EP1028807A1 - Systemes et procedes pour la synthese combinatoire d'arrangements de reaction chimique - Google Patents

Systemes et procedes pour la synthese combinatoire d'arrangements de reaction chimique

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Publication number
EP1028807A1
EP1028807A1 EP98953791A EP98953791A EP1028807A1 EP 1028807 A1 EP1028807 A1 EP 1028807A1 EP 98953791 A EP98953791 A EP 98953791A EP 98953791 A EP98953791 A EP 98953791A EP 1028807 A1 EP1028807 A1 EP 1028807A1
Authority
EP
European Patent Office
Prior art keywords
reagent
fluid
cassette
reaction vessel
tubular structures
Prior art date
Legal status (The legal status 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 status listed.)
Withdrawn
Application number
EP98953791A
Other languages
German (de)
English (en)
Other versions
EP1028807A4 (fr
Inventor
Daniel M. Bernstein
Peter Wright
Steve Miller
Christopher Kilcoin
James Wasson
Jan Hughes
Thomas Brennan-Marquez
Dominic Kyrie
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Argonaut Technologies Inc
Original Assignee
Argonaut Technologies Inc
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.)
Filing date
Publication date
Application filed by Argonaut Technologies Inc filed Critical Argonaut Technologies Inc
Publication of EP1028807A1 publication Critical patent/EP1028807A1/fr
Publication of EP1028807A4 publication Critical patent/EP1028807A4/fr
Withdrawn legal-status Critical Current

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Classifications

    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J19/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J19/0046—Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07B—GENERAL METHODS OF ORGANIC CHEMISTRY; APPARATUS THEREFOR
    • C07B39/00—Halogenation
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00281—Individual reactor vessels
    • B01J2219/00283—Reactor vessels with top opening
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00306—Reactor vessels in a multiple arrangement
    • B01J2219/00308—Reactor vessels in a multiple arrangement interchangeably mounted in racks or blocks
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00306—Reactor vessels in a multiple arrangement
    • B01J2219/00308—Reactor vessels in a multiple arrangement interchangeably mounted in racks or blocks
    • B01J2219/0031—Reactor vessels in a multiple arrangement interchangeably mounted in racks or blocks the racks or blocks being mounted in stacked arrangements
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00331—Details of the reactor vessels
    • B01J2219/00333—Closures attached to the reactor vessels
    • B01J2219/00344—Caps
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00351—Means for dispensing and evacuation of reagents
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00351—Means for dispensing and evacuation of reagents
    • B01J2219/00364—Pipettes
    • B01J2219/00367—Pipettes capillary
    • B01J2219/00369—Pipettes capillary in multiple or parallel arrangements
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00351—Means for dispensing and evacuation of reagents
    • B01J2219/00389—Feeding through valves
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00351—Means for dispensing and evacuation of reagents
    • B01J2219/00418—Means for dispensing and evacuation of reagents using pressure
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00351—Means for dispensing and evacuation of reagents
    • B01J2219/00423—Means for dispensing and evacuation of reagents using filtration, e.g. through porous frits
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00479—Means for mixing reactants or products in the reaction vessels
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00479—Means for mixing reactants or products in the reaction vessels
    • B01J2219/00481—Means for mixing reactants or products in the reaction vessels by the use of moving stirrers within the reaction vessels
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00479—Means for mixing reactants or products in the reaction vessels
    • B01J2219/00484—Means for mixing reactants or products in the reaction vessels by shaking, vibrating or oscillating of the reaction vessels
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00479—Means for mixing reactants or products in the reaction vessels
    • B01J2219/00493—Means for mixing reactants or products in the reaction vessels by sparging or bubbling with gases
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00495—Means for heating or cooling the reaction vessels
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00585—Parallel processes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/0059—Sequential processes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00596—Solid-phase processes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/00686—Automatic
    • B01J2219/00689—Automatic using computers
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B60/00—Apparatus specially adapted for use in combinatorial chemistry or with libraries
    • C40B60/14—Apparatus specially adapted for use in combinatorial chemistry or with libraries for creating libraries

Definitions

  • the standard method for searching for new chemical compounds which can effectively modulate biological processes employs the screening of pre-existing compounds in assays which have been designed to test particular properties of the compound being screened. Similarly, in designing compounds having desired physiochemical properties for general chemical applications, numerous compounds must be individually prepared and tested.
  • WO 92/09300 describe the generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery; Lam, et al . (Nature, 354, 82 (199 1) and PCT Patent Pub. No. WO 92/0009 1) describe a method of synthesis of linear peptides on a solid support such as polystyrene or polyacrylamide resin.
  • the present invention is directed to a system which is useful for the synthesis of chemical compounds, for example, for the preparation of multiple discrete compounds or for combinatorial libraries of compounds.
  • the present invention can be used for developing new drugs and chemical entities.
  • the invention is useful for rapidly generating and systematically synthesizing large numbers of molecules that may vary in their chemical structure or composition.
  • the invention is further useful for randomly generating a large number of candidate compounds, then later optimizing those compounds which exhibit the most desirable properties.
  • the present system is applicable to both solid state and liquid chemistries .
  • the present invention preferably allows a user to minimize the cost associated with the most expensive portions of a synthesis system, such as the fluid delivery system, while maximizing the number of reaction vessels that can be serviced by the fluid delivery system.
  • the delivery system can make its delivery of reagents to one or more reaction vessels and then move to service other reaction vessels.
  • the present invention can form reliable air/liquid tight seals between the delivery system and the reaction vessel without the risk of reduced seal integrity after repeated use associated with conventional septum systems.
  • the fluid pathways of the present delivery system can also be flushed prior to fluid delivery to remove contaminants which may have entered the system. This flush typically occurs after the delivery system is engaged to the reaction vessels and eliminates or significantly reduces the risk of contamination.
  • the present invention further allows delivery of small quantities of reagents without significant dilution as often required in conventional systems.
  • the present invention provides a system for the synthesis of combinatorial chemical libraries.
  • the system includes a reagent delivery/vent unit and a chemical processing unit containing a plurality of reaction vessels.
  • the reagent delivery/vent unit has a plurality of tubular structures adapted to slidably engage recesses or cavities in the chemical processing unit to form a circumferential seal about at least one of the tubular structures.
  • the delivery/vent unit typically uses a fluid interface head containing the tubular structures to engage the chemical processing unit.
  • the chemical processing unit preferably uses a cassette to house the reaction vessels and the cassette defines the plurality of cavities adapted to receive the tubular structures.
  • the tubular structures may be located on the chemical processing unit and the recesses located on the delivery/vent unit. Using the cassette advantageously allows the reaction vessels to be fluidly coupled to the interface head for reagent delivery and then be disconnected for possible offsite processing.
  • the present invention provides a system for delivering reagents into a reaction vessel where dilution of the reagent during delivery is preferably minimized.
  • the system contains an interface head fluidly couplable to the reaction vessel.
  • the interface head is preferably detachable or removable to be fluidly coupled with other reaction vessels while a first set of vessels are processing.
  • the interface head defines a fluid pathway to the reaction vessel when it is fluidly coupled to the reaction vessel .
  • the system uses a holding reservoir fluidly coupled with the interface head to help deliver reagents or solvents. In some embodiments, the holding reservoir may also be defined by the interface head.
  • a valve located at an inlet of the holding reservoir controls flow into the reservoir.
  • a pressurized gas source fluidly coupled to the valve is used to flow fluid into the reaction vessel.
  • the system preferably includes a syringe pump adapted to deliver a fluid bolus that includes a reagent portion and a solvent portion.
  • the fluid bolus generally includes a small gas gap between the reagent portion and the solvent portion. This gas gap substantially minimizes dilution between reagent and solvent, thus reducing the amount of reagent used in delivery.
  • the fluid bolus preferably extends from the syringe pump through the delivery tubing to the holding reservoir. The amount of fluid to be delivered to the reaction vessel is pushed by the syringe pump via the relatively incompressible fluid column or bolus into the holding reservoir.
  • an isolatable, holding tube from which the fluid or reagent can be delivered to a reaction vessel allows for fluid delivery without introduction of solvent rinse fluids and this minimizes dilution.
  • the liquid column used to accurately meter the reagent into the holding reservoir can be discarded or otherwise processed while the reagent is injected a short distance to the reaction vessel .
  • the holding reservoir fluid is preferably delivered in the last short distance into the reaction vessel via pressurized gas.
  • Conventional systems typically do not have such metering capability so close to the reaction vessel.
  • Conventional systems typically meter the reagent at distances far from the reaction vessel.
  • Embodiments of the present invention also use gas flow sensors fluidly coupled to the pressurized gas source to detect the flow of pressurized gas delivering fluid into the reaction vessel.
  • a method according to the present invention for testing the successful delivery of liquid in a synthesis apparatus comprise the steps of flowing liquid towards a target site, flowing gas to move the liquid, measuring the gas flow rate, emptying the liquid to the target site, and measuring an increase in gas flow rate. This allows the system to detect blockages in the delivery system when gas flow is not at the level expected.
  • Liquid sensors using optical or other sensing capability may also be used to detect whether reagents or solvents have reached their destinations.
  • the present invention provides an improved thermal agitation unit for use in chemical synthesis.
  • the apparatus includes a heat exchanger, a gas recirculation unit, and a gas distribution plate adapted to evenly distribute heat-exchanged gas around the reactions vessels within a temperature variance of ⁇ 5°C.
  • the system also includes a reciprocating agitator adapted to agitate the cassette and the reaction vessels therein.
  • the present apparatus advantageously allows for agitation of the entire cassette. Typically, no motion-limiting items such as a magnetic agitator, heating elements, or stir mechanism are attached to each reaction vessel. This provides for a more elegant design. Additionally, gas or air based thermal units advantageously allow the use of very small reaction vessels which cannot contain conventional magnetic agitation devices.
  • the present invention provides a method for minimizing mechanical motion and/or reagent washes used in the synthesis of combinatorial chemical libraries using a plurality of reagents.
  • the method uses a Hubert space-filling curve to calculate the desired placement of synthesis procedures.
  • the method includes generating a Hubert space by sizing upward a reagent space.
  • a fluid delivery system is slidably engaged to a reaction vessel and reagents -are delivered into the reaction vessel.
  • the use of the Hubert space minimize the amount of motion required by the fluid interface head. This is particularly advantageous since the amount of reagent and solvent used to flush and then prime the fluid lines can be significant if there are large number of connections and disconnections.
  • Fig. 1A shows a simplified schematic view of a system according to the present invention
  • Fig. IB illustrates an exemplary embodiment of the system according to the present invention
  • Fig. 2A shows a partial cross-section view of an interface head and cassette according to the present invention
  • FIG. 2B-2C illustrate alternative embodiments of a removable coupling according to the present invention
  • Figs. 3A-3B depict two embodiments of the interphase head
  • Fig. 4 shows a tubular structure about to engage a recess in a cassette of a system according to the present invention
  • Fig. 5 is a perspective view of one embodiment of a partially disassembled cassette mounted on an agitation thermal unit according to the present invention
  • Figs. 6-8 show additional views of an interface head according to the present invention
  • Figs. 9-10 are schematic plumbing diagrams of the system according to the present invention.
  • Figs. 11-14 illustrate fluid delivery using the system of Figs. 9-10 to minimize reagent dilution;
  • Fig. 15A is a cross-sectional view of one embodiment of the agitation thermal unit
  • Fig. 15B illustrate embodiments of the heat exchange element and gas distribution plates according to the present invention
  • Fig. 16 shows an agitation thermal unit having a fan positioned to generate air or gas flow over a cassette on the unit ; and Fig. 17A-17C shows the use of gas flow meters to detect the successful delivery of fluids into a reaction vessel .
  • the present invention is directed to the synthesis of chemical compounds, such as for the generation of combinatorial chemical libraries.
  • the present invention provides an apparatus by which any variety of single compounds or combinatorial libraries may be created.
  • the reaction apparatus of the present invention provides numerous advantages over known instrumentation. With large numbers of samples to process, the present apparatus facilitates the synthesis by allowing for common introduction of reagents and the simultaneous washing of a plurality of reaction vessels. This processing is preferably performed under an inert atmosphere in the reaction vessels.
  • the present invention may also provide an agitator for uniformly and gently mixing the reaction media. Constant and evenly distributed heating and cooling may be provided during synthesis.
  • certain functions of the present invention such as agitation of the reaction mixture, heating and cooling of the reaction vessel, inlet of inert atmosphere, introduction of reagents and solvents, rinsing and draining of reaction mixtures, and the like are preferably conducted by robotic automation or computer control. Accordingly, certain embodiments of the present invention are directed to the use of the apparatus which is partially or entirely conducted by robotic automation or under computer control .
  • the present invention is useful for the solid phase synthesis of organic compounds, including peptides.
  • This device may be used for both solid phase chemistry and liquid- liquid chemistry.
  • the present invention may be employed for the synthesis of organic compounds in the solution phase.
  • appropriate starting materials may be attached to a support.
  • Preferred support materials include solid polymeric materials, such as polyacrylamide, polydextran, polyethylene glycol, polystyrene, cellulose, sephadex, resins, combinations thereof, and the like.
  • Alternate support materials include glass, acrylic, latex, and ceramics.
  • the present invention is useful in almost all of the synthetic reactions which are known to one of skill in the art, including, for example, peptide synthesis, acylation, alkylation, condensation, cyclization, halogenation, heterogeneous catalysis, hydrolysis, metallation, nitration, nucleophilic displacement, organometallic reactions, oxidation, reduction, sulfonation, acid chloride formation, Diels-Alder reaction, Friedel-Crafts reactions, Fischer indole synthesis, Michael reactions, and the like (see e.g., H. 0. House, "Modem Synthetic Reactions", 2nd ed. (Benjamin/Cummings, Menlo Park 1972) ; J.
  • the present invention has application in essentially any synthetic reaction which may be conducted in solution or on solid phase supports, including acetal formation, alkylations, alkynation, chiral alkylation, reductive alkylation, carbanion reactions, Grignard reactions, organocadmium/manganese reactions, organolidiim reactions, organozinc reactions, carbene insertion, condensations, Claisen reactions, aldol reactions, Dieckmann cyclization,
  • a "combinatorial library” is a collection of compounds in which the compounds comprising the collection are composed of one or more subunits or monomeric units (i.e. synthons) .
  • the subunits may be selected from natural or unnatural moieties including amino acids, nucleotides, sugars, lipids, carbohydrates, dienes, dienopholes, and the like.
  • the compounds of the combinatorial library differ in one or more ways with respect to the type(s), number, order or modification of the subunits comprising the compounds.
  • Combinatorial libraries generated by the methods of the present invention may be screened for pharmacologically or diagnostically useful compounds, as well as for desired physical or chemical properties. It will be clear to one skilled in the art that such screening may be conducted on a library of compounds which have been separated from the polyvalent support, or may be conducted directly on the library of compounds which are still linked to the polyvalent support .
  • tubular structure as used herein includes objects of a variety of shapes and containing at least one lumen. It should be understood, however, that the structure may also have a plurality of lumens.
  • the structure is preferably an elongate member where the lumen therein extends from a proximal end to a distal end of the member. They may have circular, square, octagonal, or other cross-sectional shapes.
  • the structure has a smooth outer surface along which a circumferential seal may be formed.
  • a system 10 for the synthesis of combinatorial chemical libraries is depicted in a simplified schematic diagram.
  • Fig. 1 shows an overview where the elements are generally grouped as either part of a reagent delivery/vent unit 20 or as part of a chemical processing unit 30.
  • the delivery/vent unit 20 may include the diversity reagent sources, the solvent sources, pumps for delivering the reagent and solvents, and/or final product collection devices.
  • the chemical processing unit 30 may include the cassette, reaction vessels, and/or agitation/thermal processing units used to bring about synthesis once the reagents have been delivered.
  • a fluidic interface head 40 is used to removably couple the elements of the delivery/vent unit 20 to the chemical processing unit 30.
  • the interface head 40 uses tubular structures to slidably engage cavities or openings in chemical processing unit 30. These openings or cavities are typically elongate openings located in the cassette 110, usually in lid 111.
  • the tubular structures are preferably non-coring, non-piercing structure. They may have a variety of configurations, so long as they provide an air/liquid tight seal with the cassette.
  • the seal is preferably formed near the distal end of the tubular structure and is most preferably a circumferential seal.
  • This releasable coupling allows the delivery/vent unit 20 to form releasable air tight seals that do not degrade over time like conventional septum seals.
  • the releasible quality allows high-cost equipment such as the interphase head 40 and the delivery/vent unit 20 to service a plurality of chemical processing units 30. This increases production throughput at a lower cost.
  • the present invention as described below, also allows for the flushing of the tubular structures of unit 20 and its fluid pathways so that the risk of contamination is reduced.
  • Fig. IB shows an overview of an exemplary embodiment of the present automated synthesis system 10.
  • the system 10 manufactured as the TridentTM Automated Library Synthesis System by Argonaut Technologies, Inc. of San Carlos, California, typically has four agitation thermal units (ATU) 468.
  • the interface head 40 may be designed to mate with various numbers of openings on the cassette 110 of each ATU 468.
  • the interface head 40 may also have various sensors, such as light-based sensors, to monitor and visually verify the lowering and raising of the head 40 to and from cassette
  • a computer or logic device is used to control the synthesis process.
  • the interface head 40 and chemical processing unit 30 are typically located in fume hoods evacuating area 41.
  • the area 44 houses both the autosampler 60 and the fraction collector (Fig. 10B) .
  • the needles for the autosampler 60 and/or the fraction collector may be installed on one sliding carriage 320 which is typically powered by step motors (not shown) to move as desired.
  • the interface head 40 is depicted as moving on a gantry 45 and is typically moved by an x-z axis motor, which allows motion in two degrees of freedom. While not limited to such chemistries, preferred embodiments of the present invention are adapted for use with highly corrosive chemicals used in solid phase synthesis and solution synthesis.
  • Preferred embodiments also fill the reaction vessels 50 with inert gas such as argon or nitrogen to prevent contaminating air or moisture sensitive chemistries. As shown, the entire system 10 may be enclosed by its own fume hood and exhaust system.
  • One of the components of the present invention is the fluidic interface head that is described in co-pending, commonly assigned U.S. Patent Application No. 60/063,134 (Attorney Docket No. 16925-001900) filed on October 22, 1997, the full disclosure of which has been previously incorporated herein by reference.
  • FIG. 2A shows a cross-section of one embodiment of the interface head 40 mated to a cassette 110.
  • the head 40 may be a single linear array 90 or a larger matrix 92.
  • Different interface head 40 sizes typically embody different advantages.
  • the larger matrix 92 can fill many more reaction vessels 50 simultaneously, but it also requires additional fluid conduit lines. This may be a disadvantage when very small quantities of chemicals are being sent down to the reaction vessels 50. However, for concentration-tolerant processes, this may be a nonissue.
  • the interface head 40 has two extensions or tubular structures 100 and 102 which engage recesses or cavities 104 and 106 when the interface head 40 is lowered into the top of cassette 110 (as shown more clearly in Fig. 5) .
  • the cavity 104 may have an elongate or other shape to seal with the tubular structures.
  • the tubular structures 100 and 102 form an air/liquid-tight seal with the cavities 104 and 106.
  • the seal is preferably a circumferential seal, but it should be understood that in alternative embodiments, the seal may be a distal, end seal if sufficient compression is supplied to push the tubular structure 100 against cavity 104.
  • Further alternative embodiments of the releasible coupling between a cassette 110 and an interface head are shown in Figs. 2B-2C and also described in commonly assigned, copending U.S.
  • the tubes/extensions and recesses may assume a variety of shapes such as cylindrical or rectilinear so long as they conform to form an air/liquid-tight seal between the interface head 40, the cassette 110, and reaction vessel 50. In some embodiments, they are blunt, non-piercing and typically non-coring members. This releasable coupling provides a closed system with the reaction vessels 50 as shown in Fig. 10 when the interface head 40 and cassette 110 are engaged.
  • the interference to provide the desired seal between the tubular structure 100 and the side wall of cavity 104 is about 0.003" to 0.006".
  • this seal is a circumferential seal between the structure 100 and the side walls 103 of the cavity 104 as illustrated in Fig. 4.
  • the tubular structure 100 may have a diameter between about 0.080- 0.100", preferably about 0.090" diameter. This provides an air/liquid-tight connection and ensures an inert environment for delivery of reagents or solvent washes.
  • the tubing or conduits leading to the reaction vessels 50 of cassette 110 may also be flushed while the head 40 is connected to the cassette and prior to delivery of fluid.
  • the cap valve 474 may be rotated to a position where a fluid connection 113 can be formed between tubular structures 100 and 102 when they engage the lid 111 of cassette 110. This flushing further ensures the removal of contaminants prior to introduction of reagents or solvents into the reaction vessel . Details regarding contamination flushing can be found in co- pending, commonly assigned U.S. Patent Application No. 09/095,731 (Attorney Docket No. 16925-001710) filed on June 10, 1998, the full disclosure of which is incorporated herein by reference for all purposes.
  • the structure 100 is preferably made of a resilient, chemically inert material such as Teflon ® or specifically Fluorinated Ethylene Propylene (FEP) .
  • FEP Fluorinated Ethylene Propylene
  • Other fluoropolymers such as Polytetrafluoroethylene (PTFE) , Tefzel (ETFE) , and PFA may also be used. This provides for a reliable seal while maintaining this fluid pathway inert to the chemistries used in chemical synthesis. Further details can be found in co- pending, commonly assigned U.S. Patent Application No. 09/095,731 previously incorporated herein by reference.
  • the tubular structure 100 is a smooth extruded tube of FEP.
  • FEP is a material which cannot be easily shaped or drilled without causing brittleness or an unsmooth surface, except in an extrusion process.
  • the present invention uses an extruded tube which is inserted into support 42 of the interface head 40.
  • the tube 100 may be press-fit into the support 42.
  • threading such as that provided by an internally and typically externally threaded annular body 43 is used to hold the connector to the support body 42 during coupling an decoupling with the cassette 110.
  • the tube 100 typically made of FEP, is screwed through threads such as 3-56 threads in the annular body 43 using a pin vise.
  • the threads 45 (Figs. 4 and 7) prevent the tube 100 from being pulled out of the interface head 40 when the head is removed from the cassette 110.
  • Excessive temperature variation such as between 150°C and -40°C of the cassette 110, may cause the cavity 104 of the cassette 110 to tightly grip the connector 100 when the interface head is being decoupled.
  • the inert pathway is maintained since a proximal end of connector or tube 100 extends beyond the threaded annular portion 43 to connect with port 95 in the support 42 (Fig. 7) .
  • chemicals entering the reaction vessel 50 typically force gas out as indicated by arrow 114.
  • this process may be reversed to force chemicals out of the reaction vessel 50 by pressurizing the reaction vessel with inert gas.
  • the connections for both delivery and extraction are located on one side of the cassette.
  • an exemplary embodiment of an interface head 40 and a cassette 110 mounted on an agitation thermal unit 120 is depicted. Having a releasable coupling ability, the interface head 40 may be moved successively as indicated by arrows 122 to sequentially engage all of the reaction vessels 50 housed in the cassette 110.
  • the lid 111 of the cassette has openings 113 for aligning with guidepins in the interface head 40 as described in co-pending, commonly assigned U.S. Provisional Patent Application No. 60/097,511 (Attorney Docket No. 16925-002200) filed on August 21, 1998, the full disclosure of which has been incorporated herein by reference for all purposes.
  • the guidepins prevent engagement of the lid 111 and interface head 40 when they are not in alignment.
  • the releasable coupling ability of system 10 is particularly advantageous as one major cost of these synthesis systems lies in the fluidics, plumbing, and metering devices used to deliver chemicals to the interface head 40. Once the chemicals are delivered, the services of the interface head 40 may not be needed for several more hours while reactions take place in the reaction vessels 50. Hence, by making the interface head 40 movable, many more reaction vessels 50 may be serviced without substantially increasing cost. Additionally, since the present invention uses a releasible air-tight coupling with the cassette 110 and the reaction vessels 50, the closed atmosphere in the reaction vessels 50 can be maintained even though the interface head 40 engages and disengages the device.
  • cassettes 110 may also be removed from the system 10 for offsite processing or long term incubation while other cassettes are loaded onto the system for service from the interface head 40. Details on the cassette 110 and reaction vessels 50 may be found in commonly assigned, copending U.S. Patent Application Serial No. 09/095,731 (Attorney Docket No. 16925-001710) filed on June 10, 1998, the complete disclosure of which has been previously incorporated herein by reference. Also shown in Fig. 5, the cassette 110 is reciprocated by a cam device 130 powered by a motor 140. This is an exemplary embodiment of an agitation device used to agitate the reaction vessels 50 in the cassette 110. The cassette 110 preferably moves in a reciprocal manner as indicated by arrow 132.
  • Reaction vessel 50 agitation is also described in commonly assigned, copending U.S. Patent Application Serial No. 09/095,731 (Attorney Docket No. 16925- 001710) filed on June 10, 1998. Agitation is also described below in the description of the agitation thermal unit (ATU) .
  • the cassette 110 is removable from the agitation thermal unit 120 by pulling on a resin handle 111, as indicated by arrow 112 (Fig. 5 and Fig. 16) .
  • the handle 111 is preferably made of a material which is substantially thermally resistant.
  • the fluidic interface head 40 may be designed to connect with one row of openings on the lid 111 of cassette 110.
  • the interface head 40 shown in Fig. 6 is designed for use with an automated synthesis device as shown in Fig. IB.
  • the interface head 40 is typically mounted on an x-z axis manipulator that can move the interface head 40 to various positions over the cassettes 110 (Fig. IB) and lower the head onto the cassettes.
  • the openings 92 are typically occupied by an interface tube 100. Additional details regarding the interface head and connections with the cassette may found in co-pending, commonly assigned U.S. Provisional Patent Application No. 60/097,511 (Attorney Docket No.
  • the tube 100 is preferably held in place by a threaded device 43 to hold the tube to the head 40.
  • the threaded device 43 is not exposed to the fluid flow path as the tube 100 extends past the threaded device and prevents liquid contact with the device 43. Hence, an inert fluid pathway is maintained even though the device 43 may be made of materials such as stainless steel or iron which may corrode when exposed to reagents.
  • the threaded device 43 has both internal and external threads so that it can be screwed into support 42 of the head 40.
  • the head 40 also has a plurality of connectors 93 and 94 which preferably provide connections to delivery and vent lines of the system 10, respectively.
  • Fig. 7 shows a cross-section of the interface head 40 shown in Figs. 6 and 8.
  • the opening 96 contains connector 93 which provides a connection with the valving and manifold on the delivery side as shown schematically in Fig. 14.
  • the holding tube or reservoir 206 may extend into the passage 97 shown in Fig. 7 from connector 93.
  • the holding reservoir 206 may be either completely apart from passage 97 or passage 97 may be the entire holding tube and have a valve located at position 98.
  • the connectors 93 and 94 are typically offset from each other to be aligned with the tubular structures 100 and 102, respectively.
  • Fig. 9 shows a preferred embodiment of the plumbing and fluid elements of a fully automated combinatorial synthesis system 10.
  • the plumbing and interface used with the present invention allows for precise delivery of reagents without diluting the fluids in the reaction vessel with solvents used as rinse fluids.
  • Fig. 10 provides a simplified plumbing schematic of the system of Fig. 9 when the interface head 40 is engaged to eight reaction vessels 50.
  • the syringe pumps 170 and 171 are used to provide delivery and/or extraction of fluids from the delivery side and the vent side of the reaction vessels 50.
  • Fig. 11 shows one configuration used to deliver reagent to the reaction vessel.
  • reagent in some synthesis apparatus, as reagent is sent into the reaction vessel, it leaves a trail of small droplets or coatings of material as the bolus of reagent is sent through tubing to the target reaction vessel. Hence, if 1 ml of reagent were meant for delivery, some amount less than 1 ml would reach the final destination.
  • a rinse fluid of solvent is delivered after the reagent delivery to clean the tubing and also to ensure than any amounts of reagent left in the tubing is picked up by the solvent rinse fluid and sent to reaction vessel. Introducing large amounts of solvent into the reaction vessel, however, is undesirable in some processes.
  • reagent is accurately metered into the reaction vessel without the introduction of rinse solvents into the reaction vessel.
  • the general theory behind this concept is the use of a pump such as a syringe pump to push on an entire tubing or line filled with liquid, except for a small air or gas gap of about 0.22 ml to separate reagent and solvent portions.
  • the air gap is introduced into the fluid bolus by valving which can switch the syringe pump to a gas source to add the air or gas into the line.
  • the air gap is preferably included to prevent dilution between the reagent and solvent portions. Without the gap, for example, 400 microliters of reagents are required to deliver 200 microliters into the reaction vessel 50. With the gap, only 250 microliters are needed to deliver 200 microliters into the reaction vessel.
  • the extra volume of reagent is used to fill the common passage between the holding reservoirs as discussed below.
  • the substantially incompressible column This creates a substantially incompressible liquid column.
  • This enables an accurate amount of reagent to be delivered into a holding tube or reservoir 206 immediately upstream from the reaction vessel 50.
  • the substantially incompressible column should push 5 microliters into the holding tube or reservoir 206.
  • a valve 208 then seals off the holding tube from the liquid column in connecting passage 204.
  • the reagent in the tube 206 is injected into the reaction vessel through gas pressure, typically after the connecting passage is cleared of liquid and fluidly coupled to a gas source.
  • no solvent rinse fluid is delivered into the reaction vessel with the reagent.
  • the reservoir 206 is about 250 microliters, where any volumes in excess of 250 microliters flows directly into the reaction vessel before the reservoir valve 208 is closed.
  • a syringe pump 170 is typically first used to prime the manifolds 172 and 174 with solvent.
  • the manifolds are connected together with a passage 476.
  • the passage may be designed to be large enough to be a reservoir.
  • Solvent is first drawn into the syringe pump 170 as indicated by arrow 177.
  • a valve 178 leading to the solvent source 179 is then closed.
  • Solvent is then typically injected through the system to prime the manifolds 172 and 174.
  • Reagent is then withdrawn via the syringe pump 170 using the solvent to help pull reagent as indicated by arrow 180.
  • a valve 182 to reagent source 184 is closed.
  • a small air or gas gap G preferably exists between the solvent S and the reagent R as shown in Fig. 12.
  • the entire fluid column is then delivered under syringe pressure down towards the interface head 200 and the reaction vessels 50 as indicated by arrows 202.
  • a manifold or block 203 is typically used to contain conduits such as connecting passage 204 and/or holding reservoirs 206.
  • the amount of reagent drawn from the reagent source 184 is preferably enough to fill slightly more than the connecting passage 204.
  • Holding tubes 206 may be filled as desired based on the amount of reagent to be introduced for each reaction vessel. As shown in Fig. 19, the syringe pump 170 will meter reagent into the holding tube or reservoir 206 when reservoir valve 208 is open.
  • the column of reagent R completely fills the common or connecting passage 204, the desired number of holding tubes 206, and extends slightly beyond the connecting passage 204.
  • the syringe pump, connecting passage, and holding tubes are all illustrated in co-pending, commonly assigned U.S. Patent Application No. 60/063,134 (Attorney Docket No. 16925-001900) filed on October 22, 1997, the full disclosure of which has been previously incorporated herein by reference.
  • the entire connecting passage 204 is then exhausted or blown into fluid waste container 210 via gas pressure from gas source 212. Once the connect passage 204 is cleared, the individual holding tubes 206 may then be pressurized to deliver the reagents into the reaction vessels.
  • a pressure line may be connected directly to holding tube 206. After reagent delivery, the line or tubing upstream from the reaction vessel may be flushed with solvent to clean the flow path.
  • the preferred embodiment of the synthesis apparatus has two syringe pumps 170 and 171.
  • Pump 171 is used with an autosampler which can provide additional diversity reagents than those stored in containers R1-R9.
  • solvent may still be withdrawn from the solvent sources via tube 220.
  • Additional reservoir or ballast tubes 222 and 224 may be used with the system.
  • other types of pumps may also be used besides a syringe pump. On such pump is described in co-pending, commonly assigned U.S. Patent Application No. 60/063,137 (Attorney Docket No. 16925- 002010) filed May 29, 1998, the full disclosure of which is incorporated herein by reference for all purposes.
  • the fluid delivery system may use plumbing different than those shown in Fig. 9.
  • these other embodiments would be able to separate some portion of the reagent plug or bolus, either the leading edge portion or some portion in the middle.
  • gas pressure can be used to inject the isolated portion of reagent towards to desired reaction vessel.
  • the distance to be traveled by the isolated reagent bolus is small, between about 0.01" to 0.60" inches.
  • the holding tube 206 may not be needed if the isolation portion is the connecting passage 204.
  • the system may comprise of a tubing, a valve upstream of the tubing, a pressurized gas source, and a waste vent in some embodiments. The waste vent would be connected and switched at the valve.
  • the sealable reaction vessels 50 allow for the use of gaseous reagents, particularly under positive pressures.
  • the cassette and reaction vessel configuration of the present invention allows the reaction vessel to be charged with gas and then sealed to process at the desired pressures. Openings created in septum systems will leak at positive pressures.
  • the present system may also be closed after delivery at positive pressures such as 5 to 10 psi above ambient pressure or have a low pressure supply continuously flow and charging the vessel with gaseous reagent.
  • the positive pressure may be required to get the desired molecular concentration of elements in the reaction vessel 50. At ambient pressures, the number of molecules may not be sufficient for synthesis.
  • ATU Agitation Thermal Unit
  • the present invention is preferably based around the cassette 110 which contains the reaction vessels 50 used for combinatorial chemistry synthesis.
  • the cassette 110 which may be designed to hold various numbers of reaction vessels, advantageously allows for the injection and extraction of liquids, reagents, or fluid washes from a reaction vessel 50 while maintaining an inert environment. Further details regarding the cassette 110 can be found in co-pending, commonly assigned U.S. Patent
  • the reaction vessels 50 used in the present invention typically have a relatively small or moderate volume such as about 5 ml. This is due in part to the relatively small volume of reagents used per reaction vessel when generating combinatorial chemistry libraries. This minimizes total cost of synthesis. Furthermore, large volumes of resulting product are typically not necessary until the product has been analyzed for beneficial or desired properties .
  • the reaction vessels 50 also contain tubing (Fig. 2A) which extend to the bottom of the reaction vessel. Because it is preferred that the cassette 110 be able to mate with an interface head 40 as previously described, the reaction vessel 50 is not open ended at its bottom surface and all connection are preferably located on upper ports 404 of the cassette 110. The tube or tubes inside the reaction vessel allows for the removal of liquids through the upper ports 404.
  • the relatively small size of the preferred embodiment of the reaction vessel 50 and the presence of tubing within the reaction vessel makes it difficult to use agitation devices placed within the reaction vessel.
  • Such device include various shaped items which are moved in an axially reciprocal manner by an external magnet.
  • the small stroke displacement allowed and the interference from internal tubes limits the effectiveness of such items placed in the reaction vessel.
  • the cassette 110 is connected to an agitator 410 which reciprocates the entire cassette as indicated by arrows 132.
  • the motion is typically a lateral reciprocating motion but it should be understood that a variety of other motions such as circular or even vertical may be used.
  • Fig. 15A is preferably a step motor 140 (Fig. 5) coupled to a cam mechanism 130 where the step motor can provide precise positioning of the cassette when the cassette comes to a stop. This is particularly desirable in automated synthesis systems where a consistent stopping position is required so that a robotically controlled interface head can mate with the cassette.
  • the system 10 may have sensors such as optical sensors mounted on the cassette 110, the cam 130, the interface head 40, and/or the ATU 468 to confirm the final position of the cassette.
  • a less accurate motor may be used for agitation since final position is less important as the user visually aligns the interface head with the cassette 110. Further details regarding the agitator can be found in copending, commonly assigned U.S. Provisional Patent Application No.
  • the motor generally reciprocates the cassette at a rate between about 100 and 300 strokes per minute, preferably about 250 strokes per minute.
  • the total stroke displacement may be between about 0.25 and 0.75 inches, preferably about 0.5 inches.
  • Some embodiments may agitate that cassette at 0.25 inches per side.
  • the reaction vessels 50 of the present invention may be operating in a temperature range from about -40°C to 150°C. These temperature changes are preferably attained by using a heated or cooled gas that is diffused into the hollow underside 430 of the cassette 110 as indicated by arrows 432. Although a variety of gases may be used, it is preferred that the gas is dry to prevent ice formation on the cassette. To stay within a ⁇ 5°C temperature variance, the dispersion of gas into the hollow underside 430 is maintained in a controlled fashion by a gas distribution plate 440 located below the cassette 110.
  • the distribution plate 440 typically does not agitate with the cassette 110.
  • the plate 440 has a plurality of holes 442 positioned in a grid pattern shown in Fig. 15B.
  • the grid pattern varies with the number of reaction vessels 50 in the cassette 110. In some embodiments, there is approximately one hole for each reaction vessel.
  • the holes are typically circular with a diameter between about 0.05 to 0.30 inches. They are typically about 0.6 to 1.2 inches apart, again depending on the number of reaction vessels 50 present.
  • the gas or dry air is typically recirculated and pumped around using a fan 450.
  • the fan 450 pulls air or gas down through vent 452 in the plate 440.
  • the air or gas is then circulated through the heating/cooling element 460 and distributed back into the underside 430 of the cassette 110.
  • the recirculation of gas or air minimizes the energy needed to maintain a desired temperature.
  • the heating/cooling element 460 preferably contains tubing 462 for liquid nitrogen or other coolant.
  • the element 460 also contains a heating element, typically resistive heating wire such as a kapton heater, to increase the gas or air temperature.
  • the element 460 is typically made of a thermally conductive material such as aluminum. Additional plates of conductive material may be attached to the element 460 to increase thermal conductivity.
  • fins 464 in a mostly hollow heating/cooling element 460 provides additional surface area for heat transfer with the circulating gas or air.
  • the stroke displacement of the cassette 110 is such that the area above the plate 440 remains sealed or overlapped by the cassette or related part .
  • the opening to the underside of the cassette 110 is larger than the opening exposing the cassette to heated or cooled gas to maintain enclosure during agitation.
  • heating using direct contact with the reaction vessels 102 may be designed with the cassette.
  • Such a direct contact heater may require the cassettes to have enclosures for surrounding the surface of each reaction vessel or recesses for the reaction vessels formed in a solid block.
  • Such a design may increase the weight of the cassette and also introduce additional thermal variances, such as insulation and expansion/contraction issues. Referring to Fig.
  • the combination of the agitator 410, the housing, the plate 440, the fan or gas recirculation unit 450, and heating/cooling element 460 form an agitation thermal unit (ATU) 468.
  • ATU agitation thermal unit
  • the cassette 110 can be removed and replaced with another cassette so that the agitation and thermal process can continue while the other cassette awaits other processing.
  • the plate 440 may also be designed to be replaceable so that even heat distribution can be achieved for cassettes of different sizes and numbers of reaction vessels 50. Insulation may also be provided around the ATU to minimize condensation and ice formation on the device. For example, insulative material may be placed on the interior of the side walls of the cassette.
  • a cassette fan 470 is preferably positioned to generate air or gas flow over the upper surface of cassette 110 during cooling procedures.
  • the air or gas flow over the upper surface minimizes or eliminates moisture accumulation which can be difficult to remove from cavities 104 and 106. Moisture in these cavities may degrade organic reactions in the reactions vessels 50 if the moisture is not removed prior to injection or extraction of materials into or from the reaction vessels.
  • the integrity of the air/liquid seal with the reactions vessels 50 and the lid 111 of the cassette 110 further benefit from having a fan or gas flow generator 470 generating flow over the upper surface of the cassette 110.
  • the fan 470 is positioned to blow directly at the lid 111 of the cassette 110 or across the lid.
  • the elastomeric material 472 (Fig. 2A) forming a seal between a cap valve 474 on the reaction vessel 50 and the lid 111 of cassette 110, hardens and no longer guarantees seal integrity.
  • the hardened elastomeric material 472 will not be sufficiently compliant to reshape and form a seal with the upper surface of the cap valve 474 when the cap valve is rotated to open or close access to the reaction vessel 50. This non-compliance may allow for air or liquid to seep past the elastomeric material 472 and contaminate the reactions in the reaction vessels 50.
  • the elastomeric material 472 and cap valve 474 are described in commonly assigned, copending U.S. Patent
  • the system 10 preferably includes devices for ensuring that liquid delivered from the syringe pumps 170 and 171 actually reach the reaction vessels. Since the nature of combinatorial synthesis involves creating substances from many different combinations of materials, the unknown nature of the reactions which may occur may result in precipitates or solids coming out of solution and blocking the fluid lines connected to the reaction vessels 50. With these synthesis apparatus typically running 24-hours a day under automated control, errors may occur in the middle of the night, without personnel around to respond to the error. This may create problems such as fluid lines backed up with reagents (which is costly) or may result in lost processing time.
  • the reliability aspect of the present invention provides devices and methods for detecting nondelivery of reagents or solvents and preferably devices to troubleshoot the problem.
  • FIG. 17A a simplified system comprising of a reaction vessel 50 and a metering system 580 is shown.
  • Fig. 17A shows that a plug or bolus 582 of reagent is being delivered to the vessel 50 by pressurized gas as indicated by arrow 584.
  • the gas from source 586 flows behind the bolus 582 and is typically flowing at a constant rate at this time.
  • the resistance in front of the gas is no longer there the gas indicated by arrows 584 flows at a much higher rate towards vent 588.
  • reagents or solvents there is a signature increase or spike in the gas flow as shown in Fig.
  • the line to the vessel 50 may also have an optical liquid sensor which can detect the passage of fluid through the delivery line.
  • the sensor uses a photosensor to register the changes in the index of refraction of the transparent or translucent delivery line.
  • the flow meter may be installed along other portions of the system to detect delivery of material thorough a particular line.
  • a flow meter 550 monitors fluid, typically gas flow, from locations 552, 554, 556, and 558. The gas flow measured at these locations can be used to determine whether chemicals have been properly delivered to their destinations.
  • Position 552 reads delivery to manifold 172
  • position 554 reads delivery from manifold 172 to manifold 174
  • position 556 read output from the autosampler 560. Additional sensors may also be placed at different locations along the flow path.
  • liquid sensors 570 using optical or other detection methods are installed along the flow path to verify that solvent or reagent has actually reached the desired locations.
  • the detection methods are non-invasive and will not contaminate the environment of the flow path.
  • the sensors 570 are preferably located along the holding tubes 206 and also at the end of the connecting or common passage 204.
  • the syringe pump serves to simplify the operation of the syringe pump 170 during fluid delivery. Instead of having to know the exact volume to push from the syringe pump 170 to fill the connecting passage 504, the syringe pump operates until the sensor 570 detects the presence of fluid at the end of the connecting passage 504. This simplifies operation and possible slippage from the liquid column being pushed to the interface head. It should be understood, of course, that the sensors 570 may be located at a variety of positions along the fluid flow path such as near the reagent sources and near the waste containers .
  • the system 10 uses a specific control algorithm to minimize the motions of the interface head 40. Since the coupling and decoupling of the interface head 40 with cassette 110 typically requires the filling of connecting or common passage 204 which is then discarded, excessive interface head movements result in wasted reagents which can be costly. To minimize movements and also to reduce time use to create combinatorial libraries, the interface head motion may be based on a Hilbert curve motion.
  • the Hilbert curve is a recursion process that is used to solve the positioning of desired products on the cassette and also to control head motion.
  • the Hilbert curve is used prior to synthesis to determine where the desired products should be located to minimize head motion.
  • the Hilbert curve algorithm is used to determine head motion if the location of the products of each reaction vessel is predetermined. The algorithm is typically used before the head starts to move, but alternatively, the algorithm may be activated during processing. It should be understood that the automated system 10 may also be used in combination with a hand held apparatus to minimize the number of locations the Hilbert curve needs to solve for if manual operation will simplify calculations. Such a manual interface head is described in co-pending, commonly assigned U.S. Provisional Patent Application No. 60/097,511 (Attorney Docket No. 16925- 002200) filed on August 21, 1998, the full disclosure of which has been previously incorporated herein by reference for all purposes.
  • the combinatorial libraries contain most or all combinations of the reagents organized by groups called dimensions.
  • reagents A and B might be combined with reagents 1, 2, and 3, to produce compounds Al , A2 , A3, BI, B2 , and B3.
  • the reagent collections are organized into steps, or dimensions, each consisting of a subset of the reagent collection.
  • the previous example used reagents A and B in dimension one and reagents 1, 2, and 3 in dimension two.
  • reagent space is used herein to refer to the n-dimensional information space comprising the combinations of reagents from each of n dimensions. Each combination of reagents corresponds to one compound and occupies one vertex in the reagent space .
  • the system 10 contains a series of vials or reaction vessels 50 into which the reagents are dispensed.
  • the reaction vessels 50 are grouped, preferably 48 per cassette 110.
  • the system 10 stores the reagents and delivers them to the reaction vessels through a plumbing system comprising reagent storage containers, electronically controlled valves, flow sensors, tubing, and a robotic mechanism.
  • a robotic mechanism containing a fluid interface head 40 connects the tubing that delivers the reagents, to the reaction vessels.
  • the plumbing system has access to eight reaction vessels 50.
  • the fluid interface head 40 must be disconnected, moved, and reconnected to gain plumbing access to other vessels 50.
  • the system 10 delivers a reagent to all reaction vessels on a cassette 110 that need it before the plumbing is rinsed and the next reagent is delivered. After all reaction vessels on a cassette receive their deliveries, the next cassette is similarly processed.
  • a space-filling curve is a mapping between one- dimensional space and n-dimensional space. In simple terms, it folds a line into n dimensions, somewhat like a string could be routed to fill a plane or a volume. Given a point in one-dimensional space, it produces a vertex in n-dimensional space.
  • the Hilbert curve is especially useful because of its clustering property, in that, as it fills the n-dimensional space, it tends to minimize excursions out of the local region that is filling at the moment. It is this clustering property that helps minimize rinsing and mechanical motion.
  • the clustering property is further described in "Analysis of the Clustering Properties of Hilbert Space-Filling Curve", submitted to IEEE Transactions on Knowledge and Data
  • a Hilbert space is constructed having the same number of dimensions as the reagent space in the target library.
  • a Hilbert space is cubic in that there are the same number of coordinates along each dimension, as in 8 X 8 X 8. The number of coordinates in each dimension must also be a power of two.
  • the reagent space dimensions are adjusted upward in size so that they are cubic, and so that each dimension contains a number of coordinates that is a power of two.
  • a 3 X 7 X 9 reagent space would require the generation of a 16 X 16 X 16 Hilbert space.
  • the desired reagent space is a sub-cube of the Hilbert space.
  • Each vertex in the Hilbert space is assigned to zero or more reaction vessels.
  • a vertex is assigned to zero reaction vessels if it lies outside the sub-cube comprising the reagent space, or if the chemist has "pruned" the associated target compound from the library.
  • a vertex is assigned to more than one reaction vessel if the chemist desires multiple instances of a compound.
  • the Hilbert space results in an ordering of all vertices, by virtue of its n-dimensional to one-dimensional mapping. It enables the construction of a sequence of vertices that must be assigned to at least one reaction vessel. This list is then assigned, one-by-one to the list of available reaction vessels, leaving empty those reaction vessels that the chemist sets aside for controls.
  • reagent list For each dimension, there is a list of reagents. This list is ordered so as to minimize rinsing. This is done by partitioning the reagent list according to compatible solvent groups. For example, if a dimension uses reagents A, B, C, D, E, F, and G, it might be partitioned as ⁇ A, C, F) ,
  • ⁇ B, G ⁇ , ⁇ D, E ⁇ if the reagents shown here in a bracketed group are compatible.
  • the partitions are ordered, resulting in an optimal reagent ordering. For example, if ⁇ B, G ⁇ would require an intermediate rinse if it followed ⁇ A, C, F ⁇ , a better partition ordering might be ( ⁇ A, C, F ⁇ , ⁇ D, B ⁇ , ⁇ B,G ⁇ ) , yielding an ordered reagent list of (A, C, F, D, E, B, G) . It is this ordered list of reagents that is assigned to the coordinates of the reagent space .
  • the system may use a reagent delivery unit without extraction capability in place of a reagent delivery/vent unit.
  • the circumferential seal could be formed by an O-ring of sufficient circumferential contact area to seal against a tubular structure. As seal of non-circular shape, but in contact all around the tubular structure may alos be used. Reaction vessels of different sizes and shapes may also be used. It is intended, therefore, that the invention be defined by the scope of the claims which follow and that such claims be interpreted as broadly as is reasonable.

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Organic Low-Molecular-Weight Compounds And Preparation Thereof (AREA)
  • Feeding, Discharge, Calcimining, Fusing, And Gas-Generation Devices (AREA)
  • Physical Or Chemical Processes And Apparatus (AREA)

Abstract

L'invention concerne un système utile pour la synthèse de composés chimiques, qui peut être utilisé en chimie de phase solide ou liquide. Selon une variante, le système (10) comprend une unité de libération/sortie de réactif (20) et une unité de traitement chimique (30) contenant une pluralité de cuves à réaction (50). L'unité de libération/sortie de réactif comporte une pluralité de structures tubulaires (100) conçues pour s'engager coulissantes dans des cavités (104) à l'intérieur de l'unité de traitement chimique, de manière à former un joint circonférentiel autour de chaque structure tubulaire. Généralement, l'unité de libération/sortie de réactif utilise une tête d'interface de fluide englobant les structures tubulaires, pour engagement avec l'unité de traitement chimique. Cette unité fonctionne de préférence avec une cassette (110) abritant toutes les cuves à réaction et définissant la pluralité de cavités allongées conçues pour recevoir les structures tubulaires.
EP98953791A 1997-10-22 1998-10-21 Systemes et procedes pour la synthese combinatoire d'arrangements de reaction chimique Withdrawn EP1028807A4 (fr)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US6313497P 1997-10-22 1997-10-22
US63134P 1997-10-22
US9750898P 1998-08-21 1998-08-21
US97508P 1998-08-21
PCT/US1998/022193 WO1999020395A1 (fr) 1997-10-22 1998-10-21 Systemes et procedes pour la synthese combinatoire d'arrangements de reaction chimique

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EP1028807A1 true EP1028807A1 (fr) 2000-08-23
EP1028807A4 EP1028807A4 (fr) 2006-12-13

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JP (1) JP2001520116A (fr)
AU (1) AU1107099A (fr)
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US6395235B1 (en) 1998-08-21 2002-05-28 Argonaut Technologies, Inc. Devices and methods for accessing reaction vessels
GB2347141B (en) * 1998-09-26 2002-01-16 Brendan James Hamill Combinatorial synthesiser
US7932213B2 (en) 1999-05-11 2011-04-26 President And Fellows Of Harvard College Small molecule printing
ATE237399T1 (de) 1999-09-29 2003-05-15 Tecan Trading Ag Thermocycler sowie hebeelement für mikrotiterplatte
US7169355B1 (en) 2000-02-02 2007-01-30 Applera Corporation Apparatus and method for ejecting sample well trays
US7435392B2 (en) 2000-02-03 2008-10-14 Acclavis, Llc Scalable continuous production system
US7413714B1 (en) * 2000-07-16 2008-08-19 Ymc Co. Ltd. Sequential reaction system
DE10036602A1 (de) 2000-07-27 2002-02-14 Cpc Cellular Process Chemistry Mikroreaktor für Reaktionen zwischen Gasen und Flüssigkeiten
EP1207396A1 (fr) 2000-10-20 2002-05-22 Seyonic SA Dispositif dispensateur de fluide
DE10121103A1 (de) * 2001-04-27 2002-10-31 Bayer Ag Parallelreaktor mit Begasungskassette zum Test von heterogenen Katalysatoren
WO2002099003A2 (fr) * 2001-06-06 2002-12-12 Monsanto Technology Llc Systeme de reacteur parallele et procede correspondant
FR2831081B1 (fr) * 2001-10-24 2004-09-03 Commissariat Energie Atomique Dispositif d'injection parallelisee et synchronisee pour injections sequentielles de reactifs differents
US6902704B2 (en) * 2002-02-28 2005-06-07 Equistar Chemicals, L.P Injection pump assembly for a combinatorial reactor and related method
US7101515B2 (en) 2003-04-14 2006-09-05 Cellular Process Chemistry, Inc. System and method for determining optimal reaction parameters using continuously running process
US20050265905A1 (en) * 2004-04-20 2005-12-01 Akribio Corp. Multifunctional multireactor chemical synthesis instrument
JP6607653B1 (ja) * 2019-04-09 2019-11-20 ヤマト科学株式会社 固相合成装置
DE102021204572A1 (de) * 2021-05-06 2022-11-10 Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung eingetragener Verein Dosierkopf und Dosiersystem zur Aufnahme und Dosierung wenigstens zweier Medien

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EP1028807A4 (fr) 2006-12-13
WO1999020395A1 (fr) 1999-04-29
WO1999020395A9 (fr) 1999-08-05
AU1107099A (en) 1999-05-10
JP2001520116A (ja) 2001-10-30

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