Atoms form herds that evolve into social organisms called molecules
Perception in molecules, parallels with atomic systems.
Top Predators are species which take advantage of the other species of the ecosystem, either feeding and destroying lesser species, to reproduce, or enslaving them in master-slave systems of social bonding. This second case is the best analogy to explain how top predator atoms create molecular systems, using lesser atoms as relative energy species that control territorial surfaces around the central top predator atom. Take the case of water. The Oxygen atom captures two Hydrogen atoms, which act as 'eyes' of the oxygen, protecting the oxygen central zone, and processing in a first stage electromagnetic energy/information. The oxygen uses also those atoms to bond with other atoms through Hydrogen bridges, in which single atoms share the "Hydrogen orbitals". In a way we could consider molecules as we consider single atoms: the nucleon-brain is now the top predator atom, and the slave-electrons are now the lesser atoms, controlled by the top predator central atom, that acts as the brain of the molecule.
In a single atom the first territorial zone of control is given by the first orbital, or S1 spherical electron which is not shared. In molecules, the central atom, has also a first formal, regular body-territory of photonic herds, used to control his slave atom, which is his organic space hardly shared with other molecules.
We find in that zone the feeding/informative forces that the central top predator atom perceives and feeds on. They are social composite forces made of electromagnetic flows of great density, called by abstract scientists, Van der Waals and London forces. That territory is the organism of the molecule, and those forces are its blood/nervous systems, which reach till the external slave atoms.
In essence in molecules as in atomic organisms, the brain, in this case the top predator atom (Nucleons in a single atom), will try to design with its territorial atomic energy (electrons in the single atom) a zone of total control that ensures its feeding on electromagnetic energy, and gravitational stability for a correct virtual perception of the external world.
This means their slavish atomic eyes, will be harmonic around the central atom to ensure total vision without dangerous blind spots.
The body territory is secondary for the atom, and so it can also share part of it, to create molecular bondage and evolve into the next social plane of existence (crystals, and complex macro-molecules.) Accordingly as single atoms have a first Spherical harmonic orbital in which we imagine electromagnetic and gravitational perception takes place (as it happens in your spherical eye, or the black hole in a galaxy), molecules require a harmonic spherical form that can focus at similar distances the energy/information about the external world that arrives from the slavish atoms - which act as intermediate organs of feeding and perception for the inner top predator brain.
So as the distribution of those first S-electrons in atoms follow spherical shapes to provide an efficient 'scanning' of the territory according to the laws of organic geometry, the search for harmonic territorial shapes in molecules limits the shape of molecules to certain organic geometries of spherical or polyhedral nature. All other molecular forms do not exist, because when they are formed they become prey of more efficient molecular species - as unstable sub-particles are destroyed by our efficient 4-universal species, that feed on them.
In the next graph we consider the first simplest molecular systems of social organization according to the organic geometries inorganic molecules follow.
In the graph forms who are not efficient scanning the Universe (B) do not exist. So all molecules are either in an informative spherical state, or in an energetic lineal shape (molecules of high energetic content). They are equivalent to d(lineal)-s(cyclical) orbitals of lineal shape in atoms and the sigma (lineal)-Pi (cyclical) orbitals of simple molecules.
Thus we find that the basic two forms of molecules are spherical-polyhedral T-forms, and lineal, wave like S-forms. Thus geometrical designs towards spherical, lineal or wave forms, continues in all scales - from atoms to molecules, from Urbanism, to military formations in our macro-social plane of existence. Because the game is always the same: organic geometries created with the goal of capturing energy/information, and socialize with parallel forms.
Energy processes in top predator molecules that use lesser atoms.
Molecules exist for a simple reason. A society, a herd, is more efficient than an individual. Molecules beat up individual atoms. They are more efficient. And they survive as Top Predators.
Take a simple case: The Haemoglobin.
The red color of your blood is caused by haemoglobin. Iron moves the four arms of the haemoglobin macromolecule, and captures energy, an oxygen molecule, an active gas, that becomes trapped, caged inside. The movement of trapped oxygen allows the haemoglobin to store energy and then share it with the cells of your body. The small energy species is now a slave.
Or think about water,
the energy of cells. How water acts as energy of bigger molecules?
Now imagine yourself a simple carbohydrate molecule, an amino acid, the basic brick of life, dissolved in water. It has in one extreme a Head, the amino, and in the other extreme 2 legs, the carboxyl, that walk on water. How?
The amino-Head throws his hydrogen antennae to perceive the subtle molecular forces that map out within the Nitrogen atomic brain, the surrounding space. It decides where to go: Then the carboxyl legs move the amino acid, with its two oxygen, energetic, atomic legs. An O-leg which attracts H+ ions, and an OH-leg, which repels OH- particles alternatively; as your legs are repelled and attracted to the floor y electric/gravitational forces. So by pushing around the two pieces of the free liquid water, OH- and H+, the amino acid moves. The perfect legs of amino acids permits the existence of life, constantly moving with water molecules.
The amino acid form shows how easy is to apply morphological laws to determine the living elements of any species. The amino-acid looks like an animal that has acid-legs, an amino-Head, and the intermediate Carbonic body.
How we do know which role plays each atom? Obviously, the Nitrogen is less active, less energetic that Oxygen, a natural energy atom. So one is the Head, the other the tail. In the middle, the body is a carbon structure, thinner or fatter depending on species. And as it walks, the Nitrogen Head with 2 H-eyes goes first.
Take now the case of the haemoglobin. It is not a "tree" but a "spiral" structure. The 4 Iron atoms are the Head, dense, smaller in space, in the center, from where it commands and moves 4 long arms to capture oxygen. It is also a repetitive strategy: galaxies have a black hole in the center that moves their arms to capture in rotational movement the space-time energy of the Universe
Molecules perceive as atoms do, gravitation and electro-magnetism, the two forces of our light-based Universe, which act normally as the informative, knotting force (gravitation, from atomic nucleus to sound waves) and the energetic, reproductive force of molecules (electro-magnetism).
Reproduction: re actions of chemical compounds.
How molecules reproduce? Merely by assembling their atomic components, stealing them from lesser species, in what chemists call a chemical re action:
As in all other systems of the Universe there are two kinds of reproduction in molecules associated to the two basic social events: Darwinian events of capture by top predator molecules of lesser forms, and social communication between similar top predator molecules.
In molecules, Reproduction normally implies 'feeding on simpler molecules". Chemical re actions are reproductive molecular radiations. When a first top predator molecular form appears in a field rich in its atomic components, then we observe a growing 'radiation' of new molecules repeating that form, when the minimal energy required to activate the reproduction exists [threshold of activation of exogenic re actions]. This happens in all reproductive processes which only occur when the parental species find a field rich in energy, given the exhausting nature of such processes, which in a field poor in energy would jeopardize the survival of the parental form (so most animals reproduce in spring, most molecular crystals reproduce when temperature reaches a certain levels, and so on.) The radiation is explosive and designs a curve of growing existence, well known to chemists: the re action starts as a vortex of growth of the new product, when energy is hyper abundant. After the threshold of activation is crossed, the radiation will expand till it 'saturates' and exhausts the energy ecosystem in which it feeds [the lesser atoms in the molecular re action, the space-time constants in the big bang, the plants or herbivores in a macro-ecosystem of animal life]. Finally the explosive re action will end in a steady state dynamic balance, which creation of very few new molecules as some of the old molecules become destroyed or new simpler atoms enter the ecosystem. The homology with the big bang present steady state, with the trophic pyramids of nature, is evident... We talk then of a new ecosystemic balance between the two top predator/victim molecular and atomic species.
When the re action occurs between two symbiotic, similar top predator molecular forms, we talk not of a Darwinian feeding process, but of social alternating creation and destruction of both types of molecules, till reaching a balance known by abstract scientists as the 'law of equilibrium' of chemical re actions.
Social evolution: From molecules to cells
Self organization connects the evolution of big molecules with the next macro level of existence (cells). Indeed, self organization following the Laws of Universal organisms is how life surely appeared: Heads became rings, bodies structured in circles.
Together they created the first membranes: the next stage towards the cell.