WO2018093728A1 - Systèmes et procédés pour la mécanosynthèse - Google Patents

Systèmes et procédés pour la mécanosynthèse Download PDF

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Publication number
WO2018093728A1
WO2018093728A1 PCT/US2017/061363 US2017061363W WO2018093728A1 WO 2018093728 A1 WO2018093728 A1 WO 2018093728A1 US 2017061363 W US2017061363 W US 2017061363W WO 2018093728 A1 WO2018093728 A1 WO 2018093728A1
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WO
WIPO (PCT)
Prior art keywords
tip
tips
workpiece
feedstock
reactions
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PCT/US2017/061363
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English (en)
Inventor
Robert A. FRIETAS
Ralph C. Merkle
Jeremy Barton
Aru Hill
Michael Drew
Damian Allis
Tait Takatani
Michael Shawn Marshall
Matthew Kennedy
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Nanofactory Corporation
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
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Publication date
Priority claimed from US15/353,380 external-priority patent/US10067160B2/en
Application filed by Nanofactory Corporation filed Critical Nanofactory Corporation
Priority to US16/325,241 priority Critical patent/US10822229B2/en
Publication of WO2018093728A1 publication Critical patent/WO2018093728A1/fr
Priority to US17/035,844 priority patent/US11148944B2/en
Priority to US17/474,472 priority patent/US11592463B2/en
Priority to US17/531,998 priority patent/US11708384B2/en

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    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82B—NANOSTRUCTURES FORMED BY MANIPULATION OF INDIVIDUAL ATOMS, MOLECULES, OR LIMITED COLLECTIONS OF ATOMS OR MOLECULES AS DISCRETE UNITS; MANUFACTURE OR TREATMENT THEREOF
    • B82B3/00—Manufacture or treatment of nanostructures by manipulation of individual atoms or molecules, or limited collections of atoms or molecules as discrete units
    • B82B3/0009—Forming specific nanostructures
    • B82B3/0038—Manufacturing processes for forming specific nanostructures not provided for in groups B82B3/0014 - B82B3/0033

Definitions

  • the present invention relates generally to the field of mechanosynthesis and in particular to improved methods, systems, and devices for mechanosynthesis.
  • FCL Feedback Controlled Lithography
  • Horizontal atom manipulation relies upon dragging atoms across flat surfaces to place them at specific locations, in effect decorating a surface with atoms.
  • Vertical atom manipulation often referred to as mechanosynthesis, includes the deposition of single atoms or molecules, such as CO, as well as vertical atom interchange, which allows a surface and tip atom to be swapped.
  • each of these atom manipulation techniques modifies a single atomic layer on a surface, does so using a very limited palette of reactions and reactants, and cannot manufacture complex, three-dimensional products.
  • tip materials have been used for atomic manipulation and other uses of SPM.
  • Materials used including metals (e.g., aluminum, iridium, palladium, platinum, tungsten), non-metals (e.g., silicon, germanium, diamond, carbon nanotubes). Combinations may also b used. For example, Pd, Pt, Au, Ir, or Rh films grown on a W(l 11) surface.
  • doped materials other types of inhomogeneous materials (by which we mean the material is not limited to a single type of atom, such as hafnium carbide, tungsten carbide, zirconium carbide), and metals electroplated over other materials.
  • the basic structure of these tips is frequently a very large (compared to a molecule) monolithic piece of material. A point is created on the material, using various techniques such as ablation, chemical functionalization (e.g., CO may be added to the end of some tips to increase resolution), electric field-based techniques (which may include heating the tip while applying the field), etching, electroplating, ion milling, or sputtering.
  • tips may end up having a single atom at their apex, this is not synonymous with being atomically-precise because the bonding pattern of the apical atom to the rest of the tip, and the bonding pattern within the rest of the tip, is not known. Additionally, even if the structure of such tips could be determined via characterization after manufacture, such a process does not have the utility of being able to quickly, reliably, and accurately produce an atomically-precise tip to a particular design specification. Also, with respect to some tips in the literature, including tips functionalized with, e.g., CO, note that CO is adsorbed, not chemically bonded to the tips. Additionally, the geometric relationship of CO with the rest of the tip is not stiff. And, CO in this context is quite unreactive. These properties are fine for the intended use of enhancing scanning resolution, but not for the purposes of the instant invention, as will be seen from the detailed description.
  • FIG. 1 depicts the modular parts of an exemplary tip.
  • FIG. 2 depicts the modular parts of another exemplary tip.
  • FIG. 3 depicts the AbstractionO tip surface-mounted on Silicon.
  • FIG. 4 depicts the HDonationO tip surface-mounted on Silicon.
  • FIG. 5 depicts the C2DonationO tip surface-mounted on Silicon.
  • FIG. 6 depicts the MeDonationO tip surface-mounted on Silicon.
  • FIG. 7 depicts a tip surface-mounted on Silicon which can be SiFBDonationO,
  • GeFBDonationO SiMe3DonationO or GeMe3DonationO.
  • FIG. 8 depicts the AbstractionNH tip surface-mounted on Silicon.
  • FIG. 9 depicts the HDonationNH tip surface-mounted on Silicon.
  • FIG. 10 depicts the C2DonationNH tip surface-mounted on Silicon.
  • FIG. 11 depicts the MeDonationNH tip surface-mounted on Silicon.
  • FIG. 12 depicts a tip surface-mounted on Silicon which can be SiFBDonationNH, GeFBDonationNH, SiMe3DonationNH or GeMe3DonationNH.
  • FIG. 13 depicts the Abstractions tip surface-mounted on Gold.
  • FIG. 14 depicts the UDonationS tip surface-mounted on Gold.
  • FIG. 15 depicts the C2DonationS tip surface-mounted on Gold.
  • FIG. 16 depicts the MeDonationS tip surface-mounted on Gold.
  • FIG. 17 depicts a tip surface-mounted on Silicon which can be SiFBDonationS, GeFBDonationS, SiMe3DonationS or GeMe3DonationS.
  • FIG. 18 depicts a synthetic route for the AbstractionO tip.
  • FIG. 19 depicts a synthetic route for the UDonationO tip.
  • FIG. 20 depicts a synthetic route for the C2DonationO tip.
  • FIG. 21 depicts a synthetic route for the MeDonationO tip.
  • FIG. 22 depicts a synthetic route for the SiFBDonationO tip.
  • FIG. 23 depicts a synthetic route for the GeFBDonationO tip.
  • FIG. 24 depicts a synthetic route for the SiMe3DonationO tip.
  • FIG. 25 depicts a synthetic route for the GeMe3DonationO tip.
  • FIG. 26 depicts a synthetic route for the Abstraction H tip.
  • FIG. 27 depicts a synthetic route for the UDonationO tip.
  • FIG. 28 depicts a synthetic route for the C2DonationO tip.
  • FIG. 29 depicts a synthetic route for the MeDonationO tip.
  • FIG. 30 depicts a synthetic route for the SiFBDonationO tip.
  • FIG. 31 depicts a synthetic route for the GeFBDonationO tip.
  • FIG. 32 depicts a synthetic route for the SiMe3DonationO tip.
  • FIG. 33 depicts a synthetic route for the GeMe3DonationO tip.
  • FIG. 34 depicts a synthetic route for the Abstractions tip.
  • FIG. 35 depicts a synthetic route for the UDonationS tip.
  • FIG. 36 depicts a synthetic route for the C2DonationS tip.
  • FIG. 37 depicts a synthetic route for the MeDonationS tip.
  • FIG. 38 depicts a synthetic route for the SiFBDonationS tip.
  • FIG. 39 depicts a synthetic route for the GeFBDonationS tip.
  • FIG. 40 depicts a synthetic route for the SiMe3DonationS tip.
  • FIG. 41 depicts a synthetic route for the GeMe3DonationS tip.
  • FIG. 42 depicts a synthetic route for the FHD-104X intermediate.
  • FIG. 43 depicts a synthetic route for the FID-103X intermediate.
  • FIG. 44 depicts photo-activation of a halogen-capped tip.
  • FIG. 45 depicts photo-activation of a Barton ester-capped tip.
  • FIG. 46 depicts an exemplary synthesis of a tip with Barton ester cap.
  • FIG. 47 depicts the use of surface-mounted tips where the workpiece moves.
  • FIG. 48 depicts the use of surface-mounted tips where the surface moves.
  • FIG. 49 depicts a metrology setup for measuring six degrees of freedom.
  • FIG. 50a-f depicts a way of implementing the sequential tip method.
  • FIG. 51 depicts a conventional mode tip that can be used for the sequential tip method.
  • FIG. 52a-o depicts a build sequence for building a half-Si-Rad tip.
  • FIG. 53 depicts a synthetic pathway for synthesizing an AdamRad-Br tip.
  • FIG. 54 depicts exemplary methods of using strain to alter affinity.
  • FIG. 55 is a flowchart of an exemplary process for specifying a workpiece.
  • FIG. 56 is a flowchart of an exemplary process for designing reactions.
  • FIG. 57 is a flowchart of an exemplary process for performing reactions.
  • FIG. 58 is a flowchart of an exemplary process for testing reaction outcomes.
  • An "adamantane” molecule comprises a 3D cage structure of ten carbon atoms, each terminated with one or two hydrogen atoms, having the chemical formula C10H16 in its fully hydrogen-terminated form.
  • Adamantane is the smallest possible unit cage of crystalline diamond.
  • An "adamantane-like" structure includes one or more adamantanes, one or more adamantanes where one or more atoms have been substituted with atoms or molecular fragments of like or similar valence, including e.g., Nitrogen, Oxygen, and Sulfur-substituted variations, and similar molecules comprising polycyclic or cage-like structures.
  • adamantane-like structures would include adamantane, heteroadamantanes, polymantanes, lonsdaleite, crystalline silicon or germanium, and versions of each of the foregoing where, for example, Fluorine or another halogen is used for termination instead of Hydrogen, or where termination is incomplete.
  • An "aperiodic" structure e.g., a workpiece or tip
  • a periodic structure is one where the overall shape or atomic constituents do not result directly from the crystal structure or lattice of the workpiece.
  • diamond crystals tend to form an octahedral shape due to the bond angles of the underlying atoms.
  • An octahedral diamond crystal, or variations thereof, could be said to be periodic because both the internal structure and the external shape is determined by the periodic structure of the crystal.
  • a diamond shaped like a car cannot be said to be periodic because, internal structure aside, there is no way the lattice cell of diamond could have specified the shape of a car.
  • aperiodic diamond would be a crystal composed largely of diamond, but with irregular (with respect to the crystal matrix) substitutions made within its matrix, such as the replacement of some carbon atoms with silicon or germanium. Almost any complex shape or part is going to be aperiodic because of its shape, its atomic constituents, or both. Note that aperiodic does not necessarily mean irregular. Take, for example, a conventional gear made of diamond. The round, symmetrical shape of a gear and its teeth are radially symmetric and have a kind of periodicity. However, this periodicity is not derived from the underlying crystal structure. For a structure to be periodic, it is not enough that it be regular; it must be regular in a manner that is derived from its crystal structure.
  • An "atom" includes the standard use of the term, including a radical, which, for example, may be just a proton in the case of H + .
  • atomically-precise in the context of a reaction means where the position and identity of each atom is known to a precision adequate to enable the reaction to be directed to a particular atomic site ("site-specific").
  • site-specific atomic site
  • atomically- precise refers to the actual molecular structure being identical to a specified structure (e.g., as specified by a molecular model or build sequence).
  • Characterization of a non-atomically-precise structure does not render it atomically-precise, as this misses one of the key advantages of atomically-precise materials: That they can be designed ahead of time to have specific characteristics which are unavailable to non-atomically-precise materials, such as having precisely-known chemical behavior, or having superior physical or electrical properties by virtue of being defect-free.
  • the "bridgehead" position in an adamantane-like molecular structure refers to a structural atom that is bonded to three other structural atoms and may be terminated by one or more nonstructural atoms. This is contrasted with a "sidewall” position which refers to a structural atom that is bonded to two other structural atoms and is terminated by one or more nonstructural atoms.
  • a "build sequence” is one or more mechanosynthetic reactions arranged in an ordered sequence that permits the assembly, disassembly, or modification of a workpiece.
  • a "chemical bond” is an interatomic covalent bond, an interatomic ionic bond, or interatomic coordination bond, as these terms are commonly understood by practitioners skilled in the art. Physical adsorption is not a chemical bond.
  • a "chemical reaction” is said to occur when chemical bonds are formed, broken, or altered.
  • Conventional mode is where one or more tips are affixed to a positional means / device (e.g., an SPM probe) to facilitate mechanosynthetic reactions between the tips and a workpiece.
  • a positional means / device e.g., an SPM probe
  • inverted mode where a workpiece is affixed to a positional means and the workpiece moves to the tips.
  • both tips and workpiece could be affixed to a positional means, another way to distinguish between the modes would be to say that if the workpiece is connected to apparatus which indicates that the workpiece is being used as a probe (e.g., if STM is being done through the workpiece), the system is operating in inverted mode. Otherwise, the system is operating in conventional mode.
  • Conventional mode tips are generally affixed to a positional means singly or in small numbers, while in inverted mode, a larger, generally stationary, presentation surface allows the
  • inverted mode and surface mounted tips may be used together, inverted mode should not be conflated with surface-mounted tips.
  • surface-mounted tips can be used in a system which is operating in conventional mode.
  • a "conventional mode tip” is a tip affixed to a positional means or otherwise being employed in conventional mode as described in that definition, just as an “inverted mode tip” is a tip affixed to a presentation surface or otherwise being employed in "inverted mode” as described in that definition.
  • Diamond is a crystal of repeating adamantane cage units arranged in various well- known cry stall ographic lattice geometries.
  • Diamond materials include any stiff covalent solid that is similar to diamond in strength, chemical inertness, or other important material properties, and possesses a three- dimensional network of bonds. Examples of such materials include but are not limited to (1) diamond, including cubic and hexagonal lattices and all primary and vicinal crystallographic surfaces thereof, (2) carbon nanotubes, fullerenes, and other graphene structures, (3) several strong covalent ceramics of which silicon carbide, silicon nitride, and boron nitride are representative, (4) a few very stiff ionic ceramics of which sapphire (monocrystalline aluminum oxide) is representative, and (5) partially substituted variants of the above that are well-known to those skilled in the art.
  • “Feedstock” is the supply of atoms used to perform mechanosynthetic reactions.
  • Feedstock may take the form of one or more atoms, including radicals (e.g., .GeH2, .CH2).
  • Feedstock includes atoms removed from a workpiece.
  • a hydrogen atom from a workpiece may be the feedstock for a hydrogen abstraction tip.
  • feedstock since frequently nothing is subsequently to be done with atoms removed from a workpiece, such feedstock may be referred to as "waste atoms.”
  • Feedstock must be atomically-precise.
  • a "handle structure” comprises a plurality of atoms whose bonding pattern is not altered during a site-specific mechanosynthetic chemical reaction and whose primary function is to hold a tip(s) or workpiece(s) to facilitate a mechanosynthetic chemical reaction when the handle structure is manipulated by a positional device.
  • Handle structure may include the null case (e.g., a tip or workpiece bound directly to a positional means).
  • An "inert environment” includes, but is not limited to, ultra-high vacuum (UHV), argon, nitrogen, helium, neon, or other gases or liquids, either individually or in combination, that do not react with the tip(s), feedstock, or workpiece(s) during mechanosynthetic operations.
  • UHV ultra-high vacuum
  • argon nitrogen, helium, neon, or other gases or liquids, either individually or in combination, that do not react with the tip(s), feedstock, or workpiece(s) during mechanosynthetic operations.
  • Mechanical force may include applied mechanical forces having positive, negative, or zero magnitude.
  • Chemical reactions driven by the application of mechanical force include reactions that are (1) driven through its reaction barrier by mechanically forcing reactants or products through the transition state, or (2) driven away from an undesired reaction by mechanically restraining potentially reactive sites from attaining closer physical proximity, or (3) allowed to occur by bringing potentially reactive sites into closer physical proximity when zero mechanical force is required to do so, as for example when no reaction barrier exists, or when thermal energy alone is sufficient to surmount the reaction barrier.
  • a "meta-tip” is a handle to which multiple tips are attached.
  • a meta-tip could be prepared using a conventional SPM probe with a flat surface on the end, which is then functionalized with multiple tips.
  • a "modular tip” is a tip with a modular design. Modules include an active site, a body, feedstock, legs, and linkers. Some of these modules may be considered to be modular
  • a body contains an active site, and the active site may be said to include feedstock.
  • linkers can be thought of as part of the leg module.
  • a modular tip may be referred to as simply a "tip" when context makes the type of tip clear. Modular tips are atomically-precise. Modular tips, may not be uniform structures (e.g., a pure crystal of silicon or diamond, even if atomically-precise) as this renders the distinction between modules
  • a "positional device” is a device capable of exerting atomically-precise positional control on a mechanosynthetic tip, tool, or workpiece, and may include, but is not limited to, scanning probe microscopes (SPM) and atomic force microscopes (AFM) and related devices, a miniaturized or MEMS-scale SPM or AFM, a robotic arm mechanism of any size scale, or other appropriate manipulation system capable of atomically-precise positional control and appropriate force application.
  • SPM scanning probe microscopes
  • AFM atomic force microscopes
  • Many types of such positional devices are known to those skilled in the art, but for example, actuators can be based upon piezo elements or electrostatics. Metrology based upon piezo elements, or optical (e.g., interferometry), capacitive, or inductive techniques, or other technology, can be used for positional feedback if required.
  • a “presentation surface” is a surface which can be used to bind feedstock or tips for use in mechanosynthesis, and as a base on which to build a workpiece. Although generally monolithic, a presentation surface can be composed of more than one material (e.g., gold and silicon could both be used where each has advantageous aspects), or composed of multiple non- adjacent surfaces. A presentation surface may be referred to simply as a "surface” when context makes the meaning clear. Presentation surfaces include the appropriate area(s) on handle structures and meta-tips. Presentation surfaces are preferably as close as possible to atomically- flat, but this is largely a convenience having to do with standard equipment design, and to facilitate higher speeds and reduced scanning (e.g., to create topological maps of non-flat surfaces), rather than an absolute requirement.
  • Site-specific refers to a mechanosynthetic reaction taking place at a location precise enough that the reaction takes place between specific atoms (e.g., as specified in a build sequence).
  • the positional accuracy required to facilitate site-specific reactions with high reliability is generally sub-angstrom. With some reactions that involve large atoms, or those with wide trajectory margins, positional uncertainty of about 0.3 to 1 angstrom can suffice. More commonly, a positional uncertainty of no more than about 0.2 angstroms is needed for high reliability. Some reactions, for example, due to steric issues, can require higher accuracy, such as 0.1 angstroms. These are not hard cutoffs; rather, the greater the positional uncertainty, the less reliable a reaction will be.
  • a "structural atom" in an adamantane-like molecular structure refers to an atom comprising the cage framework, for example a carbon atom in an adamantane molecule. More generally, a structural atom is an atom that comprises part of the backbone or overall structure in a highly-bonded molecule.
  • a "synthetic tip” is an atomically-precise tip manufactured via a bulk method, such as gas or solution-phase chemistry, rather than via mechanosynthesis.
  • a synthetic tip be referred to as simply a "tip” when context makes the type of tip clear.
  • a synthetic tip does not include uniform structures (e.g., a pure crystal of silicon or diamond, even if atomically-precise).
  • a "terminating atom” refers to an atom that does not serve as a structural atom but absorbs unused valences of a structural atom. For example, a hydrogen atom in an adamantane molecule.
  • a "three-dimensional" workpiece means a workpiece including a lattice of atoms whose covalent structure occupies more than a single plane, discounting bond angles. Under this definition, for example, most proteins (discounting e.g., disulfide inter- or intra-molecular bonds) and other polymers would be two dimensional, as would a plane of graphene. A covalent network solid or a carbon nanotube would be three-dimensional.
  • Tips do not include uniform, unsubstituted structures (e.g., a pure crystal of silicon or diamond); one of the benefits of the atomically-precise tips of the invention is the ability to create a wide range of tips which, by virtue of their heterogeneous atom composition and/or bonding pattern, can have their feedstock and workpiece affinities precisely tailored. Unless otherwise specified, a tip of the invention is atomically-precise.
  • Tip swapping is the process of connecting a new tip and handle structure to a positional means. In conventional SPM, this may be done by, for example, manually changing the probe, or using equipment with probe magazines which hold multiple probes and can automate tip swapping.
  • a "tool” comprises a tip, potentially bonded to a handle, controlled by a positional device or means.
  • a "workpiece” is an apparatus, article of manufacture, or composition of matter, built via mechanosynthesis (and as such is atomically-precise).
  • a system may have more than one workpiece.
  • a workpiece may be connected to, but does not include, non-atomically-precise structures such as a support substrates or pre-existing structures onto which a workpiece is built.
  • a dot is may be used in chemical structures herein to represent an electron, as in the radical group ".CH2".
  • the notation herein generally omits subscript or non-standard characters. Superscript may be written using the " A " character when required for clarity.
  • Feedstock depots are presentation surfaces to which feedstock has been directly bound.
  • Trash depots are surfaces which provide for waste disposal by allowing a tip to transfer unwanted atoms from the tip to the surface.
  • One drawback to this method is the lack of chemical diversity available on the surface(s). On a uniform surface, different feedstock will have different affinity, potentially higher or lower than optimal.
  • Synthetic tips because they can be made via bulk chemistry techniques, are available in very large numbers after synthesis (like the molecules in most bulk chemical reactions, "very large numbers” can mean up to millions, billions, or even far more). Therefore, a large number of synthetic tips could be affixed to a presentation surface.
  • the synthetic tips can be pre-charged (meaning, the tips are already in the chemical state desired to carry out the intended reactions, such as already being bonded to feedstock), and they can include large numbers of every type of tip required for a given build sequence.
  • the presentation surface can serve purposes including being a feedstock depot (the synthetic tips already being charged with their feedstock), a trash depot (e.g., radical tips could be used to bind waste atoms), and a varied collection of tips that can carry out all necessary reactions (for example, almost any number of tips, including all the tips described herein, or in previous work such as
  • WO2014/133529 could be present on a presentation surface, and all in large numbers). Using a large number of synthetic tips also allows each tip to be disposable, rather than requiring recharge for subsequent use, avoiding the need to design and perform recharge operations.
  • a build sequence as a workpiece moving around a presentation surface, aligning itself with a desired tip, and then being brought into contact with that tip with sufficient force to trigger a mechanosynthetic reaction.
  • the tip that was used is then spent, but the presentation surface can provide large numbers of tips.
  • the build sequence proceeds by then aligning the workpiece with the next appropriate unspent tip and bringing them together. This process repeats until the entire workpiece is built.
  • the process of mechanosynthesis may involve scanning the presentation surface to establish a topological map and the positions of the tips to be used. If the tips have been mapped, software can be used to keep track of which locations have been used and which have not.
  • An alternative implementation would be to simply scan for unused tips as they are needed, since a used tip and an unused tip would have markedly different characteristics when evaluated via, e.g., STM.
  • the overarching point is a design which has at least some of the following characteristics and advantages, among others.
  • a plurality of tips can be made available. These tips could be all the same, or could include many different types of tips. If multiple tip types are present, they could be randomly intermingled, segregated by sector or position, or the tips could be laid out in an order which maximizes the efficiency of a build sequence (for example, by arranging different tip sectors in a manner that minimizes the movement required to perform the mechanosynthetic operations to build a particular workpiece, or considering a more general design, locating tips that are apt to be used more frequently closer to the workpiece, or locating tip sectors concentrically around a workpiece to minimize total tip to workpiece distance regardless of the order of reactions).
  • tip recharge may be reduced or eliminated during a build sequence.
  • Each tip can be used once, and then ignored once it is spent. By eliminating recharge reactions, shorter, faster build sequences are facilitated. If additional tips were still required, e.g., for a workpiece requiring a number of tips beyond that which are available, the strategy of mounting a large number of tips, preferably in their ready-to-use state, on a surface, allows the bulk replacement of tips by swapping in a new surface. In this scenario, tip recharge is not completely eliminated, but it is greatly reduced.
  • tips do not have to be swapped for chemical diversity because every type of tip needed for a given build sequence can be present somewhere on the presentation surface. This reduces or eliminates the need for multiple positional means or tip swapping.
  • mechanosynthetic operations are the rate limiting step of a manufacturing process.
  • Exemplary synthetic pathways for multiple synthetic tips are described herein.
  • a presentation surface on the order of square nanometers could provide anywhere from a dozen, to a hundred, or a thousand tips or more.
  • a presentation surface on the order of square microns could provide room for a million, a billion, or more tips.
  • long-distance metrology can allow presentation surfaces on the order of square millimeters or centimeters while still maintaining the requisite positional accuracy.
  • the tips could all be the same (helping to reduce recharge reactions, as described herein), but as chemical diversity is also useful, there could also be almost any number of different types, from two different types, to the at least eight main tip/feedstock combinations described in, e.g., Figs. 3 - 7 (or nine including the later-described AdamRad-Br tip), or even substantially more given the different types of linkers, feedstock, other tip designs that could be used, and the potential desire for tips to facilitate new reactions or that would work under different conditions.
  • Synthetic tips if properly designed, can be chemically bound to a presentation surface, or "surface-mounted.” In addition to being amenable to synthesis using traditional chemistry, and carrying out one or more mechanosynthetic reactions, surface-mounted tips are designed to allow efficient bonding to a presentation surface (often in large quantity).
  • Surface-mounted tips differ from the tips normally used in SPM work in that they are not simply integral to a handle structure (e.g., commercially available tips often have a tip where the crystal structure of the tip is contiguous with the handle structure; essentially the tip is just the end of the handle structure), nor are they a handle structure to which only a trivial functionalization has been added (e.g., a single CO molecule adsorbed to the end of an standard SPM probe tip is a common technique to increase resolution).
  • Surface-mounted tips differ from previously-proposed mechanosynthetically-created tips in that they do not require
  • Binding orientation is one issue that must be addressed when designing surface- mounted tips. It would be preferable that the tips only affix themselves to a surface in a manner that renders them properly oriented for use in mechanosynthetic reactions (although multiple possible orientations could be acceptable given the number of redundant tips that could be present - the system could scan to identify and use only tips in the desired orientation, but this reduces efficiency).
  • the legs need to be reactive enough that they will bind to the presentation surface, but they must resist pathological reactions with themselves or other tips (e.g., forming a leg-leg bond instead of a leg-surface bond, or undergoing any other undesired reactions).
  • themselves or other tips e.g., forming a leg-leg bond instead of a leg-surface bond, or undergoing any other undesired reactions.
  • surface-mounted tips can be thought of as being modular.
  • Each tip can be thought of as having an active site (one or more atoms that bind a desired atom or group of atoms, which could be, e.g., feedstock for a donation reaction, or some moiety to be removed from a workpiece for an abstraction reaction), a body (adamantane or an adamantane derivative in our examples, but other structures could be used given the teachings herein), and one or more legs that serve to attach the tip to a surface.
  • the feedstock of a tip could also be considered a module, as could the surface, which, although not technically part of the tip, can be important to tip design and function.
  • adamantanes are known, and their stiffness (in general, bridged polycyclic structures are one way to provide the stiffness and other characteristics useful in a tip), small size, computational tractability and other favorable characteristics lead us to use these structures as exemplary tips, although many different molecules, including other adamantane-like structures, could serve the same purpose.
  • the active site's main characteristic is that it reliably facilitate the desired reaction on a workpiece.
  • how to efficiently synthesize and deliver tips to a surface, and prepare them for use must be considered in their design.
  • a tip's ready-to- use form includes a radical
  • a tip may incorporate a protective cap (what in solution-phase chemistry is commonly referred to as a "protecting group").
  • This cap reduces the active site's reactivity prior to use to avoid, for example, tip-tip dimerization, binding of the active site to the surface, or other undesired reactions.
  • the cap must be removable so that the tip can be activated for use.
  • the active site frequently comprises a different atom type than the support atoms of the body, due to the advantages of adjusting the chemical reactivity of the active site to be different than that which the base structure might have. This is not always necessary (for example, an all-carbon tip is disclosed here, but it is not appropriate for all reactions).
  • the body may contain, or serve as a point of attachment for, the active site.
  • the body also serves as a point of attachment for one or more legs.
  • the body can also serve to tune the active site, and to isolate it from other chemical influences.
  • tuning the active site for example, substitutions which alter bond lengths, angles, or electronegativity may be used to increase or decrease the affinity of the active site for its feedstock.
  • isolation the body provides chemical isolation from, for example, the legs. Such isolation is one of the aspects of this modular design paradigm that eases the design of new tips by allowing modules to be put together combinatorially.
  • an active site and body combination that accomplish the desired reaction are already known, but one desires to use a different surface which necessitates different legs, it is likely that the new legs can be swapped in without redesign of the body and active site. If the legs were connected directly to the active site, their chemical nature would tend to have more of an effect on the active site, potentially requiring redesign of the body, or unnecessarily constraining the choice of legs.
  • Another characteristic of the body is that it is preferably rigid. A rigid body will tend to be more versatile because a rigid body will better resist deformation when forces are applied to it during mechanosynthetic reactions.
  • the legs serve to attach the body to the surface.
  • the legs preferably have a geometry that permits them to bind the body to a surface without excessive strain, including surfaces that are functionalized prior to leg attachment.
  • Functionalized surfaces such as chlorinated Si, may make longer legs preferable because the, e.g., CI atoms, can be directly under the tip body, making some clearance between the body of the tip and Si surface preferable.
  • Legs are also preferably fairly rigid, and strong enough so that reactions require the application of force proceed reliably rather than the tip tilting, otherwise moving, or breaking a leg bond. While legs that are too short may be unable to bond to the surface reliably, legs that are too long may be too flexible, adding to the positional uncertainty of the tip atoms during a
  • legs can be very short (e.g., a single oxygen atom could serve as each leg).
  • the examples provided depict tips with three legs. Three legs helps provide stability against forces acting upon the active site or feedstock at varied angles, and can reduce the force on any given leg by spreading it amongst all legs.
  • tips with one or two legs could be used, as could tips with four, or more, legs.
  • tips with more than one leg may be usable when not all of their legs have bound to the presentation surface, as long as the required stability is provided.
  • Legs may incorporate linkers (if not, the leg may be considered to also be the linker, or vice versa), which serve to provide a bridge between the rest of the leg and the body or surface.
  • linkers are in providing an appropriate chemistry with which to bind a surface. For example, if the rest of the leg does not have the necessary reactivity or bond strength with a surface, a linker may address the issue. This is demonstrated with the exemplary tips described herein, wherein each tip may have, e.g., a trifluorobenzene leg, and to that leg may be attached a linker which is, e.g., NH, O, or S.
  • Linkers may also be used to adjust the geometry of the legs, for example, helping them to fit the surface lattice spacing better, adjusting their length, or altering their rigidity.
  • Feedstock serves as a source of atoms which can be added to a workpiece and is generally attached to the "top" (with respect to the orientation depicted in, e.g., Fig. 1-17, although the real-world orientation may differ) of the tip to provide access to the feedstock without steric interference from other parts of the tip or the surface.
  • Feedstock is chosen not only by what atom or atoms it contains, but by how it binds to a tip's active site and the desired location on a workpiece. There are many ways, for example, to donate carbon atoms to a workpiece, and examples using C2, CH2, and CH3 are all presented herein. Context will determine which is most appropriate, though often more than one could be used to build a given workpiece, assuming appropriate alterations in the build sequence.
  • the surface must bind to the linkers during the tip binding process, but preferably not to other parts of the tip.
  • the surface's lattice spacing must allow linker binding without excessive strain.
  • the linker-surface bond strength must suffice so that the bonds do not rupture if pulling forces are required.
  • the internal (surface-surface) bonds must be of sufficient strength that, if pulling forces are required, the entire tip, along with one or more surface atoms, is not ripped from the surface.
  • Fig. 1 depicts one version of an abstraction tip that may be used to remove hydrogen, among other moieties, from a workpiece.
  • Radical 101 is used to bind the moiety to be abstracted, and serves as the tip's active site.
  • the active site is connected to body 102, which in this example is adamantane.
  • the body is connected to three methyl group legs, exemplified by leg 103.
  • Each leg contains a sulfur linker, exemplified by linker 104.
  • Each linker is bound to surface 105.
  • Fig. 2 depicts one version of a tip capable of donating hydrogen to many atom types.
  • Active site 201 is a Ge atom, which in this case is part of a substituted adamantane body 202.
  • Trifluorobenzene (which could be viewed as
  • leg 203 trifluorophenol if considered together with the linkers
  • each leg is connected to an oxygen linker 204, which connects to surface 205.
  • Feedstock 206 is connected to active site 201.
  • the set of tips described includes an abstraction tip with a C2-based active site
  • a hydrogen donation tip (capable of extracting many atoms from many different types of workpieces, including, e.g., hydrogen from diamond), a hydrogen donation tip, a C2 donation tip, a Methyl donation tip, and a donation tip which can donate SiH3, GeH3, Si(CH3)3, or Ge(CH3)3, depending on the feedstock attached to the Ge active atom in its substituted adamantane body.
  • each tip is shown with three trifluorobenzene legs which can be linked to either a chlorinated silicon surface, or a partially-hydrogenated partially-chlorinated silicon surface, via an oxygen linker or an NH linker.
  • a version of each tip is also depicted where the legs are methyl groups, using sulfur linkers to connect to an Au surface.
  • FIG. 3 depicts an abstraction tip having a C2-radical-based active site, an adamantane body, trifluorobenzene legs, and oxygen linkers, on a silicon surface (all Si surfaces include, e.g., chlorinated, partially-chlorinated, and partially- hydrogenated, partially-chlorinated Si). This tip will be referred to as AbstractionO.
  • Fig. 3 depicts an abstraction tip having a C2-radical-based active site, an adamantane body, trifluorobenzene legs, and oxygen linkers, on a silicon surface (all Si surfaces include, e.g., chlorinated, partially-chlorinated, and partially- hydrogenated, partially-chlorinated Si). This tip will be referred to as AbstractionO.
  • Fig. 3 depicts an abstraction tip having a C2-radical-based active site, an adamantane body, trifluorobenzene legs, and oxygen linkers, on a silicon surface (all Si surfaces include,
  • FIG. 4 depicts a hydrogen donation tip with hydrogen feedstock, a Ge-based active site incorporated into a substituted adamantane body, trifluorobenzene legs, and oxygen linkers, on a silicon surface.
  • This tip will be referred to as FIDonationO (or "FIDonation,” omitting the specific linker group, to denote any of the variants, a conventional which can apply to any of the tip names).
  • Fig. 5 depicts a C2 donation tip with .C2 feedstock, and otherwise the same structure as Fig. 4.
  • This tip will be referred to as C2DonationO.
  • Fig. 6 depicts a methyl donation tip with .CH2 feedstock, and otherwise the same structure as Fig. 4. This tip will be referred to as
  • MeDonationO Fig 7 depicts a donation tip that can be used to donate a variety of feedstock moieties depending on the identity of the M and R groups.
  • M can be Si or Ge
  • R can be H or CH3, allowing the tip to donate SiH3, GeH3, Si(CH3)3 or Ge(CH3)3.
  • These tips will be referred to, respectively, as SiFBDonationO, GeFBDonationO, SiMe3DonationO, and
  • Fig. 7 has otherwise the same structure as Fig. 4.
  • Figs. 8 - 12 depict tips with the same feedstock (if present), active site, bodies, and legs as Figs. 3 - 7, respectively, but each tip in Figs. 8 - 12 uses NH linkers instead of oxygen linkers to connect to a silicon surface.
  • These tips will be referred to, respectively, as Abstraction H, FIDonation H, C2Donation H, MeDonation H, and for the various versions of Fig. 12, SiFBDonation H, GeFBDonation H, SiMe3Donation H, and GeMe3DonationNH.
  • Figs. 13 - 17 depict tips with the same feedstock (if present), active site, and bodies as Figs. 3 - 7, respectively, but each tip in Figs. 13 - 17 uses methyl legs and a sulfur linker to connect the tip to a gold surface. These tips will be referred to, respectively, as
  • phenylpropargyl alcohol stands for "methyl donation” since that is what the tip does.
  • methyl donation tips With respect to naming via structure and payload, for example, many of the donation tips described herein have Ge- substituted adamantane bodies. With no feedstock, the Ge atom would be a radical, and so may be referred to as "GeRad.”
  • “AdamRad” is an adamantane molecule without the C to Ge substitution, but rather having a radical carbon at the active site. An adamantane can also be substituted with a silicon atom at its active site, which may be called SiRad.
  • Exemplary synthetic pathways for each tip are depicted in Figs. 18 - 41. Note that multiple synthetic pathways for the tip depicted in Figs. 7, 12 and 17 due to the various possible combinations of M and R. Tips with radicals in their active form are synthesized with a protective cap. Procedures for cap removal are described herein.
  • Fig 18 depicts a synthetic pathway for AbstractionO.
  • the synthesis steps are as follows: Commercially available 1,3,5-trihydroxyadamantane reacts with 2,4,6-trifluorophenol while heated between 50-80° C under acidic conditions to give OFA-1. Treating OFA-1 with an excess dimethyldioxirane (DMDO) in acetone at room temperature selectively oxidizes the tertiary C-H bond to give alcohol OFA-2. Using Koch-Haaf conditions (Stetter, H., Schwarz, M., Hirschhorn, A. Chem. Ber. 1959, 92, 1629-1635), CO is formed from the dehydration of formic acid by concentrated sulfuric acid between -5-0° C.
  • DMDO dimethyldioxirane
  • the CO forms a bond with the tertiary carbocation formed from the dehydration of the bridgehead alcohol at room temperature.
  • the carboxylic acid OFA-3 is obtained.
  • Esterifi cation of the carboxylic acid OFA-3 with dry methanol and catalytic sulfuric acid between 40-60° C yields the methyl ester OFA-4.
  • the phenolic -OH groups in OFA-4 are protected with tert-butyldimethylsilyl chloride (TBSC1) in the presence of imidazole at room temperature to give the TBS- silyl ether OFA-5.
  • TBSC1 tert-butyldimethylsilyl chloride
  • the terminal alkyne can be iodinated with N-iodosuccinimide/AgN03 or, alternatively, with 12 in basic methanol.
  • the final global deprotection of the TBS- silyl ether groups is performed with tetra-n-butylammonium fluoride (TBAF). Upon aqueous workup, the AbstractionO tip with free phenol linkers OFA-9 is obtained.
  • Fig 19 depicts a synthetic pathway for FIDonationO.
  • the synthesis steps are as follows: FFID-104X is reduced by excess lithium aluminum hydride in TFIF solvent at 0° C, converting the germanium halide to the germanium hydride FFID-105. Tetra-n-butylammonium fluoride is used to deprotect the tert-butyldimethylsilyl protecting groups from FFID-105 in TFIF to yield the triphenol FHD-106, the HdonationOHtip.
  • Fig 20 depicts a synthetic pathway for C2DonationO.
  • the synthesis steps are as follows: The Grignard reagent ethynylmagnesium bromide in THF solution is added to FHD- 104X dissolved in dry THF and cooled to -78 C dropwise with rapid stirring. The reaction is stirred for 1 hour, warmed to 0 C for 1 hour, and stirred for 1 hour at room temperature to form FC2D-101. FC2D-101 is dissolved in dry THF and cooled to -78 C. A solution of n-butyllithium in hexanes is added and the reaction is stirred for 1 hour at -78 C.
  • FC2D-102 A solution of iodine in dry THF is added and the reaction is allowed to warm to room temperature to yield FC2D-102.
  • FC2D-102 is dissolved in THF and stirred rapidly at room temperature.
  • Tetra-n-butylammonium fluoride is added and the reaction is stirred for 1 hour to yield FC2D-103, the C2DonationO tip.
  • Fig 21 depicts a synthetic pathway for MeDonationO.
  • the synthesis steps are as follows: The germanium halide FHD-104X in THF solution is reduced with lithium metal to generate a lithiated germanium species in situ. The solution is then slowly added dropwise to a solution of 10-fold excess methylene iodide (CH2I2) in THF cooled to 0 C. This method of addition favors the formation iodomethyl germane FMeD-101 over methylene-bridged germanes.
  • CH2I2 10-fold excess methylene iodide
  • Stoichiometric tetra-n-butylammonium fluoride is used to deprotect the tert- butyldimethylsilyl protecting groups from FMeD-lOlin THF to yield the triphenol FMeD-102, the MeDonationO tip.
  • Fig 22 depicts a synthetic pathway for SiH3DonationO.
  • the synthesis steps are as follows: The phenols of FHD-106 are acylated with mesitoyl chloride in dichloromethane with pyridine base. (Corey et al., JACS 1969, 91, 4398) The mesitoate protecting group is utilized due to its stability to the lithiation conditions necessary for FSiHD-102.
  • FSiHD-101 in dry THF solution is deprotonated with n-butyllithium in hexanes at -78 C and slowly warmed to room temperature.
  • FSiHD-102 silylated with chlorotriethoxysilane in THF solution to yield FSiHD-102.
  • FSiHD-102 in dry THF solution is cooled to 0 C and lithium aluminum hydride in THF solution is added to cleave the mesitoate esters and reduce the triethoxysilyl group, yielding FSiFID-103, the SiFBDonationO tip.
  • Fig 23 depicts a synthetic pathway for GeFBDonationO.
  • the synthesis steps are as follows: To form FGeFID-101, the germanium halide FFID-104X in TFIF solution is reduced with lithium metal to generate a lithiated germanium species in situ. The solution is then removed by syringe to separate the lithiated germanium species from the unreacted lithium metal and then slowly added dropwise to a solution of chloro(phenyl)germane (Ohshita, J.; Toyoshima, Y.; Iwata, A.; Tang, H.; Kunai, A. Chem. Lett. 2001, 886-887) in THF cooled to 0 C.
  • chloro(phenyl)germane Ohshita, J.; Toyoshima, Y.; Iwata, A.; Tang, H.; Kunai, A. Chem. Lett. 2001, 886-887
  • FGeHD-101 is dephenylated with trifluoromethanesufonic acid in dichloromethane at 0 C.
  • the crude reaction isolate after neutralization and workup is then dissolved in dry THF.
  • the reaction is cooled to 0 C and lithium aluminum hydride is added dropwise to produce the germane FGeHD-102, the GeH3DonationO tip.
  • Fig 24 depicts a synthetic pathway for SiMe3DonationO.
  • the synthesis steps are as follows: To prepare FSiHD-101, the phenols of FHD-106 are acylated with mesitoyl chloride in dichloromethane with pyridine base. (Corey et al., JACS 1969, 91, 4398) The mesitoate protecting group is utilitized due to its stability to the lithiation conditions necessary for FSiHD- 102.
  • FSiHD-101 in dry THF solution is deprotonated with n-butyllithium in hexanes at -78 C and slowly warmed to room temperature.
  • FSiMeD-102 silylated with trimethylsilyl chloride in THF solution to yield FSiMeD-102.
  • FSiMeD-102 in dry THF solution is cooled to 0 C and lithium aluminum hydride in THF solution is added to cleave the mesitoate esters, yielding FSiMeD-103, the SiMe3DonationO tip.
  • Fig 25 depicts a synthetic pathway for GeMe3DonationO.
  • the synthesis steps are as follows: To prepare FGeMeD-101, the germanium halide FHD-104X in THF solution is reduced with lithium metal to generate a lithiated germanium species in situ. The solution is then removed by syringe to separate the lithiated germanium species from the unreacted lithium metal and then slowly added dropwise to a solution of trimethylgermanium chloride in THF cooled to 0 C. It is necessary to separate the lithiated germanium species from excess lithium metal before addition to the trimethylgermanium chloride because lithium is capable of exchange reactions with germanium halides. Stoichiometric tetra-n-butylammonium fluoride is used to deprotect the tert-butyldimethylsilyl protecting groups from FMeD-101 in THF to yield the triphenol
  • Fig 26 depicts a synthetic pathway for Abstraction H.
  • the synthesis steps are as follows: Commercially available 1,3,5-trihydroxyadamantane reacts with 2,4,6-trifluoroaniline while heated to 50-80° C under acidic conditions in 1,2-dichloroethane to give NFA-1. Treating NFA-1 tetrafluorobonc acid forms the tetrafluorob orate amine salt in situ to prevent oxidation of the amines. (Asencio, G., Gonzalez-Nunez, M. E., Bernardini, C. B., Mello, R., Adam, W. J. Am. Chem. Soc, 1993, 115, 7250-7253) Following the salt formation, an excess of
  • Esterification of NFA-3 with dry methanol and catalytic sulfuric acid yields the ester NFA-4 that can be reduced readily with diisobutylaluminum hydride.
  • Di-tert-butyl-dicarbonate (Boc20) is used to protect the -NH2 groups and to be removable by acid hydrolysis.
  • Treating NFA-4 with Boc20 yields the protected compound NFA-5.
  • Reduction of the methyl ester with LiAlH4 in tetrahydrofuran (TFIF) gives the methyl alcohol NFA-6.
  • Oxidation of the methyl alcohol to the aldehyde NFA-7 proceeds with catalytic tetrapropylammonium perruthenate (TPAP) and stoichiometric N-methylmorpholine-N-oxide (NMO). The presence of 4 A
  • the aldehyde in THF is added to a premixed solution of iodoform (CHI3), triphenylphosphine, and potassium tert-butoxide at room temperature in THF to undergo a carbon-carbon bond forming reaction to give the 1, 1- diiodoalkene.
  • iodoform CHI3
  • triphenylphosphine triphenylphosphine
  • potassium tert-butoxide iodoform
  • Single elimination of iodide with careful temperature (-78° to -50° C) and excess potassium tert-butoxide control yields the iodoalkyne NFA-8.
  • the terminal alkyne can be iodinated with N-iodosuccinimide/AgN03 or, alternatively, with 12 in basic methanol.
  • the final global deprotection of the Boc- groups is performed with trifluoroacetic acid (TFA) in dichloromethane at RT.
  • TFA-9 trifluoroacetic acid
  • Fig 27 depicts a synthetic pathway for HDonation H.
  • HD-103X in dry THF solution is cooled to 0 C and lithium aluminum hydride in THF solution is added to reduce the germanium halide, yielding HD-104.
  • HD-104 is dissolved in dry MeOH and added to a reaction vessel suitable for pressurized hydrogenations. Palladium hydroxide catalyst is added and the vessel pressurized with hydrogen gas. Agitation of the reaction under the pressurized hydrogen atmosphere yields HD-105, the HDonationNH tip.
  • Fig 28 depicts a synthetic pathway for C2DonationNH.
  • the synthesis steps are as follows: (Triisopropylsilyl)acetylene is dissolved in dry THF and cooled to -78 C. n- Butyllithium solution in hexanes is slowly added dropwise to deprotonate the acetylene hydrogen. The solution is stirred for 1 hour, allowed to warm to room temperature, and is added dropwise to NHD-103X in dry THF solution cooled to -78 C. The reaction is stirred for 1 hour, warmed to 0 C for 1 hour, and stirred for 1 hour at room temperature to form NC2D-101.
  • NC2D-101 is dissolved in dry MeOH and added to a reaction vessel suitable for pressurized hydrogenations. Palladium hydroxide catalyst is added and the vessel pressurized with hydrogen gas. Agitation of the reaction under the pressurized hydrogen atmosphere yields NC2D-102.
  • the steric bulk of both the triisopropylsilyl group and the germaadamantane core prevent
  • NC2D-102 is dissolved in THF and stirred rapidly at room temperature. Tetra-n-butylammonium fluoride is added and the reaction is stirred for 1 hour at RT to yield NC2D-103.
  • NC2D-103 is dissolved in MeOH and rapidly stirred. Potassium hydroxide is added and a solution of iodine in methanol is added slowly dropwise at RT to yield NC2D-104, the C2DonationNH tip.
  • Fig 29 depicts a synthetic pathway for MeDonationNH.
  • the synthesis steps are as follows: The germanium halide NHD-103X in THF solution is reduced with lithium metal to generate a lithiated germanium species in situ. The solution is then slowly added dropwise to a solution of 10-fold excess methylene iodine (CH2I2) in THF cooled to 0 C. This method of addition favors the formation iodom ethyl germane NMeD-101 over methylene-bridged germanes.
  • NMeD-101 is dissolved in dry MeOH and added to a reaction vessel suitable for pressurized hydrogenations. Palladium hydroxide catalyst is added and the vessel pressurized with hydrogen gas. Agitation of the reaction under the pressurized hydrogen atmosphere yields NMeD-102, the MeDonationNH tip.
  • Fig 30 depicts a synthetic pathway for SiH3DonationNH.
  • the synthesis steps are as follows: The germanium halide NHD-103X in THF solution is reduced with lithium metal at - 78 C to generate a lithiated germanium species in situ. The solution is then removed by syringe to separate the lithiated germanium species from the unreacted lithium metal and then slowly added dropwise to a solution of excess chlorotriethoxysilane in THF cooled to 0 C and the reaction is allowed to warm to room temperature to produce NSiHD-101. NSiHD-101 in THF solution cooled to 0 C is reduced with lithium aluminum hydride to generate NSiHD-102.
  • NSiHD-102 is dissolved in cyclohexane and added to a reaction vessel suitable for pressurized hydrogenations. Palladium hydroxide catalyst is added and the vessel pressurized with hydrogen gas. Agitation of the reaction under the pressurized hydrogen atmosphere yields NSiHD-103, the SiH3DonationNH tip.
  • Fig 31 depicts a synthetic pathway for GeH3Donation H.
  • the synthesis steps are as follows: The germanium halide HD-103X in THF solution is reduced with lithium metal at - 78 C to generate a lithiated germanium species in situ. The solution is then removed by syringe to separate the lithiated germanium species from the unreacted lithium metal and then slowly added dropwise to a solution of chloro(phenyl)germane in THF cooled to 0 C and the reaction is allowed to warm to room temperature to produce NGeHD-101. It is necessary to separate the lithiated germanium species from excess lithium metal before addition to the
  • NGeHD-101 is dephenylated with trifluoromethanesufonic acid at 0 C.
  • the crude reaction isolate after neutralization of acid and workup is then dissolved in dry THF.
  • the reaction is cooled to 0 C and lithium aluminum hydride is added to produce the germane NGeHD-102.
  • NGeHD-102 is dissolved in cyclohexane and added to a reaction vessel suitable for pressurized hydrogenations. Palladium hydroxide catalyst is added and the vessel pressurized with hydrogen gas. Agitation of the reaction under the pressurized hydrogen atmosphere yields NGeHD-103, the GeH3DonationNH tip.
  • Fig 32 depicts a synthetic pathway for SiMe3DonationNH.
  • the synthesis steps are as follows: The germanium halide NHD-103X in THF solution is reduced with lithium metal at -78 C to generate a lithiated germanium species in situ. The solution is then removed by syringe to separate the lithiated germanium species from the unreacted lithium metal and then slowly added dropwise to a solution of excess chlorotrimethylsilane in THF cooled to 0 C and the reaction is allowed to warm to room temperature to produce NSiMeD-101. NSiMeD-101 is dissolved in cyclohexane and added to a reaction vessel suitable for pressurized hydrogenations. Palladium hydroxide catalyst is added and the vessel pressurized with hydrogen gas. Agitation of the reaction under the pressurized hydrogen atmosphere yields NSiMeD-102, the SiMe3DonationNH tip.
  • Fig 33 depicts a synthetic pathway for GeMe3Donation H.
  • the synthesis steps are as follows: The germanium halide HD-103X in THF solution is reduced with lithium metal at -78 C to generate a lithiated germanium species in situ. The solution is then removed by syringe to separate the lithiated germanium species from the unreacted lithium metal and then slowly added dropwise to a solution of trimethylgermanium chloride in THF cooled to 0 C and the reaction is allowed to warm to room temperature to produce NGeMeD-101. It is necessary to separate the lithiated germanium species from excess lithium metal before addition to the trimethylgermanium chloride to prevent lithium reduction of the germanium chloride.
  • NGeMeD- 101 is dissolved in cyclohexane and added to a reaction vessel suitable for pressurized hydrogenations. Palladium hydroxide catalyst is added and the vessel pressurized with hydrogen gas. Agitation of the reaction under the pressurized hydrogen atmosphere yields NGeMeD-102, the GeMe3DonationNH tip.
  • Fig 34 depicts a synthetic pathway for Abstractions.
  • the synthesis steps are as follows: Commercially available 1-bromoadamantane undergoes a Friedel-Crafts alkylation with three separate benzene molecules under Lewis acidic conditions with A1C13 at 90 C to yield SHA-1. Careful control of the stoichiometry of the tert-butyl bromide (2.0 equivalents) yields the 1,3,5-triphenyl adamantane (Newman, H. Synthesis, 1972, 12, 692-693). Treatment of SHA-1 in fluorobenzene and 50% aqueous NaOH solution with a phase transfer catalyst gives SHA-2.
  • Fig 35 depicts a synthetic pathway for HDonationS.
  • the synthesis steps are as follows: Allowing RHD-101 to react with benzene and trifluoroacetic acid (TFA) at room temperature in dichlorom ethane forms the triphenylgermaadamantane SHD-101. Oxidative cleavage of the phenyl groups with catalytic RuC13 in a solvent mixture of CC14, CH3CN, and H20 with periodic acid added as stoichiometric oxidant cleaves the aromatic rings between 0° C to room temperature gives the tricarboxylic acid SHD-102.
  • TFA trifluoroacetic acid
  • Treating the resulting Ge-X compound SHD-106X with LiAlH4 at 0° C to room temperature reduces the Ge-X bond as well as simultaneously removing the thioacetate groups from the thiols to yield the trithiol SHD-107, the HDonationS tip, upon aqueous workup.
  • Fig 36 depicts a synthetic pathway for C2DonationS.
  • the synthesis steps are as follows: The intermediate SHD-106X from the HDonationS synthesis is allowed to react with an excess of commercially available ethynylmagnesium bromide solution in diethyl ether at 0° C to room temperature to form SC2D-101. The excess of the ethynylmagnesium bromide ensures full deprotection of the thioacetate protective groups upon aqueous workup. The thiols in SC2D-101 are protected with acetate groups by treating it with acetic anhydride (Ac20).
  • Fig 37 depicts a synthetic pathway for MeDonationS.
  • the synthesis steps are as follows: The synthesis of the thiol methyl donation tool begins from intermediate SHD-105. The acetate groups must be exchanged with a thioether protective group, specifically the tert-butyl group, to withstand the synthetic conditions.
  • SMeD-101 The acetate groups are removed in basic methanol at room temperature and then subsequently treated with an acidic solution of tert-butanol at room temperature to form SMeD-101.
  • the Ge-Me bond is cleaved with a Lewis acid between -78° C and room temperature with a reagent such as SnC14, 12, or Br2 to yield the Ge-Cl bond in SMeD-102X.
  • a reagent such as SnC14, 12, or Br2
  • Fig 38 depicts a synthetic pathway for SiH3 Donations.
  • the synthesis steps are as follows: Intermediate SMeD-102X with t-butyl protected thiols is treated with lithium metal in THF at 0° C followed by the addition of triethoxychlorosilane to give SSiHD-101 upon workup. This reaction forms the Ge-Si bond necessary for the SiH3 donor.
  • the removal of the t-butyl groups is performed with the reagent 2-nitrobenzenesulfenyl chloride in acetic acid at room temperature to give the mixed disulfide.
  • Treatment with LiAlH4 cleaves the S-S bonds to give the free thiols in SSiHD-102, the SiH3DonationS tip, as well as simultaneously reducing the triethoxysilyl group to -SiH3.
  • Fig 39 depicts a synthetic pathway for GeH3DonationS.
  • the synthesis steps are as follows: Intermediate SMeD-102X with t-butyl protected thiols is treated with lithium metal in THF at -78° C. The solution is then removed by syringe to separate the lithiated germanium species from the unreacted lithium metal and then slowly added dropwise to a solution of PhGeH2Cl at 0° C to give SGeHD-101 upon workup. This reaction forms the Ge-Ge bond necessary for the -GeH3 donor. Treatment of SGeHD-101 with triflic acid cleaves the Ph-Ge bond to form a Ge-OS02CF3 bond.
  • Triflic acid also removes of the t-butyl thioether groups.
  • Treatment of the this intermediate with LiAlH4 in diethyl ether at 0° C cleaves any S-S bonds to give the free thiols in SGeHD-102, the GeH3DonationS tip, as well as simultaneously reducing the Ge triflate group to -GeH3.
  • Fig 40 depicts a synthetic pathway for SiMe3DonationS. The synthesis steps are as follows: Intermediate SMeD-102X with t-butyl protected thiols is treated with lithium metal in THF at -78 C followed by the addition of chlorotrimethylsilane upon warming to 0° C.
  • Fig 41 depicts a synthetic pathway for GeMe3DonationS.
  • the synthesis steps are as follows: Intermediate SMeD-102X with t-butyl protected thiols is treated with lithium metal in THF at -78 C. The solution is then removed by syringe to separate the lithiated germanium species from the unreacted lithium metal and then slowly added dropwise to a solution of chlorotrimethylgermane at 0 C. Upon workup the compound SGeMeD-101 with the Ge-Ge bond is obtained. The removal of the t-butyl groups is performed with the reagent 2- nitrobenzenesulfenyl chloride in acetic acid at room temperature to give the mixed disulfide. Treatment with NaBH4 in chloroform and methanol at room temperature cleaves the S-S bonds to give the free thiols in SGeMeD-102, the GeMe3DonationS tip.
  • Fig 42 depicts a synthetic pathway for intermediate FHD-104X, from which some of the other syntheses begin.
  • the synthesis steps are as follows: Cis, cis-Tri-O-alkyl 1,3,5- Cyclohexanetricarboxylate is reduced with lithium aluminum hydride in refluxing THF and vigorous mechanical stirring to yield cis, cis- l,3,5-tris(hydroxymethyl)cyclohexane HD-1.
  • the procedure used resembles that found in Boudjouk et al., Organometallics 1983, 2, 336.
  • Cis, cis- l,3,5-Tris(hydroxymethyl)cyclohexane, HD-1 is brominated utilizing triphenylphosphine dibromide generated in situ. This is accomplished by slow addition of bromine to a solution of the triol and triphenylphosphine in DMF at room temperature to yield cis, cis-1,3,5- tris(bromomethyl)cyclohexane, HD-2.
  • the procedure used resembles that found in Boudjouk et al., Organometallics 1983, 2, 336.
  • the tri-Grignard is generated in situ by adding cis, cis-1,3,5- Tris(bromomethyl)cyclohexane, HD-2, at room temperature to magnesium turnings in THF and heating to reflux.
  • the tri-Grignard is then transferred to a second reaction vessel to separate the reagent from the excess magnesium turnings (Mg is capable of inserting into a Ge-Cl bond).
  • Trimethylchlorogermane previously dried over calcium hydride and degassed, is added slowly dropwise to the reaction at 0 C. After 2 hours, the reaction is warmed to room temperature for two hours, and finally refluxed overnight.
  • the reaction yields predominantly cis, cis-1,3,5- Tris(trimethylgermylmethyl)cyclohexane, HD-3.
  • Cis, cis-l,3-dimethyl-5- (trimethylgermylmethyl)cyclohexane and cis, cis-l-methyl-3,5- bis(trimethylgermylmethyl)cyclohexane are also produced in small amounts.
  • the procedure used is similar to that found in Boudjouk and Kapfer, Journal of Organometallic Chemistry, 1983, 296, 339.
  • HD-3 in benzene solution is subjected to redistribution reaction conditions using high purity anhydrous aluminum trichloride and heating to reflux to yield 1 -methyl- 1- germaadamantane.
  • HD-3 side products cis, cis-l,3-dimethyl-5- (trimethylgermylmethyl)cyclohexane and cis, cis-l-methyl-3,5- bis(trimethylgermylmethyl)cyclohexane may also be present in the reaction or isolated and reacted under these conditions to yield HD-4 as well.
  • HD-4 is reacted with excess "ketone free" dimethyldioxirane (DMDO) (Crandall, J. K. 2005. Dimethyldioxirane. e-EROS Encyclopedia of Reagents for Organic Synthesis.) in methylene chloride solution at -20 C to yield l-methyl-3,5,7- trihydroxy-l-germaadamantane RHD-101.
  • DMDO dimethyldioxirane
  • RHD-101 The absence of acetone in the reaction conditions allows for RHD-101 to precipitate from the reaction mixture, preventing over-oxidation.
  • isopropyl alcohol is used to quench the excess DMDO, preventing over-oxidation by excess reagent during reaction workup.
  • RHD-101 is subjected to strongly acidic conditions in the presence of 2,4,6-trifluorophenol at room temperature to yield FHD-102.
  • the use of Bransted acidic conditions favors carbocation formation at the 3,5,7 bridgehead positions of the adamantane cage structure over redistribution reactivity at the germanium center.
  • Reagents include, but are not limited to: Lewis acids such as SnC14 or GaC13, elemental halides Br2 and 12 with Lewis acid catalyst, alkyl halides such as isopropyl chloride with Lewis acid catalyst, and interhalogen compounds such as IBr and IC1.
  • heavier FHD-103X halides can be converted to lighter halides utilizing the appropriate lighter silver halide (e.g. FHD-103Br and AgCl will produce FHD-103C1).
  • Fig. 43 depicts a synthetic pathway for intermediate HD-103X, from which some of the other syntheses begin.
  • the synthesis steps are as follows: RHD-101 is subjected to strongly acidic conditions such as methanesulfonic acid in the presence of 2,4,6-trifluoroaniline at room temperature to yield HD-102.
  • strongly acidic conditions such as methanesulfonic acid
  • 2,4,6-trifluoroaniline at room temperature
  • HD-103 HD-102 is alkylated at room temperature with 4-methoxybenzyl bromide in DMF with potassium carbonate base in the presence of potassium iodide.
  • Reagents include, but are not limited to: Lewis acids such as SnC14 or GaC13, elemental halides Br2 and 12 with Lewis acid catalyst, alkyl halides such as isopropyl chloride with Lewis acid catalyst, and interhalogen compounds such as IBr and IC1.
  • Lewis acids such as SnC14 or GaC13
  • elemental halides Br2 and 12 with Lewis acid catalyst alkyl halides such as isopropyl chloride with Lewis acid catalyst
  • interhalogen compounds such as IBr and IC1.
  • heavier NHD-103X halides can be converted to lighter halides utilizing the appropriate lighter silver halide (e.g. NHD-103Br and AgCl will produce NHD-103 CI).
  • Various exemplary surfaces are described herein, including diamond, silicon and gold. Preferably, these surfaces would more specifically be depassivated diamond, partially- hydrogenated partially-chlorinated Si(l 11), and Au(l 11). Of course, similar surfaces could be used, including germanium, and lead, although they may require leg or linker modifications.
  • Partially-hydrogenated partially-chlorinated Si(l 11) is used in preference to a fully-chlorinated Si surface because the partial chlorination reduces the energy barrier to the tip molecules binding as compared to just chlorinated Si(l 11) because the hydrogen, being smaller in size than CI, helps reduce steric congestion as the tip approaches the surface. Hydrogenation is preferably in the 33% - 50% range, although wider ranges will work, as will not using hydrogenation at all. Partially hydrogenated partially-chlorinated Si(l 11) can be prepared in a number of ways. One is the following.
  • the Si(l 11) surface can be chlorinated by depositing C12 from an electrochemical cell similar to the one in J Vac Sci and Tech A 1, 1554 (1983), while the Si(l 11) is heated to -400C. Atomically flat halogenated Si(l 11) surfaces have been prepared this way, as in Phys Rev Lett 78, 98 (1997).
  • Si(l 11)-C1 surfaces can then be partially hydrogenated by exposing the surface to
  • a tip can be bound to a presentation surface, including large surfaces , and smaller surfaces such as meta-tips or a single-tip tool surface. Many ways of binding tips to surfaces are possible, and these may vary with the exact nature of the tip and the surface.
  • a simple way to evaporate molecules is to place the molecules in a glass or alumina crucible with a tungsten wire wrapped around the crucible. Passing a current through the wire heats the crucible and molecules, generating a molecular gas that exits the front of the crucible. A thermocouple on the crucible measures its temperature. A quartz crystal
  • microbalance can be used to determine how much is evaporating as a function of time and temperature.
  • Tips particularly those with exposed radicals at their active site, may be bonded to a surface in an inactive form.
  • One method of activating such tips is through photo-cleavage of the structure.
  • the halogen-capped tip examples herein can be activated through exposure to 254nm light.
  • Fig. 44 depicts an activating reaction for halogen-capped tips.
  • Other wavelengths and chemistries can also be used. For example, if different synthetic steps were used, a tip could be protected with a Barton ester, which can then be cleaved, activating the tip, with 365nm light.
  • Fig. 45 provides an example of the activation reaction that could be used with a Barton ester.
  • photo-activation is convenient in that different areas of a surface can be masked. Different wavelengths can also be used, choosing wavelengths which affect some tips but not others. This makes photo-activation a versatile technique even when multiple types of tips are present, or when potentially-complex layout patterns are desired.
  • Fig. 46 depicts the synthesis of the Barton ester AbstractionO tip, which is as follows: To synthesize the Barton ester for photoactivation, propynoic acid OFAB-1 is made from OFA-7 using the traditional Corey -Fuchs procedure and quenching by bubbling gaseous C02 through the reaction mixture. (Corey, E. J., Fuchs, P. L. Tetrahedron Lett. 1972, 36, 3769- 3772) The first step forms the 1,1-dibromoalkene in solution at -78 C. The addition of 2 more equivalents of butyllithium forms the lithium acetylide in the reaction mixture.
  • carboxylic acid derivative OFAB-1 is activated to the acid halide by oxalic acid and catalytic ⁇ , ⁇ -dimethylformamide (DMF) in dichloromethane at room
  • Another method is to use OFAB-2 and catalytic solid tetra-n-butylammonium fluoride (TBAF) or cesium fluoride in 100: 1 THF -buffer solution to produce OFAB-3.
  • TBAF catalytic solid tetra-n-butylammonium fluoride
  • CFA cesium fluoride
  • handle 4701 is connected to surface 4702.
  • Surface 4702 is optional, serving to provide the desired materials and chemistry to bind workpiece 4703 in the case where the material of the handle is unsuitable for doing this directly. It may be possible to bind workpiece 4703 directly to handle 4701.
  • Handle 4701 would be connected to a positional means (not shown) for the purposes of moving handle 4701, and thereby workpiece 4703 with respect to tips (of which tip 4704 is representative) mounted on surface 4705.
  • workpiece 4703 could be descending upon a tip, or it could be rising from just having been acted upon by a tip. Regardless, the point is that surface 4705 can contain many tips, of many different types, including non-functional tips (which either failed to synthesize correctly or have already been used).
  • Knowledge of tip position for example, because sectoring was used to place certain tip types in certain locations, or via scanning the surface (before or during a build sequence), allows the workpiece to be moved to a desired tip, at which time a mechanosynthetic reaction occurs, and the workpiece then moves to the next desired tip. This process is repeated until the workpiece is complete.
  • FIG. 48 depicts this mode of using surface-mounted tips, where handle 4801 is connected to (optional) surface 4802. Handle 4801 is also connected to a positional means (not shown). Tips, of which tip 4804 is representative, are shown mounted on surface 4802, but could be mounted directly to handle 4801. In this scenario, the tips move to act upon workpiece 4803, which resides upon surface 4805.
  • Fig. 48 perhaps provides the clearest illustration of the advantages surface- mounted tips have over previous mechanosynthesis techniques. If surface 4802 only had one tip affixed to it, it would be analogous to the tips commonly used for mechanosynthesis. In this scenario, to create complex workpieces, the affixed tip would have to a) be capable of multiple reactions and b) be regenerated frequently, or, frequent tip swapping employed. Using either the scenario of Fig. 47 or Fig. 48 (and modifications thereof which would be possible given the teachings herein), many tips are available to provide mechanosynthetic reactions, potentially (depending on the number of tips initially available and the number of reactions required to build the workpiece) without tip recharge and without tip swapping. Any reduction in tip recharge or tip swapping can help decrease the average time it takes to perform a reaction.
  • the total number of available tips could span a very wide range, depending on factors such as the total number of reactions needed to make a workpiece, the number of different types of reactions needed to make a workpiece, the available size of the presentation surface, and the exact methods being used. Also, it is conceptually important to distinguish between the total number of available tips, and the number of different types of tips.
  • the number of tips might be limited to only providing one tip for each type of reaction needed by a build sequence. For example, as described herein, one way of building diamond requires four different tips (and row initiation and termination each take only three tips, while row extension requires four). Ignoring feedstock and differences only in legs or linkers, about 7 different types of tips are described herein. Counting feedstock, given the structures in Table 1, in addition to those in, e.g., Figs. 1- 17 and Fig. 51, this number becomes about 20 or more since some tips can use a variety of feedstocks. Given these examples, it will be obvious that the number of types of tips present in a system can include less than 4, 4 to 7, 8 to 20, or more. Note that this says nothing about the number of positional means in a system, since multiple types of tips can be affixed to a single positional means.
  • each type of tip would be present at least as many times as that tip is used in a build sequence. Given that build sequences can essentially be arbitrarily long, this is one example where it becomes useful to have the total number of tips present be, e.g., 10 to 100 for even quite small workpieces, and between one hundred and a thousand, or between a thousand and a million, or between a million and a billion, or more, for larger workpieces.
  • the presentation surface can hold a very large number of tips.
  • the number of reactions required to a build a workpiece may not be synonymous with the number of atoms within that workpiece. For example, it if quite possible for a 100 atom workpiece to require 200 reactions due to intermediate passivation steps or other complications. Conversely, e.g., if dimers were used as feedstock, it is possible that a 100 atom workpiece could require less than 100 reactions.
  • Typical commercial atomic microscopy systems combine course and fine motion controllers to provide both long range of motion, and atomic resolution.
  • LT Nanoprobe provides a pre-integrated SPM, having 4 probe tips, a course motion controller with a range of 5mm x 5mm x 3mm, a fine motion controller with a range of lum x lum x 0.3um, and atomic resolution in STM mode.
  • Such equipment suffices for mechanosynthesis work, and given that mechanosynthesis work has been carried out for decades, even what would currently be considered outdated equipment can suffice.
  • typical SPM equipment is not optimized for carrying out high-volume mechanosynthetic reactions.
  • Typical SPM work involves analysis rather than manufacture, the point generally being to scan specimens to create an image or collect other data. Scan speed is frequently the limiting factor, and increasing scan speed is an active area of research (Dai, Zhu et al., "High-speed metrological large range AFM,” Measurement Science and Technology. 2015. 26:095402).
  • Scan speed is less important to systems for mechanosynthesis as long as the system can obtain the necessary accuracy without scanning, which is well within the state-of-the- art.
  • systems adapted for mechanosynthesis would not need to scan, at least for position determination or refinement.
  • some scanning will probably be necessary, including an initial surface scan to map surface topology and tip location and identity, and, if desired, small areas around a reaction site could be scanned after a reaction to verify that the reaction occurred correctly (it should be noted that this may not be necessary given the extremely high reliability of many of the exemplary reactions). Note that such scanning and tip or workpiece
  • the tip is generally not exactly at the point being measured (which may be, e.g., a reflective flat when using laser interferometry), such metrology has to be carefully implemented to avoid, e.g., Abbe error which can be induced by slightly nonlinear movement of the tip or workpiece with respect to, e.g., the reflective flat.
  • One way to address this issue it to measure not only the X, Y and Z coordinates of the reflective flat, but also to measure (and so be able to account for) any rotation that might be occurring around these axis as well.
  • Fig. 49 illustrates one way
  • interferometers can be used to measure six degrees of freedom (X, Y, and Z, and rotation about each of those axes).
  • BeamZl 4907, BeamZ2 4908, BeamZ3 4909, BeamXl 4910, BeamYl 4911 and Beam Y2 4912 can be used together to determine position in all six degrees or freedom.
  • the spacing between various pairs of beams must be known to compute rotations.
  • BeamXl provides the X position.
  • BeamYl or BeamY2 provide the Y position.
  • BeamZl, or BeamZ2, or BeamZ3 provides the Z position.
  • BeamZl and BeamZ2 together with the distance between the two beams allows the rotation about the X axis to be calculated.
  • BeamZ2 and BeamZ3, together with the distance between the two beams allows the rotation about the Y axis to be calculated.
  • BeamYl and BeamY2 together with the distance between the two beams allows the rotation about the Z axis to be calculated.
  • inverted mode Ideally, one would like to combine the benefits of both inverted mode and conventional mode, keeping the high aspect ratio, versatile mode capabilities and other desirable characteristics of conventional mode, without sacrificing the important improvements that inverted mode with surface mounted tips offers, such as the reduction or elimination of tip swapping due to the availability of large numbers of any type of tips required for a given build sequence, and the elimination of feedstock provisioning and trash depots as separate entities from surface-mounted tips.
  • the sequential tip method consists of a surface-mounted tip interacting with a conventional mode tip.
  • the conventional mode tip interacts with the workpiece.
  • the surface mounted tips thus serve as what can be conceptualized as a surface with tunable affinity. Since the surface mounted tips can be engineered to have any desired affinity for their feedstock, they can present or accept a much wider range of feedstocks to the conventional tip than would be possible if the feedstock was attached directly to the presentation surface.
  • the workpiece is preferably located on the presentation surface along with the surface mounted tips, although this is not always true, as is explained herein.
  • Fig. 50a-f shows one way of implementing the sequential tip method, with sub- figures 50a-e depicting sequential states of the same system and Fig. 50f showing an overhead view.
  • Fig. 50a which we arbitrarily use as a starting state, shows handle 5001 (which would be connected to positional control means, not shown) with a tip 5003 (a conventional mode tip) bound to its apex.
  • Tip 5003 has an active site 5002, which in this case, is empty and awaiting feedstock.
  • a presentation surface 5007 holds tips, of which tip 5004 (an inverted mode tip) is exemplary, and a workpiece 5006.
  • the tip 5004 includes feedstock 5005.
  • feedstock 5005 is bound to both tip 5003 and tip 5004.
  • handle 5001 brings tip 5003 and its feedstock 5005 to a specific location on workpiece 5006, facilitating a mechanosynthetic reaction between feedstock 5005 and workpiece 5006. At this point feedstock 5005 is bound to both tip 5003 and workpiece 5006.
  • feedstock 5005 leaving feedstock 5005 bound to workpiece 5006.
  • feedstock 5005 remains bound to workpiece 5006, instead of pulling away with tip 5003, because tip 5003 has been engineered to have lower affinity for feedstock 5005 than does the chosen specific location on workpiece 5006.
  • Fig. 50f depicts a top view of the system shown in side views in Fig. 50a-e.
  • Workpiece 5006 is shown partially under handle 5001 (dotted lines representing the hidden borders of the workpiece) and tip 5003 (denoted with dotted lines as it is under handle 5001).
  • Tip 5004 is representative of many surface-mounted tips arrayed in sectors set off by a grid of dotted lines, such as exemplary sector 5008. Of course, this is not to scale, nor necessarily the actual arrangement that would be used.
  • the workpiece could be next to the surface-mounted tips, in the middle of the surface-mounted tips, or at any other convenient location, even on a different presentation surface.
  • the sectors could be rectangular, concentric, shaped like pie wedges, or any other convenient shape, or sectors could not exist at all, with tips of different types being intermingled.
  • Fig. 51 depicts one possible structure of a conventional tip for use in the sequential tip method.
  • the tip is built on surface 5101 (which would be connected to a positional means, not shown) and comprises support atoms 5102, 5103 and 5104, and active atom 5105.
  • active atom 5105 is a radical, ready to e.g., bind feedstock from surface-mounted tips, or abstract one or more atoms from a workpiece.
  • Passivating atom 5106 is used to satisfy unused valences, and is representative of many such atoms bonded to the tip and surface.
  • surface 5101 is silicon
  • support atoms 5102, 5103 and 5104 are carbon
  • active atom 5105 is silicon.
  • this embodiment has an affinity which is conveniently between that of the described surface-mounted tips and the workpiece for multiple different feedstocks and reactions.
  • passivating atom 5106 and other passivating atoms could be any atom of appropriate chemical nature such as hydrogen or fluorine.
  • the active atom is silicon, connected to three support atoms which are carbon, as half-Si-Rad (because it is a partial or "half adamantane structure with an apical silicon radical in its basic form).
  • the tip can take forms which include half-Si-Rad-CC (a carbon dimer bound to the active atom, and a radical itself, which for some reactions actually makes the apical carbon of the carbon dimer the active atom as it can be used to abstract other atoms from tips or workpieces), half-Si-Rad-H (a hydrogen bound to the active atom), and half-Si-Rad-CH2 (CH2 bound to the active atom), among others.
  • half-Si-Rad-CC a carbon dimer bound to the active atom, and a radical itself, which for some reactions actually makes the apical carbon of the carbon dimer the active atom as it can be used to abstract other atoms from tips or workpieces
  • Exemplary reactions that various versions of the half-Si-Rad tip can carry out include: H Abstraction from C(l 11) to half-Si-Rad-CC, H Donation to from half-Si-Rad-H to C(l 11)-Radical, H Abstraction from C(l 11)-CH3 to half-Si-Rad-CC, H Donation from half-Si- Rad-H to C(l 11)-CH2, CH2 Donation from half-Si-Rad-CH2 to C(l 11)-Radical, CH2 Donation from half-Si-Rad to C(l 11)-CH2 and C2 Dimer Donation from half-Si-Rad-CC to C(l 11)- Radical.
  • half-Si-Rad can carry out many useful reactions, it is not capable of carrying out all reactions, particularly when different classes of workpieces are considered. For example, silicon bonds tend to be weaker than carbon bonds, and germanium bonds tend to be weaker still. Given this, for Si- or Ge-based workpieces, the half-Si-Rad tip will often have an affinity for feedstock that is higher than the affinity of the workpiece for the feedstock. This means that it could not donate the feedstock to the workpiece. A systematic method of adjusting tip affinity would be useful to assist in the rational design of tips with different feedstock affinities. There are two main ways of adjusting tip affinity without departing from the basic bonding structure of the tip depicted in Fig. 51.
  • active atom 5105 can be substituted with an atom of different affinity.
  • carbon could be substituted for silicon
  • germanium, tin, or lead could be used (although it should be recognized that this is a rule of thumb and will not be accurate for all tip-feedstock combinations; those familiar with the relevant arts will understand more nuanced ways of predicting affinity).
  • one or more of the support atoms 5102, 5103 and 5104 can be substituted with different atoms which can affect the affinity of active atom 5105.
  • the embodiment described above where the support atoms are each carbon is, for most diamond- based reactions, superior to an all-silicon tip because the affinity of the all-silicon tip is lower than desired.
  • the carbon atoms strengthen the bond between the active atom and the feedstock.
  • Our computational studies indicate that active atom affinity for feedstock, in general, is affected by the support atoms in the following manner: 0 > N > C > S > P > Si.
  • the half-Si-Rad tip described above was the initial tip bound to a handle, a build sequence could be carried out up until the point when a tip of different affinity was needed. At that point, the conventional tip (half-Si-Rad in this example) essentially becomes a workpiece, with the system temporarily operating in inverted mode rather than sequential mode.
  • the surface-mounted tips act upon the conventional tip, modifying it as desired.
  • the surface mounted tip can be used to remove any (or all, creating a completely new structure) of the atoms in the conventional tip.
  • the surface-mounted tips then provide the new atoms to manufacture a tip that can complete the next part of the build sequence. This process can be repeated as many times as necessary to complete a build sequence, although preferably the need to change the conventional tip would be minimized to streamline the manufacturing process. This suggests a refinement to the process of creating a build sequence where build sequences are ordered, at least in part, in a manner that minimizes the need to rebuild the conventional tips.
  • Figs. 52a-o depict a build sequence which creates the half-Si-Rad tip starting from a depassivated silicon surface.
  • Depassivated silicon surfaces are well-known in the relevant fields, and can be created via bulk chemical methods or heating.
  • a patch of depassivated silicon atoms could be created using mechanosynthesis. For example, starting with a conventional passivated silicon probe, three hydrogens could be removed from a small flat area on the apical end via the abstraction tips described herein.
  • an exemplary silicon structure is depicted as a stand-alone structure terminated with passivating hydrogens, of which hydrogen atom 5201 is representative, except on its lower face, which is depassivated.
  • the structure depicted would be part of a larger structure (which may itself be connected to larger structures such as a handle and positioning means), but only the small area needed for a presentation surface is shown for clarity.
  • Three depassivated silicon atoms are present, of which silicon atom 5202 is representative. This silicon structure, with its small patch of depassivated silicon atoms, serves as the starting point for building the half-Si-rad tip.
  • depassivated silicon atoms at certain points in the sequence to prevent unwanted rearrangements.
  • the question might also be raised as to why the sequence does not just start from a hydrogenated silicon surface, since on that surface there are no unused valences to lead to potential reactivity problems.
  • the issue is one of chemical convenience. Hydrogen, and in general, passivating atoms other than bromine, could be made to work. However, using the particular tips we have chosen for this sequence, bromine is found to more reliably facilitate the desired reactions than other atoms that were investigated.
  • a CH2 group has been added to the radical silicon that was created by the bromine removal in the previous step.
  • This CH2 donation reaction is accomplished using a tip like MeDonationO or its variants, described herein.
  • a hydrogen atom is added to the CH2 radical that was added in the previous step. This is accomplished using HDonation (whether it is HDonationNH, HDonationO, or HDonationS not being relevant to the reaction).
  • a methyl group is donated to the silicon radical that was created by the bromine abstraction in the previous step.
  • the methyl donation reaction is accomplished using MeDonation (again, the specific variant not being relevant).
  • a methyl group is donated to the silicon radical that was created by the bromine abstraction in the previous step.
  • the methyl donation reaction is accomplished using an MeDonation tip. Note that unlike the previous methyl groups, this methyl group does not have its open valence satisfied via a hydrogen donation reaction.
  • one of the previously-created CH3 groups has a hydrogen abstracted from it, via an Abstraction tip, resulting in a surface that has two CH2 groups and one CH3 group.
  • a silicon atom is bound to all three CH2 groups.
  • the silicon atom is donated from an already-described tip loaded with a different payload. Specifically, the
  • Abstraction tip can have a silicon atom bound to its radical active site, and will then donate that silicon atom to the structure.
  • the Abstraction tip can be charged with a silicon feedstock atom by abstracting a Si atom from anywhere else on the conventional tip which is not crucial to the build sequence.
  • the resulting structure is the half-Si-rad tip, which will be obvious when realizing that the structure shown in Fig. 52o, although differing in how termination is depicted at the top of the diagram, is essentially the structure from Fig. 51.
  • Fig. 53 This is an adamantane radical with a bromine feedstock.
  • the synthesis for this tip is depicted in Fig. 53.
  • the synthesis starts with chemical SHA-2, previously described in Fig. 34 and the respective synthesis.
  • SHA-2 can be iodinated at the 4-position of the aromatic rings using 12 and [bis(trifluoroacetoxy)iodo]benzene in CHC13 to yield AdBr-1.
  • Sonogashira coupling conditions of AdBr-1 with triisopropylsilylacetylene (TIPS acetylene) produces the protected alkyne AdBr- 2.
  • Deprotection of the TIPS group proceeds with TBAF in THF to make the terminal acetylene AdBr-3.
  • AdBr-4 also called AdamRad- Br.
  • AdBr-4 also called AdamRad- Br.
  • this version of AdamRad-Br depicts a new leg structure, phenylpropargyl alcohol, which has been found to be useful in conjunction with adamantane-based bodies and silicon surfaces and could be coupled with any of the other tips described herein.
  • the tip shape preferably allows the tip to approach a workpiece and perform the desired reaction without steric hindrance, leading to the observation that higher aspect ratios can be advantageous.
  • tip geometry could also be exploited to hold feedstock at a particular angle.
  • equipment limitations may dictate that, e.g., an SPM probe, must be kept perpendicular to the work surface. But, there may be reactions where a perpendicular alignment of the feedstock with the workpiece is not a desirable trajectory. In that case, it is possible to design a tip that holds the feedstock at e.g., 45 degrees (or any other angle desired) to the rest of the tip or handle.
  • Tip size and shape can also be useful in holding the active atom far enough away from other atoms that the active atom is not adversely affected.
  • atomically-sharp (but not atomically -precise) tips in the literature that do not accomplish this goal in metal tips functionalized with CO, were mechanosynthesis to be attempted with such a tip (which is highly unlikely for various reasons, but if we assume for a moment that it would work), the metal atoms are so to the apical atom (O in this example) that they would affect the interaction of the apical atom with, e.g., a presentation surface, feedstock, or workpiece.
  • a tetrahedral structure with respect to the apical atom can be useful as, with a feedstock atom bound to one leg of the tetrahedron, the other three bonds serve to stabilize the apical atom when force is applied during a reaction.
  • other geometries are possible.
  • AX5 and higher hybridizations can also provide the necessary free electrons to bond a feedstock atom while having the ability to form at least three other bonds to create a rigid tip structure.
  • C9H14[A1,B,N,P] have the apical atom, to which the feedstock atom is attached, at the sidewall position of an adamantane frame.
  • C9H15[C,Si,Ge] have the apical atom, to which the feedstock atom is attached, at the bridgehead position of an adamantane frame.
  • the notation for the workpieces are the same, except that the apical atoms are listed first.
  • the reaction where a C914A1 tip using a Be feedstock atom donates the feedstock atom to CC9H15 could be expressed as:
  • strain (or “bend,” including ring) strain.
  • steric energies these steric energies, or strain, are known to influence molecular stability and chemical reaction energetics.
  • cyclobutane with 7.5% kcal/mol/bond strain, is more reactive than the larger cycloalkanes in which the ring strain is relaxed.
  • Fullerenes are similarly affected by bond strain. Since the lowest energy configuration for individual fullerene units is planar, higher curvatures generally lead to more reactive molecules due at least in part, to angle strain. In terms of individual bond energy, less than about 2% strain tends to have little effect on reactivity. 3-5% strain tends to cause at least some increase in reactivity, while at 5-10% strain, major increases in reactivity are generally apparent. Of course, this trend cannot continue indefinitely; if strain is too high, a bond can spontaneously rupture, leading to rearrangement of the molecule.
  • One scenario is that of feedstock held to a tip by a single bond. Strain within the tip may be used to change the bond angles, and thereby energies, of the apical tip atom to the feedstock.
  • Strain within the tip may be used to change the bond angles, and thereby energies, of the apical tip atom to the feedstock.
  • adamantane structure where a bridgehead carbon is bonded to the feedstock. This bridgehead carbon would normally be bonded to three other carbons, and the uniform length of the carbon-carbon bonds throughout the adamantane structure allows the bridgehead carbon to achieve a perfect tetrahedral configuration where each bond to the bridgehead carbon is about 109.5 degrees.
  • the Ge-C-feedstock angle becomes about 112.9 degrees, causing angle strain.
  • Van der Waals strain can be created by replacing, e.g., H atoms with larger diameter atoms of the same valence, adjacent to the feedstock. In this case, the larger diameter atom need not be bonded to the feedstock or to the apical tip atom. It need only impinge upon the feedstock's Van der Waals radius to cause steric strain.
  • a tip designed in this manner can cause Van der Waals strain by having two or more parts of the same tip interfere (where one part is the feedstock site and the other part is a portion of the tip designed to at least partially impinge upon the feedstock location), a second tip could also be used to apply mechanical force to feedstock. For example, consider a first tip with feedstock bound to it. Using a second tip to apply force to the feedstock perpendicularly (or at any useful angle) to its point of attachment could weaken the bond between the first tip and the feedstock. This is conceptually similar to building such strain into a single tip, but more versatile as the timing, amount of force, and angle of force application can all be varied.
  • strain could be employed is when feedstock is held by more than one bond to a tip.
  • the bonding points can be pulled apart until the bonds are strained by the desired amount. This is more easily illustrated in a slightly larger structure than a single adamantane, so that rigidity of the tip backbone can be used to create strain without excessive deformation.
  • the native distance between two methyl groups connected by an oxygen (3HC-0-CH3) is about 2.36 A, and the angle is about 110.7 degrees.
  • this configuration cannot be obtained on (111) diamond.
  • torsion is generally irrelevant. But, if a feedstock moiety was multiply-bonded, or one or more, e.g., double bonds (or any bond type not free to rotate), were used to bind the feedstock to one or more tips, or one or more points on a single tip, torsion could also be used to create strain, as could any other well- known strain-inducing modifications.
  • strain and releasing strain are two sides of the same effect. If one considers a strained structure the default structure, releasing strain could be used to, for example, strengthen, instead of weaken, bonds. Further, strain levels need not be static. Levels of strain could be changed curing the course of a reaction. For example, to increase tip affinity when picking up feedstock, and then decreasing tip affinity when releasing feedstock.
  • Fig. 54 depicts various one way of creating adjustable strain, and hence affinity, for feedstock.
  • a first tip (5401) is connected to feedstock (5405) via bond (5403).
  • a second tip (5402) is also connected to feedstock (5405) via bond (5404).
  • Various movements of the two tips would change the bond angles and lengths, causing strain and thereby reducing the affinity of the feedstock for the tips.
  • the two tips have been moved part, stretching and changing the angle of the bonds to the feedstock.
  • Fig. 54c the two tips have been move closer together, potentially compressing and changing the angle of the bonds to the feedstock.
  • Fig. 54a a first tip (5401) is connected to feedstock (5405) via bond (5403).
  • a second tip (5402) is also connected to feedstock (5405) via bond (5404).
  • Fig. 54b the two tips have been moved part, stretching and changing the angle of the bonds to the feedstock.
  • Fig. 54c the two tips have been move closer together, potentially compressing
  • one tip has been moved vertically with respect to the other, potentially resulting in stretching of bond (5403) and compression of bond (5404), plus angle changes.
  • the tips would be attached to positional means (not shown). It is possible that each tip has its own position means. It is also possible that both tips reside on a single positional means (and actually may be considered two halves of the same tip) in which case relative movement can still be caused in various ways.
  • the surface onto which the tips are affixed could be a piezo element which can expand and contract. Or, changing temperature, charge, or other parameters could result in a conformation change in either the tips, or the surface to which they are affixed.
  • a workpiece for mechanosynthesis can be defined by specifying each atom in the workpiece and its atomic coordinates, directly or indirectly (for example, via an algorithm which generates the desired structure).
  • Many computational chemistry programs allow the creation of models based on atomic coordinates, or algorithms to generate such coordinates.
  • a build sequence can be created that specifies the order in which each atom is to be added to, or removed from, the workpiece. Reactions that do not add or remove atoms are also possible, such as those that change the bonding structure of the workpiece, or if necessary, charge or otherwise alter tips. The reactions must be ordered so that they result in the desired workpiece, while avoiding, for example, intermediate states prone to pathological reactions, or unstable structures that undesirably rearrange.
  • Figures 55 through 58 illustrate embodiments of the invention using exemplary flowcharts. Note that many variations on these processes are possible, and even without changing the steps involved, one might change the decision logic or loop through some processes more than once. For example, to optimally design a workpiece for manufacturability (55-2) may require an iterative process where the workpiece design is revised based on the outcome of subsequent steps or processes, such as the reaction design process described in Figure 56.
  • This step is similar to that for any traditionally-manufactured product in that product requirements must be defined before the product can be designed from an engineering perspective.
  • Step (55-2) Design Workpiece for Manufacturability also has an analog in traditional manufacturing. The product must be designed with the limitations of the
  • a device is preferably designed with elements and bonding patterns whose properties are understood, for which tips and build sequences have been, or can be, designed and are compatible with equipment capabilities, using geometries accessible to the relevant tips, among other limitations which will be obvious to those skilled in the art given the teachings herein.
  • step (55-3) is to "Specify Atomic Coordinates of Workpiece.” That is, define each atom type and its position within the structure. This step may also include determining bonding structure, as this step can be informative although technically redundant since the bonding structure may be fully specified via the atomic coordinates. This may be done in any molecular modeling or computational chemistry software with the appropriate capabilities, such as HyperChem, Gaussian, GROMACS or NAMD.
  • Step (55-4) "Determine Reaction Reliability Requirements" involves performing an impact analysis of potential defects and the resultant establishment of reaction reliability requirements.
  • the goal of mechanosynthesis is the production of atomically-precise products, unintended reactions can occur at frequencies which depend on factors including the chemical reactions being used, the tip design, the reaction trajectory, equipment capabilities and temperature.
  • For each reaction one could analyze the most likely pathological side reactions that might occur and their impact upon the finished workpiece. For example, one could determine the impact of a feedstock atom failing to transfer, a feedstock atom bonding to a workpiece atom adjacent to the intended position, or the workpiece undergoing an unintended rearrangement.
  • the workpiece could be simulated with each potential defect, or more general heuristics or functional testing could be used to determine the likely impact of possible errors in the workpiece.
  • Figure 56 which describes how a build sequence can be designed, begins with step (56-1) "Determine Order of Reactions, Reaction Conditions and Trajectories.”
  • step (56-1) Determine Order of Reactions, Reaction Conditions and Trajectories.
  • Each atom as specified in the atomic coordinates of the workpiece, generally (but not necessarily since, for example, one could use dimers or larger molecules as feedstock) requires that a particular reaction be performed on the workpiece to deposit that atom. Abstraction reactions may also be required, as may be reactions which alter the bonding structure of the workpiece without adding or subtracting any atoms.
  • the build sequence may be simulated to determine if it works correctly (56-2).
  • the same simulations can test reaction parameters including which tip to use, what temperature is required, and what trajectory a tip will follow. As has been previously noted, lower temperatures will favor accuracy, and frequently the coaxial trajectory will enable successful reactions.
  • CAD programs can be used to specify SPM trajectories (Chen, "CAD-guided automated nanoassembly using atomic force microscopy -based nonrobotics," IEEE Transactions on Automation Science and Engineering, 3, 2006; Johannes, “Automated CAD/CAM-based nanolithography using a custom atomic force microscope,” IEEE Transactions on Automation Science and Engineering, 3, 2006), atomic force microscopes that are programmable are commercially available, and programming languages or environments (e.g., Lab VIEW) to control scientific equipment are well known (Berger et al., "A versatile Lab VIEW and field- programmable gate array -based scanning probe microscope for in operando electronic device characterization,” Review of Scientific Instruments 85, 123702 (2014)).
  • reaction reliabilities can be calculated (for example, by energy barrier calculations or Monte Carlo simulations).
  • (56-6) is a determination as to whether the proposed reaction reliabilities meet production quality needs, and, if the answer to (56-6) is no, the process proceeds to (56-7) where requirements are reviewed to see if the build sequence restrictions can be relaxed since they were not met. From (56-7) if the answer is yes, a new iteration is started at (55-4) to determine revised reaction reliability requirements. If the answer to (56-7) is no, alternate reactions, reaction order, reaction trajectories, or reaction conditions can be simulated (56-1) to find a revised build sequence that meets the reaction reliability
  • step (57-1) If the answer to (56-6) is yes, the process continues in Figure 57, step (57-1).
  • Figure 57 describes a process for carrying out mechanosynthetic reactions per a build sequence.
  • the reactions determined in the build sequence are carried out using SPM -like equipment, or other suitable equipment.
  • This step involves, whether manually or in a computer-controlled manner, using a positionally-controlled tip to perform each mechanosynthetic reaction in the build sequence. This means picking up a feedstock atom from a presentation surface (or potentially a gaseous or liquid source of feedstock) and bonding it to the workpiece, or removing an atom from the workpiece, or changing the bonding structure of the workpiece without adding or removing an atom.
  • This step would also encompass other reactions, including reactions not involving the workpiece, such as tip refresh or pre-reaction feedstock manipulation as may be necessary.
  • Step (57-2) is a decision point. If the answer is "no,” testing is not required (for example, such as when the reactions being used are reliable enough that testing is superfluous), the process proceeds to (57-3). The action taken from (57-3) depends on whether all reactions in the build sequence have been completed. If no, reactions are repeated until the answer is yes, at which point the workpiece is complete. Back at (57-2), if the answer were "yes,” testing is required, the process continues in Figure 58, starting with step (58-1).
  • testing may done by, for example, scanning the surface of a workpiece using SPM-like techniques and checking to see that the expected structure is present. If no errors are found in (58-2), the process continues at (57-3). If an error is present at (58-2), a decision must be made in (58-3) as to whether the error is ignorable (e.g., not an error that would prevent the workpiece from functioning). If it is ignorable, the process again continues with (57- 3), although the build sequence may require adjustment if key atoms were moved as a result of the error (not depicted). If the error is not ignorable, it must be determined if the error can be fixed (58-4). This is largely a question of whether the tools and processes exist to fix the error.
  • Row Extension, or Row Termination For example, to start a new row of diamond on a build surface, one would use the Row Initiation reactions, #1 to #11. To then extend that row, Row Extension reactions #12 to #17 would be used (as many times as necessary to achieve the desired length). To terminate the row, Row Termination reactions #18 to #22 would be used.
  • Second step for row extension via abstracting a hydrogen from the
  • Second step for row termination via abstracting a hydrogen from
  • the workpiece is not a simple shape, or any periodic shape derived directly from its crystal structure (which might permit its manufacture by CVD, self-assembly, or some other known process).
  • aperiodic workpieces are interesting because as far as we know, mechanosynthesis is the only way to produce such workpieces. For example, consider an arbitrary shape such as the outline of a car (to use a familiar shape, if not a relevant scale). Even if CVD could be used to grow atomically-precise crystals, there is no way it could be used to achieve such an irregular shape.
  • aperiodic workpieces that may largely be periodic, but which have aperiodic substitutions. For example, consider a diamond cube, perfect and regular in all respects except that nitrogen vacancies have been placed in specific locations. Again, this would be impossible to create via CVD, or any other technology of which we are aware besides mechanosynthesis, yet this could be a very useful workpiece for realizing a quantum computer.
  • the vast majority of parts, whether mechanical or electronic, used in devices today, are aperiodic. Being aperiodic is the rule rather than the exception, and while such parts are easily manufactured at the macro-scale using subtractive manufacturing (e.g., machining) and other techniques, it is very difficult to manufacture such parts with atomic precision. In most cases we would say that it is impossible without mechanosynthesis.
  • DNA of essentially arbitrary length and sequence can be prepared using conventional techniques. And, given that DNA need not be simply a repetition of the same monomer, by some measures DNA sequences could have high complexity. However, DNA is essentially a floppy, one-dimensional polymer. Although DNA can fold into 3D structures, even then, DNA is not stiff or highly-bonded.
  • ADAMANTANE COMPOUNDS US Patent 3859352, United States, Eli Lilly and Company (Indianapolis, IN), 1975; Baxter, "Adamantane derivatives,” US Patent 6242470, United States, AstraZeneca AB (Sodertalje, SE), 2001).
  • the adamantane aggregates obtained from natural sources are connected randomly, and so the chances of finding any particular
  • adamantanes as the size of the molecule grows becomes vanishingly small. In practicality, these molecules are neither large nor atomically-precise.
  • the functionalized adamantanes used in the pharmaceutical industry are atomically-precise, but they are not large or highly-bonded (since such molecules tend to be, for example, a single adamantane connected to a long, flexible side chain).
  • Diamond whether natural or synthetic (e.g., grown via chemical vapor deposition) is neither complex, being (with the exception of errors) a uniformly repeated three- dimensional polymer of adamantane, nor atomically-precise, as even the most perfect such diamond has flaws at the atomic level.
  • strained bonds With respect to strained bonds, the creation of individual strained bonds is routine in chemistry, and molecules like cyclopropane and cubane exemplify the structures that can be created with strained bonds. Larger structures containing many strained bonds also exist, e.g., Fullerenes of various configurations. While the specific mechanisms of formation are very different, there is a commonality between the synthesis of cyclopropane, cubane, Fullerenes, and other strained molecules in that there are energetically-feasible sequential reaction pathways leading from the initial reactants to the final product.
  • the two ends of the linear molecule can be closely approximated in a variety of ways.
  • the molecule can be very small to begin with, so that even if the molecule is straight, the two ends are both within reach of a single reaction.
  • the molecule can be flexible enough that it can bend into the necessary
  • the linear molecule could have an inherent curve to it, making it already a partial hoop and thereby leaving only a small gap to bridge.
  • a stiff, long, potentially wide, structure with two sides which are, atomically speaking, far apart, but which need to be brought together to then undergo a bonding reaction to form a stable hoop or cylinder may sound like a very contrived class of structures. It is not.
  • Mechanosynthesis can form such structures in a variety of ways, such as by using force to approximate the necessary ends, or by building a temporary jig around the structure that forces intermediate structures into the necessary shape (and which can then be removed once the desired structure is complete).
  • Reliability is an important consideration in the design of build sequences for multi-atom workpieces. Reaction reliability can be achieved in a variety of ways, including use of reactions with energy barriers sufficient to prevent spontaneous reactions at a given temperature, reactions designed to avoid pathological side reactions (for example, by
  • reaction barriers or energy deltas are often overcome by thermal energy.
  • thermal energy is nonspecific and facilitates desired and undesired reactions alike. Reducing temperature decreases the thermal energy available to cause non-specific reactions. This reduces the likelihood of pathological side reactions while directed mechanical force, even at low temperatures, still facilitates desired reactions.
  • computational chemistry may be used in conjunction with data on net energy differences and energy barriers to determine the reliability of a given reaction at a given temperature.
  • Mathematica v8 code may be used to determine reaction reliability at a given temperature when considering the net energy difference between two structures (e.g., the before and after workpiece structures):
  • tip design is streamlined by using modules, or sub-modules, such as legs, linkers, a body, an active site, and feedstock.
  • Modular tips can be synthesized via bulk chemical methods, as demonstrated by the many exemplary syntheses described. Bulk synthesis facilitates a paradigm shift in the manner in which tips are used, allowing the binding of many tips, of many different types, to a presentation surface. This surface-mounted tip strategy can reduce or eliminate the need for tip swapping and recharge, and also allows the creation of atomically-precise tips without a bootstrap process involving non-atomically-precise tips.
  • a workpiece can be built using surface-mounted tips in inverted mode, but to circumvent some of the limitations such a process presents, also described is a sequential tip method, where, for example, a surface-mounted tip donates feedstock to a conventional mode tip, which then passes the feedstock on to the workpiece. The final reaction being via
  • a half-Si-Rad tip could be turned into a GeRad-based tip, or an AdamRad-based tip, changing its chemical nature, thereby allowing different reactions or operation under different conditions (e.g., allowing for changes in reliability or temperature).
  • surface-mounted tips can be used not only to build tips on other presentation surfaces, such as on the end of an SPM probe.
  • build sequences are required to build a workpiece via mechanosynthesis. Unlike bulk chemistry where many atoms can assemble in a stochastic manner, building workpieces via positionally-constrained chemistry requires making choices about what order the atoms as placed in, and where they are placed. While the need to create a build sequence may be considered a drawback as compared to conventional chemistry, the ability of mechanosynthesis to create products which would, as far as we know, otherwise be impossible to build, such as large, highly-bonded, complex or irregular or aperiodic, atomically- precise workpieces, makes it a very useful technology.

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Abstract

La présente invention concerne des procédés, des systèmes et des dispositifs améliorés pour la mécanosynthèse, comprenant ceux qui impliquent la préparation chimique en masse de pointes, de multiples pointes sur une surface de présentation, et de multiples pointes utilisées successivement dans une cascade thermodynamique. Ces améliorations peuvent simplifier les exigences de départ, améliorer la polyvalence, et réduire la complexité de l'équipement et du processus.
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US17/474,472 US11592463B2 (en) 2016-11-16 2021-09-14 Systems and methods for mechanosynthesis
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