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    Molymod compatible atoms - Many Additional Coordination/point group Options

    Please Note: My aim is not to replicate parts already available in the official kits. This thing is designed to enhance existing Molymod kits - not replace them. Molymod do not produce atoms with the configurations or the custom parts I have created - nor have they ever as far as I can tell.

    The officially available atom configurations are listed below and along with bond connectors of various lengths plus other accessories such as lone pairs, orbitals etc can be obtained by buying official Molymod components or kits (https://molymod.com/)

    • 1 Coordination
    • 2 Coordination (linear)
    • 2 Coordination (105 degrees)
    • 3 coordination (Planar)
    • 3 coordination (107 Degrees)
    • 4 coordination (tetrahedral)
    • 5 coordination (trigonal bipyramidal)
    • 6 coordination (octahedral/trigonal antiprismatic)

    I have created some some additional (some very uncommon - possibly even unknown/impossible) atom types that are compatible with the 'Molymod(R)' molecular modelling kit. These allow for coordination types/point groups that are not available from the official kits and should help extend the range of molecules and complexes that may be modelled using the Molymod system.

    In some cases, it is possible to use official Molymod atoms to create these configurations (e.g. Disphenoidal/"Seesaw" configuration can be created using the octahedral atom - and leaving two bond connections unfilled, or by using the lone pair connectors) - but for others such as the icosahedral pentagonal pyramid configuration - no suitable solution is available using official atoms.

    I have included versions both with the bond cutout and without it - either should work fine, but the cutout ones better replicate the look of the official Molymod atoms.

    Note - these can only be used if you have existing Molymod or Molymod compatible bonds, atoms etc (these items are not included in this thing).

    The additional atoms I have created so far are:

    Coordination 3

    • T-Shaped - point group C2v (e.g. Chlorine trifluoride CLF3)

    Coordination 4

    • Square Planar - point group D4h (e.g. Silver Tetrafluoride AgF4)

    • Disphenoidal/"Seesaw" - Point Group C2v (e.g. Sulfur tetrafluoride SF4)

    Coordination 5

    • Pentagonal Planar - point group D5h (e.g. [XeF5]−)

    • Pyramidal Square Planar - point group C4v (e.g. ClF5, MnCl5 2−)

    Coordination 6

    • Hexagonal Planar - point group D6h? (e.g. possibly some exotic transition metal complexes)

    • Pentagonal Pyramid - point group C5v (e.g. Xenon oxytetrafluoride XeOF5)

    • Pentagonal Pyramid (Icosahedral layout with bonds at 122 degrees) - point group C5v (e.g. dodecaborate(12) anion B12H12 or ortho, meta and para-Carborane B10C2H12)

    • Trigonal Prismatic - point group D3h (e.g. Hexamethyltungsten W(CH3)6)

    Coordination 7

    • Capped Octahedral - point group C3v (e.g. MoF7-)

    • Pentagonal Bipyramid - point group D5h (e.g. Iodine heptafluoride IF7)

    • Capped Trigonal Prismatic - point group C2v (e.g. TAF7 2-)

    Coordination 8

    • Trans BiCapped Octahedral - point group ?? (Ni in nickel arsenide, NiAs; 6 As neighbours + 2 Ni capping)

    • Hexagonal bipyramid - point group D6h (e.g. Dysprosium(III) single ion magnet)

    • BiCapped Trigonal Prismatic - point group C2v (e.g. [ZrF8]4−)

    • Square Antiprismatic - point group D4d (e.g. XeF8 2−)

    • Square prismatic - point group D4h (e.g. Na3PaF8)

    Cordination 9

    • Tricapped Trigonal Prismatic - point group D3h (e.g. ReH9 2-)

    • Capped Square Antiprismatic - point group C4v (e.g. [Ge9]4-)

    Coordination 10

    • Bicapped square prismatic - point group ?? (e.g. Unknown)

    • Bicapped square antiprismatic - point group D4d (e.g. Unknown)

    • Pentagonal Prismatic - point group ?? (e,g, Unknown)

    • Pentagonal Antiprismatic - point group ?? (e,g, Unknown)

    Coordination 11

    • All face capped Trigonal Prismatic - point group D3h (e.g. aqua-(12-crown-4)-tris(nitrato-O,O')-cerium(III) (12-crown-4) solvate and (15-crown-5)-tris(nitrato-O,O')-cerium(III) the Cerium ion is 11 coordinate)

    Coordination 12

    • Cuboctahedron - point group Oh (e.g. Unknown)

    • Hexagonal Prismatic - point group D6h (e.g. Unknown)

    • Hexagonal Antiprismatic - point group D6d (e.g. Unknown)

    • Bicapped Pentagonal Prismatic - point group ?? (e,g, Unknown)

    • Bicapped Pentagonal Antiprismatic - point group ?? (e,g, Unknown)

    Coordination 14

    • Bicapped Hexagonal Prismatic - point group D6h (e.g. Unknown)

    • Bicapped Hexagonal Antiprismatic - point group D6d? (e.g. V15⁺ cluster)

    Coordination 16

    • Almost Fully Coordinated? (wasn't sure what to call this one. It's essentially a square antiprismatic shape - capped with antiprismatic squares.)

    Coordination 17

    • Fully Coordinated? (wasn't sure what to call this one either. Three layers of antiprismatic pentagons, bicapped with a single at each end. This is as many molymod bonds as will fit on a 23mm sphere. The 16 and 17 may not be realistic - but I have included them for completeness - and perhaps a bit of artistic licence.)

    In addition - I have also created a few custom parts:

    • Linear Bond Connector - to connect bonds together to make longer bonds

    • Aromatic Carbon Atoms. This is a carbon atom with a trigonal planar configuration, but with an extra hole at 60 degrees offset. This allows you to use these atoms in conjunction with the short molymod space filling bonds and the custom aromatic bond arcs below to create 6 carbon aromatic rings without having to alternate single and double bonds - but also allow you to depict the carbon ring with the circle in the centre, a depiction often used in text books to denote the delocalised P orbitals. There are both cutout and non cutout variants of these atoms.

    • Aromatic Bond Arc. These are designed to be used with the custom aromatic carbon atoms above and connect via 3 holes each to the inner hole of the carbon atoms via a short molymod space filling bond (see image in the gallery comparing a standard aromatic ring with one built using these custom parts).

    • Aromatic Bond Full. As above, but a complete ring with 6 holes.

    The atoms in this thing are scaled to ~23mm (the same size as a standard molymod carbon atom). I may include a larger 24.5mm option at some point, to match the larger atom size found in in some legacy kits.

    I have only printed in PLA so far and so get layer lines. They aren't too prominent if you print with a very fine layer height (I used 0.08 for the ortho-carborane model that is the cover photo for this thing), however if you printed in a filament such as ABS or PVB that are amenable to solvent smoothing, you may be able to more closely replicate the shiny, polished look of the official kits. I'd probably advise plugging the holes somehow if you try this to prevent them from warping during solvent smoothing.

    If there are any other useful coordination types/point groups that are not not available in the official kits that I haven't covered here - or if you find issues with any of the files, let me know and i'll have a crack at fixing them or adding them to this thing.

    These atoms were modelled in Blender 4.2. I hope you find them useful :o)