Difference between revisions of "Highly polycyclic small molecule"

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Polycycles not just in in 2D but also (and perhaps predominately so) in 3D. <br>
 
Polycycles not just in in 2D but also (and perhaps predominately so) in 3D. <br>
 
Preferably with no free rotational degrees of freedom in  the molecule.
 
Preferably with no free rotational degrees of freedom in  the molecule.
 +
 +
Such molecules may eventual provide a way out of the <br>
 +
[[fat finger problem]] vs [[floppy finger problem]] dilemma <br>
 +
that one faces with natural proteins.
 +
 +
'''Highly polycyclic small molecule could be integrated as an artificial side-chain in synthetic peptides.'''<br>
 +
For integration of different technologies see page: <br>
 +
[[Combining advantages of different selfassembly technologies]]
  
 
== Examples ==
 
== Examples ==
  
−
[[Spiroligomers]]
+
=== Spiroligomers ===
−
* 2D polycyclic
+
−
* no rotational degrees of freedom
+
  
−
----
+
These are:
 +
* typically 2D polycyclic
 +
* do not allow for any rotational degrees of freedom
  
−
Molecules close to adamantane in structure. These are close in nature to diamond.
+
See main page: [[Spiroligomers]]
−
One proposal are adamantanes with corners substituted with boron sand or nitrogen.
+
 
−
* Either alternatingly wit four nitrigens and 4 borons
+
=== Adamantane related building blocks ===
−
* Or all the same either all 8 substituted with nitrogen (adamanzane) or all 8 substituted with boron.
+
 
 +
This is about molecules close to adamantane in structure. <br>
 +
These are close in nature to diamond. And the origin of the name [[diamondoid]].
 +
 
 +
One proposal is the synthesis and usage of adamantanes with corners substituted with boron and/or nitrogen.
 +
* Either alternatingly wit 4 nitrogen atoms and 4 boron atoms
 +
* Or two different molecules. <br>One with all 8 substituted with nitrogen (adamanzane aka 1,3,5,7-tetraazaadamantane). <br>The other one with all 8 substituted with boron (??? aka 1,3,5,7-tetraboroadamantane).
 +
 
 +
The idea is {{wikitodo|verify that}} that unlike open carbon bonds (carbon radicals)<br>
 +
the unreacted boron and nitrogen could be stable in some solvents.
 +
 
 +
Formed B-N [[coordinative bonds]] between the buildingblocks would be only slightly weaker than C-C bonds.<bR>
 +
As can be seen in the super-hard artificial gemstone [[boron nitride]] (today only ceramics).
 +
 
 +
There are actually quite many strong covalent bond forming reactions that can happen between in-solvent-stable molecules.<br>
 +
After all these reactions are the basis for a lot of modern chemistry.<br>
 +
For an overview over such reactions see page: [[Types of chemical reactions for synthesis]]
 +
 
 +
=== Optically active molecules ===
 +
 
 +
Many of these own their optical activity form delocalized electrons in graphitic polycycles within the molecule.<br>
 +
Some of these even do conformational changes on optical activation. <br>
 +
So these could, beside their stiffness provide the functionality of optically activated nanoscale actuators.
 +
 
 +
=== Boron clusters ===
 +
 
 +
Boron tends to form small stiff clusters with strong internal bonds. <br>
 +
Some mostly structure preserving substitutions are often possible with e.g. carbon or nitrogen.
 +
 
 +
=== Polyoxymetallate clusters ===
 +
 
 +
Polyoxymetallates (e.g. molybdenum oxides) can form nano-clusters that terminate in their selfassembly
 +
reaching atomically precise structures. These can be considered big atomically precise molecules.
 +
 
 +
=== Metalorganic structures (terminating in selfassembly) ===
 +
 
 +
Terminating selfassemblies of metalorganic structures. <br>
 +
Exclusing nonterninating metalorganic frameworks though. <br>
 +
More like multidentate tightly clasping chelates with no floppy parts sticking out. <br>
 +
Various options for how many chelating molecules clasp how many metal ions. <br>
 +
Metalorgainic bonds may me more or less covalent in character.
  
 
== Misc ==
 
== Misc ==
  
−
Aromatic polycyclic compounds are also often optically active
+
=== 2D aromatic molecules & (mechano)optical activity ===
−
and potentially of interest as basis for [[optically activated nanoscale actuators]].
+
 
 +
Due to electron energy levels in the optical range <br>
 +
aromatic polycyclic compounds are also often optically active <br>
 +
sometimes changes of electronic structure come with conformational changes of the molecules. <br>
 +
Thus '''some aromatic polycyclic molecules are potentially of interest as basis for [[optically activated nanoscale actuators]]'''. <br>
  
 
== Related ==
 
== Related ==
  
 +
* The "[[downward inward]]" aspect of: [[Expanding the kinematic loop]]
 
* [[Stiffness]]
 
* [[Stiffness]]
 
* [[Combining advantages of different selfassembly technologies]]
 
* [[Combining advantages of different selfassembly technologies]]
−
* [[Spiroligoners]]
+
* [[Spiroligomers]]
 
* [[Organometallic compound]]
 
* [[Organometallic compound]]
 
* [[Molecule fragments]]
 
* [[Molecule fragments]]
Line 34: Line 87:
  
 
== External links ==
 
== External links ==
 +
 +
=== Adamantane related work ===
 +
 +
'''Awesome graphics''' thereto (and coupling to nanotubes)
 +
[https://www.somewhereville.com/the-design-of-carbon-nanotube-based-dative-structures-from-supramolecular-principles/ on www.somewhereville.com]<br>
 +
In peculiar this slide: [https://www.somewhereville.com/rescv/foresight_2002/foresight200207.jpg Dative-Based Molecular Building Blocks – Graphic by Damian G. Allis – Idea by Ralph C. Merkle (2000)]
 +
 +
* 2020 Complexes Between Adamantane Analogues B4X6 -X = {CH2, NH, O ; SiH2, PH, S} - and Dihydrogen, B4X6:nH2 (n = 1–4)<br>[https://www.mdpi.com/1420-3049/25/5/1042/htm at www.mdpi.com]
 +
* 2018 Adamantane-Derived Carbon Nanothreads: High Structural Stability and Mechanical Strength<br>[https://pubs.acs.org/doi/10.1021/acs.jpcc.7b12603 at pubs.acs.org]
 +
* 2009 '''Functionalized adamantane: Building blocks for nanostructure self-assembly''' <br>[https://journals.aps.org/prb/abstract/10.1103/PhysRevB.80.125421 at journals.aps.org]
 +
* 2008 Electronic nature of the aromatic adamantanediyl ions and its analogues <br>[https://www.scielo.br/j/jbchs/a/dpYfcxt9bTjhWfdTWf8CCRJ/?format=html&lang=en# at www.scielo.br]
  
 
=== Wikipedia ===
 
=== Wikipedia ===

Latest revision as of 12:40, 30 May 2022

This article is a stub. It needs to be expanded.

This page is about small molecules that feature a lot of polycyclic elements.
Polycycles not just in in 2D but also (and perhaps predominately so) in 3D.
Preferably with no free rotational degrees of freedom in the molecule.

Such molecules may eventual provide a way out of the
fat finger problem vs floppy finger problem dilemma
that one faces with natural proteins.

Highly polycyclic small molecule could be integrated as an artificial side-chain in synthetic peptides.
For integration of different technologies see page:
Combining advantages of different selfassembly technologies

Examples

Spiroligomers

These are:

  • typically 2D polycyclic
  • do not allow for any rotational degrees of freedom

See main page: Spiroligomers

Adamantane related building blocks

This is about molecules close to adamantane in structure.
These are close in nature to diamond. And the origin of the name diamondoid.

One proposal is the synthesis and usage of adamantanes with corners substituted with boron and/or nitrogen.

  • Either alternatingly wit 4 nitrogen atoms and 4 boron atoms
  • Or two different molecules.
    One with all 8 substituted with nitrogen (adamanzane aka 1,3,5,7-tetraazaadamantane).
    The other one with all 8 substituted with boron (??? aka 1,3,5,7-tetraboroadamantane).

The idea is (wiki-TODO: verify that) that unlike open carbon bonds (carbon radicals)
the unreacted boron and nitrogen could be stable in some solvents.

Formed B-N coordinative bonds between the buildingblocks would be only slightly weaker than C-C bonds.
As can be seen in the super-hard artificial gemstone boron nitride (today only ceramics).

There are actually quite many strong covalent bond forming reactions that can happen between in-solvent-stable molecules.
After all these reactions are the basis for a lot of modern chemistry.
For an overview over such reactions see page: Types of chemical reactions for synthesis

Optically active molecules

Many of these own their optical activity form delocalized electrons in graphitic polycycles within the molecule.
Some of these even do conformational changes on optical activation.
So these could, beside their stiffness provide the functionality of optically activated nanoscale actuators.

Boron clusters

Boron tends to form small stiff clusters with strong internal bonds.
Some mostly structure preserving substitutions are often possible with e.g. carbon or nitrogen.

Polyoxymetallate clusters

Polyoxymetallates (e.g. molybdenum oxides) can form nano-clusters that terminate in their selfassembly reaching atomically precise structures. These can be considered big atomically precise molecules.

Metalorganic structures (terminating in selfassembly)

Terminating selfassemblies of metalorganic structures.
Exclusing nonterninating metalorganic frameworks though.
More like multidentate tightly clasping chelates with no floppy parts sticking out.
Various options for how many chelating molecules clasp how many metal ions.
Metalorgainic bonds may me more or less covalent in character.

Misc

2D aromatic molecules & (mechano)optical activity

Due to electron energy levels in the optical range
aromatic polycyclic compounds are also often optically active
sometimes changes of electronic structure come with conformational changes of the molecules.
Thus some aromatic polycyclic molecules are potentially of interest as basis for optically activated nanoscale actuators.

Related

External links

Adamantane related work

Awesome graphics thereto (and coupling to nanotubes) on www.somewhereville.com
In peculiar this slide: Dative-Based Molecular Building Blocks – Graphic by Damian G. Allis – Idea by Ralph C. Merkle (2000)

  • 2020 Complexes Between Adamantane Analogues B4X6 -X = {CH2, NH, O ; SiH2, PH, S} - and Dihydrogen, B4X6:nH2 (n = 1–4)
    at www.mdpi.com
  • 2018 Adamantane-Derived Carbon Nanothreads: High Structural Stability and Mechanical Strength
    at pubs.acs.org
  • 2009 Functionalized adamantane: Building blocks for nanostructure self-assembly
    at journals.aps.org
  • 2008 Electronic nature of the aromatic adamantanediyl ions and its analogues
    at www.scielo.br

Wikipedia

  • Adamanzane – adamantane with corners substituted by nitrogen atoms
  • The boron analogon to adamanzane
  • The alternating nitrogen boron version of adamanzane

Exotic miscellaneous:

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