Gemstone-like molecular element

Here is a rather small structural diamondoid crystolecule with some bonds (brighter red) intentionally being left open/dangling/unpassivated. A crystolecule fragment. Such surface interfaces can be fused together via seamless covalent welding in the second assembly level and perhaps higher assembly levels.

A proposed acetylene sorting pump. This is a larger diamondoid machine element (DME). Possibly assembled from several pre-produced smaller diamondoid crystolecules. The frame is one big monolithic crystolecule (it may be fused together via seamless covalent welding during assembly). Other parts are smaller independent crystolecules that may be mechanosynthesized fully passivated as a whole and integrated as a whole without any seamless welding.

Gemstone-like molecular elements (GMEs) here also called crystolecules for short. Also possible crystalecules or crystallecules.
Gemstone-like molecular elements are the basic building blocks in
gemstone based atomically precise manufacturing here aka
gemstone metamaterial technology or gem-gum-tec.

The small & simple initial idea was:
These objects are somewhat of a cross between a crystal and a molecule.
So let's use the term "crystolecule" as a portmanteau.
Below is an evolved much more extensive definition.

Definition of crystolecules

Abbreviated tl;dr
A crystolecule …
★ has fully atomically precise to specification crystal like internal structure
★ has fully atomically precise to specification molecule like surface structure
★ is a single monolithic piece, not an assembly of crystolecules
– is usually but not always on the lowermost physical size limit to fulfill its function
– has usually but not always non-bonding surface passivations

Hard criteria:

★ Crystolecules are (unless broken) fully atomically precise.
All atoms are at a known and fully intentional position that was desired not accepted.
Some errors may be acceptable so long the parts can still fulfill their tasks.
★ Crystolecules, like macroscale crystals, have a crystalline internal structure (it is allowed to be strained, stressed, and feature fully intentional and atomically precise "defect" like structures. (A more fitting name might be "perfections" maybe?)
★ Crystolecules, like nanoscale molecules, have both a finite, and atomically precisely intentionally defined outer shape i.e. surfaces, edges, corners. (Surfaces may feature intentional atomically precise surface reconstructions.)
★ Crystolecules are structural and monolithic, molecular machine elements with moving parts must contain more than one crystolecules (excluding flexures).

Soft criteria:

These are not strictly necessary but corroborate the crystolecule status.
If these requirements are not met it does not mean it is not a crystolecule.
★ Crystolecules usually but not always feature an atomically precise monolayer (or near monolayer) surface passivation such that they feature mechanical stability, thermal stability, chemical stability, and other (electrical optical, …) overall only necessarily sufficient for their intended purpose. Encapsulated crystolecules e.g. need not be stable to air. See: Fruit interior analogy.
★ Crystolecules usually but not always are created to fulfill a specific structural function as whole of (or part of) a structural element, or structural part of a machine element of various kind, (mechanical, electrical, plasmonic). Exceptions: crystolecules in recycling storage, somehow broken crystolecules, mechanosynthesis capability demonstrations (like test-prints), failed prototypes, …
★ Crystolecules usually but not always are in their size at the lowermost physical size limit to fulfill their function.
★ Crystolecules are usually but not always highly symmetrical.

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★ Diamond crystolecules are produced via force applying mechanosynthesis. There seems to be no other viable way to make diamond ones.
★ Crystolecules are generally produced via mechanosynthesis/mechanochemistry or
for some (not all) gemstones that are cook mix and stir in solvent crystallizable a method of in nano-mold crystallization may be an option.
Limits on atomic precision of surfaces are still unclear, early methods will yield rather bad crystolecules to the point of questionability of calling them crystolecules.
Some may not even be releasable from the mold.

Reactive crystolecules – subsumed edge case

Absence of surface passivation would make the more exotic crystolecules unstable in air or water.
Future larger scale crystolecule based systems will be able to provide excellent vacuum (PPV) though.
Even if passivatable some faces may intentionally be left unpassivated for seamless covalent welding.

Grey zone of definition

Glassolecules

Same as crystolecules just that
the internal structure is not crystalline but pseudoamorphous
i.e. it looks random but it is actually very intentional.
e.g. the result of an optimization process.
See page: kaehler brackets and …
These may require more advanced mechanosynthesis capabilities.

Related page: Amorphous structures

Nanotubolecules & Graphenolecules

Nanotubes & (nano)graphenes (as 2D sheet or 1D nanoribboins):
These existing established concepts do not strongly require atomically precise terminations at their edges
thus they can't be counted as-is to crystolecules
despite fitting other requirements like being crystalline
with a bit of a stretch to 2D or 1D crystallinity.
And a bit of weakening on the stiffness requirement.

Thus here we'll introduce the novel terms
nanotubolecules & graphenolecules (matching to the term "crystolecule") that
add the strong requirement of true full atomic precision, particularly the edges.

Nanotubolecules & graphenolecules
may stretch the concept of crystolecules a bit to 2D & 1D crystals
and to inclusion of lower stiffness structures (due to their typical high aspect ratios).

More formally but a horribly unwieldy mouthful:
atomically precise terminated nano(graphene/tubes).

Future more advanced mechanosynthesis may eventually
in place mechanosynthesize fused structures that contain both …
– 3D structures made from sp3 carbon and
– 2D structures made from sp2 carbon (including rolled up to 1D)
Unless the sp2 part is dominant the resulting structures are best called just crystolecules.
All the same holds for sp2 boron nitride structures. Generally sp2 structures.

As for sp2 and sp3 structures, they may occur even in intermixed ways too.
– Either in a 3D checkerboard crystal. Related page: Pseudo phase diagram
– Or glass like (this is an orthogonal classification, see adjacent section on glassolecules).

Synthesizability:
Unlike crystolecules graphenolecules can (as of 2025) be synthesized
via cook mix and stir thermodynamic synthesis.
Via step wise synthesis followed by on surface synthesis (cyclodehydrogenation) to be precise.
The crucial thing here is the presence of termination control
and some means to pick out the truly atomically precise products.
See page: graphene nanoribbons.

Delineation – what crystolecules must not be confused with

Delineation from nanocrystals

• There is very little control over the precise shape of nanocrystals.
  Nanocrystals are created by natural physical chemistry processes.
  Their shape is the result of thermodynamic equilibria during their history of formation.
  I.e. they are grown via mix cook and stir thermodynamic synthesis.
  Some crystals faces form faster some slower. The slower growing faces remain.
• Nanocrystals seem to always be convex (except in case of twinning).
• Nanocrystals are not atomically precise as there is no precise termination control.
• Larger nanocrystals tend to incur unintentional defects especially low energy ones like stacking order.

Delineation from nanoparticles

Nanoparticles are literally any stuff falling in the nanoscale size class <1000nm.
Nanoparticles are a much more broad concept than crystolecules.

The main concern with nanoparticles is of them being free floating and a health hazard.
With dedicated efforts crystolecules could eventually be made into one form of free nanoparticles.
But such efforts are not needed for getting towards advanced productive nanosystems.

Delineation from foldamer crystals

Crystolecules must not be confused with nanoscale crystals out of folded up polypeptide molecules aka proteins.
Crystals of proteins may seem weird when first encountered.
Micro- to macroscale protein crystals are made today to find the locations of their constituent atoms using X-ray diffraction.

The closest foldamer analog to a crystolecule
in the sense of precisely defined surface and surface passivation)
might be a fully termination controlled monolithic foldamer assembly (wiki-TODO: This may need a name.)
See pages: foldamer, termination control, hierarchical selfassembly

Related but different concepts – intentionally factored apart on this wiki

Crystolecular units

See main page: Crystolecular unit

These are bigger assemblies of basic structural crystolecules.
Assembled from crystolecules either via seamless covalent welding or Van der Waals force sticking and/or shape closing interlocking

Let's use a different name for crystolecules or assemblies of crystolecules that are typically:

• a bit bigger
• also functional in nature not just structural
• not monolithic
• do feature irreversibly enclosed moving parts
• may involve pick and place post assembly (from constituent crystolecules) at the next higher assembly level

Generally crystolecules and crystolecular units will be made from gemstone like compounds.
One subclass already investigated a bit in molecular detail are the crystolecular units made from diamondoid like compound. Specifically some ones made from diamond and moissanite were investigated. See: Examples of diamondoid molecular machine elements.

Diamondoid/Gemstone-based Molecular (Structural and Machine) Elements – term introductions and definitions

Note that this classification is orthogonal to the distinction between
single monolithic crystolecule ~and~ crystolecular unit.
(wiki-TODO: Make a graphic with a 2x2 matrix showing example cases. tetrpod, flexstage/flexgripper/flexhinge, ReChain, bearing/pumps)

Diamondoid or gemstone-based molecular elements (DMEs/GMEs) may come as both.

• Structural elements may lean to the smaller monolithic crystolecule side
  (exception e.g. ReChain frame systems as have slidingly movable elements and decent complexity)
• Machine elements will be crystolecular units (except for monolithic flexures).

Let's use:

• Diamondoid molecular structural elements (DMSEs) for structural ones of all sizes including beside small ones also bigger ones
• Diamondoid molecular machine elements (DMMEs) for functional ones that are typically bigger in size
• Diamondoid molecular elements (DMEs) for structures of all sized including both of the former
• ("Diamondoid" can be replaced by "Gemoid" to include more general gemstone like compounds like e.g. sapphire)
• Or G for D if it's a gemstone that is not diamondoid.

Examples:

• On this wiki: Examples of diamondoid molecular machine elements
• (DMMEs) (examples) like e.g. bearings and gears have completely passivated surfaces.
• (DMSEs) (example) these are typically only partially passivated. They can expose multiple radicals on some of their surfaces that act as AP welding interfaces to complementary surfaces. The assembly step of connecting surface interfaces is here called "seamless covalent welding" and is done in the next higher assembly level (assembly level II?). Seamless covalent welding it usually is irreversible but sparsely linking versions may be reversible.

Naming the base material makes the "crystal" part in "crystolecular" redundant.
So here the choice has been taken to go back to just "molecular" to avoid nesting custom terms.
Well, not fully consistently ATM: Diamondoid crystolecular machine element

Section possibly deprecated due to too many (eight) naming possibilities.
(Diamondoid|Gem-based)(Molecular|Crystolecular)(Structural|Machine)Element

Base material

Specific focus (diamond & co)

Of especially high interest are diamond, its hexagonal version called lonsdaleite, and diamond like compounds.
Many semiconductors fall in this class too.
As of 2025 other compounds still remain largely unexplored for use as crystolecules.

A subset of crystolecules (or gemstone-like molecular elements) are
diamondoid crystolecules (diamondoid molecular elements).

General focus (gemstones)

Gemstone-like compounds are the most suitable base material for crystolecules.
For a collection of gemstones of particular interest see page:
Base materials with high potential.

Beside classical gemstones like diamond other semi-precious minerals including
bio-minerals that are synthesizable in solution also fall under gemstone-like compounds.
Along the incremental path these may be accessible earlier.
See page: technology level IIfor semi advanced precursor technologies.

Some gemstones like periclase MgO and Transition metal nonmetallides (TiC, TiN, TiO)
transition over from mainly covalent to ionic salt like. See next section.

Exotic focus (salts, metals, …)

Use of pure metals and metal alloys is limitedly suitable for crystolecules for a number of reasons.

• Mechanical sliding interfaces can't be done with blank metal on metal surfaces due to seamless metallic welding on contact. Also, surfaces are likely difficult to passivate (for allowing sliding interfaces that way) due to the catalytic nature of metals. A full gemstone layer may suffice (possibly oxidic) but that just goes back to gemstones. Structural applications are less problematic but face issues too.
• Metallic bonds with free electron gas are not directed like covalent bonds and sort of more "slippery". High performance gemstones are notably stronger especially when sticking with one's choice to abundant elements. Best of todays steels will pale compared to say superelastic sapphire based gem-gum. Also (gemstone typical) full breakage might be a preferable digital yes/no failure mode over (metal typical) plastic deformations.
• Metal ad-atoms on metal surfaces tend to diffuse away from where they have been deposited. Likely ok with sticking to flat surfaces during crystolecule usage and with sticking with mechanosynthesis at sufficiently deep cryo temperatures in fabrication.

• Usage of salts like gemstones should face fewer issues than metals structurally in limited scale. Flawless nanoparts will be superelastic but interlocking to make large scale gem-gum faces the issue of seamless ionic welding.
• Salt like gemstones (just like metals) can't be passivated well for sliding interfaces. Salt like gemstones as base material are thus likely mostly useful for structural framework purposes. Possible exception: Enforced non-bonding spacing may allow to play some tricks with discrete notched motion.

How crystolecules will be made and used

From atoms to crystolecules

Buildability: Unfortunately crystolecules and their assemblies
crystolecular (machine) elements cannot be produced yet (state 2015..2025).
See page: Why natural chemistry can not be used to make crystolecules

Mechanosynthesis can start to be prototyped today 2025 with scanning probe microscopy technology.
This does not cover scaling yet. For that see page: Bootstrapping

From smaller crystolecules to larger crystolecules

See page: Seamless covalent welding
Any form of non-bonded assembly (form closure,vdW force, clipping, …)
is not subsumed here but is subsumed in the next section.

From crystolecules to their assemblies

Assembly in advanced productive nanosystems. In advanced nanofactories crystolecules would be:

• assembled from small molecule fragments – in the first assembly level – typically mostly irreversible
• assembled to bigger crystolecular units – in the second assembly level – typically partially irreversible

• Diamondoid molecular machine elements (DMMEs) are assemblies of some diamondoid crystolecules implementing one specific mechanical function
• Diamondoid molecular structural elements (DMSEs) are crystolecules or assemblies of some diamondoid crystolecules implementing a structural function

Misleading aspects in MD simulations of crystolecules and their assemblies

See main page: Misleading aspects in animations of diamondoid molecular machine elements

Beware of the "nanodiamond-is-jelly availability bias" misjudgement

Molecular dynamics simulations are typically run simulating extremely high speeds thus showing jelly like wobbling which would not at all occur when operated at actually proposed (steady state) speeds many orders of magnitude slower.

No, crystolecules (nanoscale diamond or other gemstones) do not normally behave like jelly. It is just that …

• it is so much easier to simulate them at extremely high speeds and …
  
• unlike strong non-rubber macroscale materials they don't break or bent at these speeds and …
  
• unlike macroscale materials they even could dissipate the heat but …
  with the important caveat of being as lone standing nanomachine coupled to cooling bulk.
  

See page: A better intuition for diamondoid nanomachinery than jelly

Beware of the stroboscopic illusion

Simulations of DMEs often show a stroboscopic effect this can be misleading and make one believe that the operation frequencies lie near the thermal frequencies, thereby giving the false impression of enormously high friction.

Why the strobe effect?
To make the machine motion visible in a movie despite them being slow compared to the thermal motions many molecular dynamics simulation frames are dropped and only a few are taken as movie frames. Thus in the movie the atoms are at a random point in their wiggle cycle at each movie frame making them jump around erratically at e.g. at gif file frame rate.

How to fix the strobe effect?
Averaging atom positions for the merged simulation frames and increasing apparent size based on their momentary wiggle amplitude would be an easy huge improvement. Blurring and following even thermal torsional motion of H atoms on OH groups more advanced possibilities.

What else is misleading?
Note that even with the stroboscopic effect fixed simulation speeds are still picked extremely high (m/s to km/s). Way above speeds that were actually proposed for productive nanosystems (mm/s). So there is jelly like wobble visible that would be the rare exception rather than the norm in nanomachine operation. Exception: Rare high energy snaps. Norm steady state near reversible operation.

At proposed speeds gemstone like molecular machine elements with sliding interfaces will work exceptionally well.
See related pages: Superlubricity, Friction in gem-gum technology
There is both experimental evidence and theoretical evidence for that.
(See e.g.: Evaluating the Friction of Rotary Joints in Molecular Machines (paper) and the friction analysis in Nanosystems)

well animated bearing The fast thermal vibrations are more realistically blurred out. The remaining localized periodic average deformations (visible here if one looks closely) are highly reversible. (See page about "superlubrication".)	badly animated bearing The present stroboscopic effect can be misleading in that friction is likely to be grossly overestimated. It deceivingly looks like as if the operating speed would be close to the speed of the thermal vibration. If that were the case it indeed would cause massive friction (strong coupling of motions with similar frequency).
DMME - bearing with blurred out fast vibrations	DMME - bearing with misleading stroboscopic effect

…

History of this page

Since the here described physical objects have no official name yet (2016..2025)
something sensible had to be invented to refer to them in this wiki.

The small & simple initial idea was:
These objects are somewhat of a cross between a crystal and a molecule.
So let's use the term "crystolecule" as a portmanteau.

With time this page amassed a lot of discussion regarding
the choice of terminology and refinement on the definition.
What was later eventually worked out into the extensive definition here.
See the intro of this page.

"crystolecule" is nice because it's:

• quite accurate in descriptiveness
• quite conveniently usable in natural language
• quite memorably (catchy) because it seems unusual (clickbait effect)

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(wiki-TODO: This section is a bit redundant with the definition, maybe to clean up later.)

Specifically let's use the term "crystolecule" for ones that are typically are:

• small – stiff – minimal
• structural
• monolithic (like illustrated)
• do (typically) do not yet feature irreversibly enclosed moving parts – (no form closure yet – there may be exceptions)
• are assembled purely at the first assembly level by force applying mechanosynthesis (direct in place assembly) – exception being seamless covalent welding

Related

• Terminology for parts
• Design of crystolecules
• For components at different size scales see: Components
• Stroboscopic illusion in crystolecule animations
• Example crystolecules
• In place assembly
• putting molecule-fragments together to crystolecules Mechanosynthesis core
• putting crystolecules together to microcomponents Crystolecule assembly robotics

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• Mechanical circuit elements

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Terms for bigger assemblies of several crystolecules but not yet as big (and disassemblable) as microcomponents

• Diamondoid crystolecular machine element – diamond like structure – See: Diamondoid
• Crystolecular machine element – more general gemstone like structure – See: gemstone like compound

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• assembled from molecule fragments
• assembled to crystolecular elements
• assembly is typically irreversible

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• Amorphous structures
• Nanoparticles

External links

At K. Eric Drexlers website:

• A shaft in a sleeve can form a rotary bearing
• Sleeve bearings have been designed and modeled in atomic detail (here shown minus the stroboscopic illusion)

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• structural elements
• machine elements
• Design of Nanomachines using NanoEngineer-1
• "Nanomachines: How the Videos Lie to Scientists" (archive) (old dead link)
• without stroboscopic illusion: Molecular dynamics simulation of small bearing design
• A Low-Friction Molecular Bearing Assembly Tutorial, v1