay mechanism of the 8Be atom
Beryllium 9Be
9Be is practically the only stable isotope of beryllium. The stability of this isotope is probably related to the fact that the supplementaryl neutron, which is common to both protons, stabilizes the system of both protons. At the same time, it changes the resulting direction of the strong nuclear interactions of the two protons, so that they no longer tend to push each other out. The whole system is thus much calmer and more stable. Covalent radius of beryllium is lower than in the case of lithium, approx. 96 pm.
3D model of 9Be atom
Action of strong nuclear interactions in the 9Be atom.
Boron
Boron has two stable isotopes. 10B has a natural abundance of about 20% and 11B about 80% (https://en.wikipedia.org/wiki/Boron). Their relationship and reason for existence is the same as in the case of lithium isotopes 6Li and 7Li.highlighted. A supplementary neutron like in the case of 9Be would be unstable because it would be pushed by radial neutron pulses from the third deuterium unit. The third deuterium building unit also acts as a nucleus stabilizer, i.e. just like a supplementary neutron in the case of 9Be. But it also presses on the hole in the 4HE plate in a perpendicular direction, so it prevents it from opening. Covalent radius of boron is approx. 84 pm. The third deuterium unit causes the original two deuterium units to tilt as shown in the picture. This then causes the boron to crystallize in a rhombohedral structure. (https://en.wikipedia.org/wiki/Boron#/media/File:Rhombohedral.svg)
It is also impossible to create a symmetrical model of the nucleus, i.e., where the third deuterium unit would be centered between the first and second deuterium units. In such a case, the proton would be caught between two neutrons, which would suppress the pulsation of this proton with their radial pulses so much that it would absorb its own electron, forming a neutron. This is also the reason for the instability of the 11C and 18F nuclei.
3D model of 10B atom
3D model of 11B atom
Carbon
Carbon contains four deuterium building blocks. Covalent radius of carbon is approx. 73 pm. It has two basic stable isotopes, 12C and 13C with a natural representation of approx. 99%, or 1.1%. There is also the isotope 14C, in trace amounts, with a half-life of 5730 years (https://en.wikipedia.org/wiki/Carbon). We will first deal with the common isotope 12C and finally mention the two minority isotopes. Since all four deuterium units are fully rotatable, the carbon nucleus can assume several forms. Firstly, let study the basic form, where two and two units always form a planar pair, as shown in the following 3D model.
3D model of 12C atom in basic configuration
According to current theory, carbon has four electrons in its valence shell. In the case of sp3 hybridization, they are equal. However, as can be seen from the model, this is not entirely true. Those electrons are indeed equal, but they are arranged in a 2+2 system. Why is this important? There are chiral compounds and many of them are the basic building blocks of living organisms. We can take the simplest chiral amino acid, L-alanine, as an example. This has the following groups attached to the chiral carbon: methyl, amino, carboxyl and hydrogen. The point is that there are in fact two forms of L-alanine. For simplicity, we will use the group amino and carboxyl for interpretation. Then we are able to create one configuration so that both of these groups are bound to paired deuterium building units, i.e. on one side of the 4He plateau, and the other configuration on unpaired deuterium units, i.e. on the opposite sides of the 4He plateau. Because current theory does not distinguish between these two configurations, we do not know whether they both have the same or different biological activity. It may be necessary to introduce the concept of biochirality in the future. Of course, this is not only a question of chiral substances, but also of most non-chiral ones.
Another property of the ground state atom is the fact that the two electrons on the paired deuterium building blocks are actually separated by the radial pulsation of the two neutrons from the other deuterium pair, and thus cannot move from one side to the other at will. In the next perpendicular direction, the 4He plateau pulsation forms a barrier for electron movement. Therefore, the carbon atom in its basic state is an electrical insulator.
As mentioned at the beginning of the chapter, all four deuterium units are fully rotatable. Each deuterium unit can pair with any other to form a plane with it. In addition to the base configuration, there are also two equivalent alternative configurations as shown in the following 3D model.
3D model of 12C atom in alternative configuration
It can be seen that the barrier for electron movement in one of the directions is no longer there, and the carbon atom in the alternative configuration can serve as an electrical conductor in this direction.
The carbon nucleus can assume many other configurations due to the free rotation of the deuterium units. However, these are no longer so advantageous and are a manifestation of the thermal energy of the atom. The following 3D model shows a carbon atom in a fully open configuration.
3D model of 12C atom in a fully open configuration
The 13C isotope is obtained by adding one neutron in the basic configuration of the 12C atom, just as in the case of the beryllium 9Be isotope. This not only reduces the level of symmetry of the 13C nucleus, but also changes the pulsation form of the corresponding protons, which is related to the position and distance of the respective electrons and therefore also the length of their chemical bonds. These changes allow the NMR analytical technique to be used to measure the 13C spectrum. The isotope 14C is obtained in the same way by adding another neutron to the second pair of deuterium units on the other side of the 4He plateau. However, the supplementary neutrons will also block the possibility of rotation of both deuterium units concerned. But even the basic configuration of the nucleus allows the carbon atom all known types of chemical bonds. One of the main roles of electrons in chemical bonding is to maintain just the right direction of all the deuterium units involved in the bond.
Single bonds between carbon and two hydrogens
A double bond between two carbon atoms
A potential triple bond may be mediated by the reversed protons on the other sides of both 4He plats.
Nitrogen
Nitrogen contains a total of five deuterium units, so one unit is not paired. The unpaired electron is probably the reason why the covalent radius of nitrogen is almost the same as in the case of the carbon atom, and is about 75 pm. The main isotope of nitrogen is 14N, which does not contain any supplementary neutron, and its natural abundance is about 99.6%. The minority isotope is 15N, with one supplementary neutron (https://en.wikipedia.org/wiki/Nitrogen). This can theoretically be both type 9Be and type 7Li. Its natural abundance is about 0.4%. You can see the 3D model of the 14N isotope in the next figure.
3D model of 14N atom
Two pairs of deuterium units are seen here, but they are not equivalent. First pair has a 4He plateau next to it and a second deuterium pair on the other side. Their axial pulses are thus in direct interaction, which limits the protons’ own pulsation. In addition, the entire system is tilted towards the 4He plateau at an angle of approximately 45°, which reduces the strength of the interaction between protons and their paired neutrons. The corresponding electrons will thus be closer to the nucleus, which reduces their reactivity. The second pair has the first pair of deuterium units adjacent to it and a fifth deuterium unit which is additionally shifted to the center. The second pair thus has much more space around it. The angle between this pair and the 4He plateau is 90°, so the interaction between protons and their paired neutrons is much stronger. The consequence of all these effects is that the electrons in question are much more reactive. The question remains how much the units of the second pair can rotate freely. Thus, the fifth deuterium unit has the most space, which allows it to presumably have unlimited rotation. Although it makes an angle of about 45° with the 4He plate, since it passes through its middle, the interaction between the proton and neutron is sufficiently strong and the result is a fairly reactive electron. Several facts emerge from the assessment carried out. The ammonia molecule will be formed by hydrogen bonds to the fifth deuterium unit and to the second, more reactive, deuterium pair. However, the three nitrogen-hydrogen bonds formed are probably not equivalent and may differ in reactivity. Furthermore, the first deuterium pair is tilted relative to central axis of these three bonds, causing further asymmetry of the molecule. This is highlighted if we replace one hydrogen with methyl to form methylamine. One of the products of such a reaction is the binding of methyl to the fifth deuterium unit. An achiral methylamine is formed, which has a plane of symmetry. Next are the products of the second pair of deuterium bonds. If this pair does not form an equivalent bond as the fifth deuterium unit, both of these products are chiral and form enantiomers. Theoretically, if there is a reason why life on earth is based on L-amino acids, the answer may be hidden precisely in the properties of the nitrogen atom.
As explained earlier, the first deuterium pair is less reactive. Therefore, nitrogen dioxide is not produced directly, but through ammonia. Its heat of combustion will then supply the necessary activation energy required for the reaction. Two oxygen molecules will bind to both deuterium pairs to form a NO2 molecule. The more correct designation should be N2O4, because the two NO2 molecules are linked through their fifth, unpaired, deuterium units. For us, however, the comparison of the O=N=O bond angle with the proposed structure of the nucleus of the nitrogen atom is more interesting. According to the literature, this value is 134.3°.
https://en.wikipedia.org/wiki/Nitrogen_dioxide
By looking at the designed 3D model, the value of 135° can be deduced quite easily!
Oxygen
Oxygen contains a total of six deuterium units. According to the assumption, its covalent radius is smaller than that of the previous atoms and amounts to about 66 pm. The main isotope of oxygen is 16O, which does not contain any supplementary neutron, and its natural abundance is about 99.8%. The minority, but stable isotopes are 17O and 18O (https://en.wikipedia.org/wiki/Oxygen). We create the 16O atom by adding a sixth deuterium unit to the 14N atom. We thus obtain one pair of protons on one side of the 4He plateau and two pairs of protons on the other side of the 4He plateau. However, these make an angle of about 45° with the 4He plateau and, like in the case of nitrogen, they are not very reactive. The only reactive pair is the one perpendicular to the 4He plateau.
3D model of 16O atom
Fluorine
Fluorine contains a total of seven deuterium units. Its only stable isotope is 19F, thus has one supplementary neutron that interacts with the seventh, non-paired, deuterium unit. In the case of the 18F isotope, the seventh deuterium unit would pass through the center of the 4He plateau hole. Both the neutron and the proton would be squeezed between three pairs of deuterium units and their pulsation would be greatly reduced. In the case of a proton, its electron would be absorbed and a neutron would be formed, followed by a rearrangement of the nucleus (https://en.wikipedia.org/wiki/Fluorine-18). The purpose of the supplementary neutron is thus to push the proton off-center, as shown in the 3D model. The additional neutron also gives the proton more energy, so that it is, according to the theory above, much more active on the opposite side. As a result, the relevant electron is moved significantly further than the other electrons, and the atom thus has a very high reactivity. Accordingly, it also has a relatively higher covalent radius, approx. 64 pm (https://en.wikipedia.org/wiki/Fluorine).
3D model of 19F atom
Neon
Neon contains a total of eight deuterium units connected in four pairs. These create fully filled two circles on both sides of the 4He plateau. All nucleons thus fully interact their axial pulsation with their neighbors and their activity is thus significantly reduced. Which is the main cause of the inert behavior of the atom. Covalent radius, approx. 58 pm. The main isotope is 20Ne, with a natural abundance of about 90,5%. The minor, stable isotope is 22Ne, with a natural abundance of approx. 9,3%. The last, but also stable, is 21Ne (https://en.wikipedia.org/wiki/Neon).
3D model of 20Ne atom