Perspective

Molecular Diversity, 1 (1995) 270-274

ESCOM

MOLDIV 027

Automating combinatorial chemistry:

A primer on benchtop robotic systems

Jill H. H a r d i n * a n d F r a n k R. S m i e t a n a
Lilly Reseamh Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, IN 46285, US.A.

Received 6 April 1996

Accepted 21 May 1996

Keywords: Robotics; Automation; Combinatorial chemistry

Summary
Benchtop robotic systems are inexpensive, flexible automation tools with potential applications in a wide
array of disciplines such as combinatorial chemistry, high-throughput screening, and genomics. We
explain the basic components of a benchtop system and explore factors to consider when purchasing
or customizing a robot, such as automation benefits, vendor selection, and current system limitations.
Issues involving system specification, software design, and hardware customization are then discussed.
Additionally, system optimization, validation, and support are detailed. Given a properly designed and
implemented system, the combinatorial laboratory can markedly increase compound synthesis and
purification.

Accompanying the growing acceptance of combina-
torial chemistry is the realization that manual processes
need to be automated. Automation establishes consistency
in the synthesis and screening of compounds, frees the
scientist from the mundane aspects of the process, and
channels scarce resources toward more productive arenas
demanding human attention. This paper explores automa-
tion from the perspective of benchtop systems specifically
designed for combinatorial chemistry.
Benchtop systems are currently being used to automate
a number of specific combinatorial chemisty applications.
These include applying microliter-scale volumes of syn-
thesized compounds to thin-layer-chromatography (TLC)
plates; adding solvents, reagents, diluents and resin slur-
ries to synthesis vessels; solid-phase extraction (SPE);
transfer of products to vials or microtiter plates; and
injection of final products into an autosampler attached
to either a high-pressure liquid chromatograph (HPLC)
or a mass spectrometer (MS). Some systems are capable
of septum piercing, a useful capability for adding product
to MS vials or removing product under an inert atmos-
phere. Several automation companies are currently mar-
keting robots specifically built for solid-phase combina-
torial chemistry. These firms include Advanced Chem-
Tech [1], Bohdan Automation Inc. [2], Science Applica-
tions International Corp. (SAIC) [3], Tomtec [4], Tecan
AG [5], Argonaut Technologies Inc. [6], and CombiChem
Inc. [7]. A host of other firms market systems capable of
automating various aspects of combinatorial chemistry,
including Beckman Instruments Inc. [8], Hamilton Co. [9],
RoSys Inc. [10], Gilson Inc. [11] and Packard Instrument
Company, Inc. [12]. Custom-built solutions can also be
purchased from Bohdan Automation Inc., Zymark Corp.
[13], and Sagian Inc. [14].
Before attempting an automation project, the limita-
tions of current benchtop systems must be clearly under-
stood. Some applications are straightforward and can be
automated using off-the-shelf systems requiring no further
customization. Other applications, though capable of
being automated, present a greater challenge since no

*To whom correspondenceshould be addressed.

1381-1991/$ 6.00 + 1.00 9 1996 ESCOM SciencePublishers B.V.


commercially available robotic system exists, necessitating
custom hardware construction.
Generally, automated systems do not perform tasks
quicker than manual alternatives. However, this does not
necessarily preclude the use of automated systems, as they
may run well beyond the typical 40-h work week without
an increase in hourly operating costs. There are reasons
to automate a task even if it does not prove cost-effective,
such as eliminating human exposure to toxic chemicals,
human 'burnout' due to the performance of repetitive
routine tasks, the necessity for very accurate and precise
deliveries of liquids, or to standardize procedures across
many laboratories within a given department or company.
Therefore, automation may be able to compete with
manual performance if the timing, expense, and accuracy
issues provide adequate justification. In order to guage
the applicability of automation, it is important to under-
stand both current functionality as well as limitations.
Functionality that is currently available for automated
systems includes intelligent error recovery; allowing ro-
bots to assess an unexpected event, take corrective action
and proceed rather than halting. Multi-tasking is a fea-
ture available with certain robotic systems software in-
volving the simultaneous operation of multiple pieces of
equipment within a given system. Multi-tasking may be
invaluable in an automated system as it maximizes system
throughput by minimizing the downtime of the various
components comprising the robot. Commercially available
databases may be used to capture relevent data generated
in an automated system and provide convenient links to
statistical data evaluation tools or allowing for the use of
data mining tools, such as neural networks, to create
'intelligent' databases.
There are some situations which commercially avail-
able robotic systems may not be able to address. The
weight of containers that will be used in the automated
process needs to be examined closely. Most robots are
restricted to moving only a few kilograms at best. Heavier
containers would demand manual intervention, eliminat-
ing the possibility of a totally automated system. If sep-
turn puncturing is to be performed, robot-arm durability
and ruggedness is paramount. Processes requiring subjec-
tive observations to determine a color change or product
formation may be difficult or impossible to automate.
Another factor to consider is the length of time a given
automation system will be operational. This factor may
prove to be substantial when comparing the cost of the
automated system with the manual process. Budgetary
constraints must be examined to determine how much of
the process can reasonably be automated. A semi-auto-
mated solution involving minimal human intervention
may meet the needs of a laboratory unable to finance a
'cradle-to-grave' solution. It is conceivable that several
robots can be used in tandem to perform the desired
automation. Complexity increases dramatically when
271
using multiple systems, and timing issues must be resolved
to eliminate workflow bottlenecks.
The length of time necessary to automate a given ro-
botic system may prove to be substantial therefore, this
factor must be weighed heavily when considering an
automation project. The length of time required to auto-
mate may be increased with the increase in complexity of
the desired task. Simple routine tasks, for example serial
dilutions, may be programmed in a vendor-provided
'point and click' environment, while a more difficult task
may need to be programmed in a more complex environ-
ment, using a language such as C++ or Microsoft Visual
Basic. With the increase in complexity of the task one can
expect the length of time required to program the robot
to increase, as well as the complexity of the program.
Other automation-system applications may require the
use of customized hardware, requiring substantial invest-
ments of time and money, as it becomes necessary to
work closely with a machine shop to design the hardware.
After the automation specialist has delivered the desired
system to the end users, requests for changes in the pro-
gramming or hardware of the system typically begin to
surface. Changes may be due to work load increases,
evolvement of underlying processes or misunderstood ex-
pectations. The latter can be minimized by the automation
specialist possessing a thorough understanding of the man-
ual application to be automated and by providing users of
the system with a system-requirements document. This is
a document detailing everything a given system needs to
do in order to be used, accepted, and valuable to the users.
Once the users have 'signed off' on this document, the
automation specialist may begin working on the system.
Ideally, the automation specialist charged with imple-
menting a benchtop system will have a clear understand-
ing of the processes to automate. Failing that, it is im-
perative that the specialist has free access to the personnel
engaged in chemical synthesis. Automation project fail-
ures are often the result of an incomplete understanding
of the end user's expectations. If the automation specialist
does not have a thorough understanding of the underly-
ing process, she may choose to shadow laboratory per-
sonnel for several cycles of the manually executed syn-
thesis to familiarize herself with the attendant details and
potential difficulties.
A number of commercially available off-the-shelf sys-
tems may currently be evaluated by a laboratory seeking
to automate its applications. It is preferable to negotiate
a risk-free evaluation period with each prospective ven-
dor, typically 1 to 2 months in duration. This allows the
specialist time to evaluate the chemistry, programming
and durability of a system, and to perform an objective
comparison between the various robots. If the applica-
tions demand a custom-built robot, the laboratory will
obviously not have the luxury of performing a risk-free
evaluation at the expense of the vendor.
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Some benchtop systems are merely retooled versions of
aqueous-based liquid-handling robots. Tubing, valves and
any other components that are subjected to prolonged
contact with organic solvents will therefore have to be re-
placed with components capable of resisting this expo-
sure. The arm's construction is also critical to the longev-
ity and success of the system. During the evaluation phase,
periods of time should be blocked off to run diagnostics
that check the reproducibility of the arm's positioning
mechanisms. Some robots such as the Tecan RSP 5000
provide utility programs that automate this procedure.
A typical benchtop robot consists of a work surface or
deck, a robotic arm, a liquid-handling system and a con-
troller, and a personal computer (PC). Roughly two feet
deep by three feet long, the deck of an instrument may
house numerous components, such as test-tube racks,
microtiter plates, wash troughs, or autosamplers and in-
jection ports.
The robotic arm manipulates and transfers samples,
reagents and diluents on the deck. The arm of the robot
is capable of movement along the x-axis with range of
motion bounded by the dimensions of the deck. The
robot may have one, four or eight probes which are ca-
pable of movement in the yz plane and equipped with a
variety of different tips used to manipulate liquids. Some
vendors offer an optional second arm that, although
identical in functionality to the primary arm, does not
necessarily double throughput. Due to sample-scheduling
demands and the synchronization of functions on the
robot, the second arm may be idle for long periods of
time. Instead of the two arms being configured identical-
ly, the second arm might operate as a plate handler ca-
pable of a wide range of motion. The RoSys Plato and
the Tecan Roma systems exemplify this type of robot.
The liquid-handling system interacts with the arm to as-
pirate and dispense liquids between designated locations on
the deck. This system is flushed and filled with a system
liquid, typically a solvent compatible with the reagents
used during the synthesis. The system is composed of the
aforementioned probes, a length of tubing connecting the
probes to the syringes, a stepper-motor mechanism capable
of driving the syringes, a switching valve that facilitates
liquid transfer and a liquid-detection mechanism. The
probes are usually individually plumbed, allowing each
probe to handle different volumes, if necessary. Various tip
configurations are commercially available. If the applica-
tion specifies a sterile or pyrogen-free pipetting appar-
atus, disposable tips must be used which are available in
polystyrene or polypropylene. These tips perform a single
transfer and are then discarded by the robot. Fixed tips
are another option and are composed of Teflon-coated
stainless steel. These tips are washed between liquid trans-
fers and generally have a lifetime of several months.
Connecting each tip to its respective switching valve is
a length of tubing with sufficient internal volume to con-
tain the maximum amount of liquid that could be drawn
up by that syringe, thereby preventing samples and re-
agents from entering the syringe. Syringes vary in size
from 0.10 ml to 25 ml. Syringes contain system liquid
that is separated from samples and reagents by airgaps
that are programmed into the liquid-handling operation.
Syringes are driven by the stepper motors, which are
capable of accurate movement at a very small step size,
perhaps 8000 increments over the path of syringe travel.
Switching valves toggle between inlet and outlet settings
to aspirate and dispense liquids through the tip. When
using organics, it is imperative to use syringes and valves
that are Teflon-coated. Most robots use syringes and
valves manufactured by either Cavro or Hamilton; some
of both companies' components are resistant to a broad
range of organics.
Liquid-level sensing is a mechanism that ensures that
the minimum amount of liquid required by an application
is present prior to aspiration from a container. If sensors
fail to detect this minimum, an error message is displayed
or logged by the system informing the user of this condi-
tion. The majority of liquid-level-sensing systems are
capacitance-based, relying on ionic activity to determine
the presence of liquid. Problems may occur when pipet-
ting organic solvents exhibiting weak ionic activity. A
second approach, termed sonic liquid-level sensing, is
used in the Beckman Biomek 2000. A sound-wave gener-
ator and a receiving device similar to a microphone em-
bedded inside the Biomek's liquid-handling tools provide
sensing capabilities that are not dependent on a liquid's
ionic activity. The analyst may also choose to disable
liquid-level sensing completely. If this approach is em-
ployed, probes are programmed to travel to the maximum
coordinate on the z-axis of the respective container before
aspirating liquids from the container. Disabling liquid-
level sensing forces the end user to maintain appropriate
levels of liquid in all containers to ensure the proper
execution of the application.
The robot is controlled by an Intel 486 or Pentium-
based PC. Communications to the robot take place either
via a custom interface card or the RS-232 port on the PC.
Peripheral devices can also be controlled through addi-
tional communication ports on the PC. A generic PC
configuration might include 8-16 megabytes of volatile
memory (RAM), a 3 1/2" floppy-disk drive, and from 100
to 500 megabytes of permanent hard-drive storage. A cur-
rent trend in the software industry is to package shrink-
wrapped software on CD-ROMs, necessitating a CD-
ROM drive. Additionally, the PC should be configured
with at least one communications port.
Two software environments are currently available for
benchtop robotic systems. One approach caters to the
scientist, providing a 'point-and-click environment' requir-
ing no in-depth programming at the expense of some
flexibility and extensibility. The Beckman Biomek 2000

provides a three-dimensional graphical depiction of the
deck. The user builds an application program by selecting
volumes, locations and containers from this depiction.
The actual machine commands are then automatically
created by the Biomek system software. Despite its ex-
treme ease of use, these environments may not support
file manipulation or peripheral device control. This may
be problematic when querying external databases or de-
vices or sending data to a laboratory-information-man-
agement system (LIMS).
A second approach to creating robotics software pro-
vides a complete programming environment for experi-
enced automation specialists. Designed for specialists
accustomed to working with languages such as Microsoft
Visual Basic, C++, or Borland Turbo Pascal, these envi-
ronments provide total flexibility and extensibility. Ro-
botics vendors generally define the software driving the
mechanical operations of their robot in a Dynamic-Link
Library (DLL). The programmer uses a language such as
Microsoft Visual Basic to create data-entry screens, re-
ports and the scheduling of the automated synthesis while
using the DLL to perform robot-specific operations.
Interfacing to an external database such as Oracle or
Sybase is also handled through the use of a DLL. If the
scientist wishes to send data directly to a spreadsheet or
statistics package, Dynamic Data Exchange (DDE) may
be used. Note that these capabilities are possible only
when the application resides under a graphical operating
system such as Microsoft Windows 3.1 or Microsoft
Windows 95. Older applications written for the Disk
Operating System (DOS) will not share this capability,
although various vendors do provide user-friendly envi-
ronments in their DOS applications.
Regardless of which approach is used for software
design, end-user acceptance is largely dependent on the
application's ease of use and the software's ability to anti-
cipate and correctly process improper or erroneous user
input. Although it requires additional programming, the
analyst may choose to create detailed audit trails that
facilitate diagnosis of hardware problems, should they
occur.
When contracting with an outside vendor for software
development, an agreement regarding source code must
be established. Source code is comprised of readable files
that can be edited by a programmer when modifications
to the application need to be made. These files are then
compiled into machine-readable form or interpreted by
the PC for use by the robot. If the vendor does not re-
lease the application's source code, the user will be depen-
dent on the vendor for all subsequent updates and main-
tenance. In this case, purchasers should negotiate for the
source code to be held in escrow by a third party in the
event that the outside vendor becomes insolvent. The
vendor may also choose to sell the source code or provide
it as part of the robot's purchase price.
273
When synthesis applications demand customized hard-
ware, an in-house machine shop may be indispensable for
rapid hardware prototyping and testing. A second ap-
proach is to use an external machine shop, though it may
be difficult to effectively communicate the exact needs of
the desired prototype, and the subsequent turn-around
time for prototype development may be unacceptably
slow. A third approach is to have a vendor specializing in
custom automation design and build a robot to meet the
laboratory's needs. Bohdan Automation Inc. specializes
in the construction of robots into which commercially
available components are integrated whenever possible.
Off-the-shelf systems are also available from this vendor.
Bohdan writes Windows software capable of integration
into external databases using text file transfers. Sagian
Inc. also builds custom robotic systems interfaced with
CRS [15] and Orca subsystems. The Orca robot is cur-
rently manufactured by Sagian Inc., as is the point-and-
click SAMI software environment which allows rapid
application development that intuitively models the work-
flow of the process being automated.
Once the hardware and software have been implemen-
ted, the robot's liquid-handling parameters must be opti-
mized. These parameters include the syringe speeds used
to aspirate and dispense liquids, the size of the airgaps
that surround the aspirated liquid and delay times that
pause the probe following liquid dispensing. Depending
on the fluids that will be used in the application, this
optimization process ranges from straightforward to tedi-
ous. Parameters are very dependent on the volume and
viscosity of the representative liquid; therefore, a universal
parameter set, robust enough to handle the entire range
of potential volumes, rarely exists. A statistical technique
available in most PC-based statistics packages that can be
used to expedite parameter optimization is E X P E R I M E N -
TAL DESIGN. Using a statistically generated matrix of
potential parameter sets, the automation specialist gener-
ates gravimetric or volumetric measurements for those
parameters, allowing the statistical routine to quickly
determine a robust optimum for a given range of volumes
and viscosities.
Following optimization, the robot must be validated to
ensure that volumes being dispensed are accurate and
precise. A batch program can be written that aspirates
and dispenses numerous aliquots across the range of
volumes used in the application. The aliquots are then
weighed and adjusted for density to determine whether
the optimized parameter set delivers the correct volumes.
If the liquid-detection unit is employed, it must be vali-
dated to determine whether detection takes place at vol-
umes and ionic concentrations typical to the application.
This is especially critical when using very small sample
volumes.
Though usually treated as an afterthought, system
maintenance costs should be considered during the robot
274
selection process. With nonrobust systems, these costs
may prove to be a significant percentage of the original
purchase price. Systems that suffer a high failure rate
tend to discourage further automation efforts and cast
doubt on the credibility of results generated by the robot.
Maintenance contracts can be negotiated with most ven-
dors and may be necessary if the synthesis laboratory
lacks trained instrumentation-service technicians.
The system will require both users and instrumention
technicians to support the hardware. It is necessary for
users to be trained to perform routine maintenance on a
given system. Though this may appear trivial, finding a
person who is motivated to perform such tasks reliably
may be difficult. Timetables for performing routine main-
tenance range from daily to yearly activities. Certain
applications may be dependent on the actual time that the
robot is in service. Time in service can be logged by the
robot's software, eliminating the need for manual track-
ing. Examples of routine maintenance are the removal of
dust and dirt from the instrument deck and arm, thor-
ough lubrication of the arm, and inspection of syringes,
valves, and tubing for wear and leaks. When done on a
routine basis this maintenance will prove to be invaluable
to the life of the automated system.
Instrumentation technicians have a more in-depth
understanding of system hardware than the typical end
user. They are capable of thoroughly dismantling and
troubleshooting an instrument down to the circuit board
level. These technicians generally obtain their training
from the system vendor, though some automation com-
panies prefer to keep this level of expertise within their
organizations, necessitating service contracts. In addition
to diagnosing and repairing unexpected system malfunc-
tions, instrumention technicians are also responsible for
performing periodic preventative maintenance, such as
removal and replacement of syringes, tubing, and valves
and checking the system's pipetting accuracy and liquid-
detection capabilities. A program that transfers replicate
aliquots across a broad range of volumes to a container
appropriate for gravimetric verification should also be
run periodically to determine whether accuracy and preci-
sion is being maintained by the liquid-handling system.
Systems that perform this calibration check using the
optical density of a dispensed solution are commercially
available and can be easily integrated into most benchtop
systems.
A properly designed benchtop robotics system can
markedly increase the throughput of a synthesis labora-
tory. Carefully determining the scope of the automation
project, clearly communicating the details of the synthesis
and analytical procedures to the automation specialist,
and becoming familiar with the host of commercially
available benchtop systems should guarantee a successful
implementation. Combinatorial chemistry applications
lacking off-the-shelf solutions may also be automated by
vendors specializing in customized systems.
References
1 Advanced ChemTech, 5609 Fern Valley Road, Louisville, KY
40228, U.S.A.
2 Bohdan Automation, Inc., 1500 McCormick Boulevard, Munde-
lein, IL 60060, U.S.A.
3 Science Applications International Corporation (SAIC), 10260
Campus Point Drive, MS C4, San Diego, CA 92121, U.S.A.
4 TomTec, 607 Harborview Road, Orange, CT 06477, U.S.A,
5 Tecan U.S. SLT Lab Instruments, RO. Box 13953, Research Tri-
angle Park, NC 27709, U.S.A.
6 Argonaut Technologies, Inc., 887 Industrial Road, Suite G, San
Carlos, CA 94070, U.S.A.
7 CombiChem, Inc., 9050 Camino, Santa Fe, San Diego, CA 92121,
U.S.A.
8 Beckman Instruments, Inc., 846 Algonquin Road, Schaumburg,
1L 60173, U.S.A.
9 Hamilton Co., 4970 Energy Way, Reno, NV 89502, U.S.A.
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Middleton, WI 53562, U.S.A.
12 Packard Instrument Company, 800 Research Parkway, Meriden,
CT 06450, U.S.A.
13 Zymark Corporation, Zymark Center, Hopkinton, MA 01748,
U.S.A.
14 Sagian Inc., 5601 West 74th Street, Indianapolis, IN 46278, U.S.A.
15 CRS Robotics Corp., 5344 John Lucas Drive, Burlington, ON,
Canada L7L 6A6.