Space-filling molecular models: Carbon expansion set

Space-filling molecular models: Carbon expansion set

cults3d

Human: Carbon generally can form four bonds with other atoms. If each bond is single, carbon resembles a tetrahedron with an atom attached to each face or vertex. When double-bonded, atoms usually occupy the same plane and are 120 degrees apart from one another. Triple bonding results in atoms aligned in a straight line. Here I present the carbon atoms for multiply bonded systems. I created CarbonDB2 for scenarios where two carbon atoms share a double bond. For instances with bulky side groups on the same side as the double bond, use CarbonDBR. When double-bonded to another atom like oxygen or nitrogen, employ CarbonDB3. It's similar to CarbonDB2 but has relaxed edges for better visuals. Choose whichever one suits your needs. You may have noticed that most of the provided atoms can be rotated around their bonds. However, this feature is unavailable for double-bonded atoms due to their fixed position, mimicking real atomic behavior. The rectangular socket in these models represents a slightly shorter bond distance than other connections. CarbonTB3 serves triple-bonded carbon, which cannot rotate but appears symmetrical with nitrogen bonding. A cumulative double bond resembles two groups locked at right angles; use CarbonCDB1 for such cases. Some might think this is unnecessary, but it's crucial for modeling carbon dioxide, a symmetrical and predictable molecule. On another note, space filling models rely on two key measurements: the covalent radius, which determines atom distances, and the Van der Waals radius, representing atomic diameters. Covalent radii can be precisely calculated, whereas Van der Waals radii are more challenging to determine. Various values exist for carbon's Van der Waals radius; I use 1.5 Angstroms, slightly smaller than some other accepted values like 1.7 Angstroms. This choice may not be the most critical factor but shouldn't be overlooked either.

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