Daedalus RM User manual

User’s Guide
RM Synthesizer
Version 1.02
Copyright ©2010
Daedalus Innovations LLC
Aston, Pennsylvania
United States

1
TABLE OF CONTENTS
LIST OF FIGURES ....................................................................................................2
WARNINGS / INFORMATION...................................................................................3
ITEMS INCLUDED WITH THE RM SYNTHESIZER..................................................4
ITEMS TO BE SUPPLIED BY THE END-USER........................................................5
INSTRUMENT SITE CONSIDERATIONS.................................................................6
CONNECTION DETAILS...........................................................................................7
THEORY OF OPERATION......................................................................................10
CONVENTIONS USED IN THIS MANUAL..............................................................14
VALVE DESCRIPTIONS .........................................................................................14
BACK PANEL CONNECTIONS...............................................................................16
FRONT PANEL CONTROL .....................................................................................17
PREPARING THE INSTRUMENT FOR USE ..........................................................17
THE MIXING CHAMBER / ADDING REAGENTS....................................................19
SEALING THE MIXING CHAMBER.........................................................................21
PROTOCOL FOR MAKING SAMPLES...................................................................22
TRANSFERRING SAMPLES FROM THE MIXING CHAMBER TO THE NMR CELL
.................................................................................................................................25
CLEANING THE MIXING CHAMBER......................................................................26
RESETTING THE SYSTEM FOR THE NEXT SAMPLE..........................................28
TIPS.........................................................................................................................29
CALIBRATING THE SYSTEM.................................................................................31
REPLACING THE WINDOW SEALS.......................................................................32
SPECIFICATIONS...................................................................................................36
FURTHER INFORMATION......................................................................................38

2
LIST OF FIGURES
Figure 1: Possible bench-top setup............................................................................6
Figure 2: Possible fume hood setup...........................................................................7
Figure 3: Cleaning manifold assembly diagram .........................................................8
Figure 4: Piston position during operation................................................................10
Figure 5: RM Synthesizer Operational Description ..................................................12
Figure 6: RM Synthesizer Flow Diagram..................................................................13
Figure 7: Example valve actuation progression........................................................14
Figure 8: Back panel port connections.....................................................................16
Figure 9: Front panel controls ..................................................................................17
Figure 10: Mixing chamber components: Poston, reagent plate, and main seal
(MCCS)....................................................................................................................19
Figure 11: View showing internal placement of the mixing chamber components ...20
Figure 12: Progression of steps for assembling and sealing the mixing chamber prior
to sample preparation...............................................................................................21
Figure 13: Increasing the sample chamber pressure using the piston .....................24
Figure 14: Progression of valve actuation for the sample transfer steps..................26
Figure 15: Removing the piston ...............................................................................28
Figure 16: Replacing the mixing chamber windows .................................................33
Figure 17: Reassembly of the window plug..............................................................33
Figure 18: Reinserting the window plug ...................................................................34
Figure 19: Face plate tightening pattern...................................................................34
Figure 20: Removing the light housing.....................................................................35
Figure 21: Internal control board schematic.............................................................37

3
WARNINGS / INFORMATION
When the system contains alkane gas the system should be left turned
on since an internal fan constantly circulates the air in the instrument
case to prevent possible build-up of flammable gases.
The maximum pressure rating of this device is 1 kbar (14,500 psi).
Use of the system above this pressure can result in component failure
and possible injury to the user.
The system has been leak tested to the maximum pressure, however
when using gases, especially expensive deuterated reagents it is
prudent to not leave gases loaded in the system for extended periods
of time. It is good practice to retract the gases from the RM
Synthesizer back into the syringe pump, and then push it back into the
gas cylinder.
The MCCS seal is single use only. Reuse of the seal or undertaking
multiple displacement cycles of the piston at high pressure can cause
the seal to fragment leading to the loss of pressure tolerance or
causing the piston to be jammed in the cap or mixing chamber.
Do not open the HP ALKANE TO BOOSTER valve on the RM
Synthesizer if the reservoir is not filled with liquid CO2. This could
displace the internal separator of the gas booster to an unknown
position. Thus it is very important that the separator be reset to the
position closest to the alkane inlet on the gas booster (see Figure 6)
for proper function and transfer of samples to the NMR tube under
pressure.

4
ITEMS INCLUDED WITH THE RM SYNTHESIZER
Below is the list of components that are supplied with the RM Synthesizer to
facilitate setup. This list includes part numbers for possible replacement sources
where appropriate.
Quantity Description Source
1 Elpac Power Systems 12V, 0.5A auto
ranging power supply
1 AC power cord
30 ft. 1/16” O.D. x 0.03” I.D. stainless steel
tubing (1 – 10 ft. coil, 1 – 20 ft. coil) High Pressure Equipment Company P/N 15-9A1-030
16 15,000 psi glands – ¼”-28 threads High Pressure Equipment
Company P/N 15-2AM1
16 15,000 psi sleeves High Pressure Equipment
Company P/N 15-2A1
4 1L Pressure resistant bottles Ace Glass P/N 5557-20
4 PTFE 3-hole GL-45 caps VICI P/N JR-9000-0001
1 PEEK Cross w/fittings – ¼”-28 threads VICI P/N CXMPK
3 packs Cheminert glands and collars – ¼”-28
threads; 5/pack VICI P/N CFL-1N
1 PEEK plug – ¼”-28 threads VICI P/N CPPK
3 PEEK shut-off valves – ¼”-28 threads Cole-Parmer P/N 02014-
00
1 PEEK check valve – ¼”-28 threads Cole-Parmer P/N 01355-
26
12 ft 1/16” O.D. polyethylene tubing Various sources
1 5/16” x 1/4” wrench
1 3/4” wrench
1 3/16” hex driver
200 MCCS mixing chamber cap seals
(primary) Daedalus
10 WS01 mixing chamber window seals
(spares) Daedalus
2 Stir bar
North America only
1 Nitrogen gas regulator; 150 psi max. out
1 Tescom Extreme Pressure Regulator;
6000 psi max in; 2,500 psi max out
1 0-3000 psi brass gauge
1 0-3000 psi brass gauge
1 CGA 320 brass nipple
1 CGA 320 brass nut
1 HiP 15-21AF1NMB adapter
1 HiP 15-21AF1NMC adapter

5
ITEMS TO BE SUPPLIED BY THE END-USER
Some additional tools may be required to complete the setup of the instrument.
Metal tubing cutter: A 1/16” metal tubing cutter and deburring tool will be
necessary to cut sections of tubing for making connections between the syringe
pump and RM Synthesizer and connections to the gas cylinders.
Teflon tape: This may be required when making attaching gas cylinder regulators.
The gas cylinder requirements are outlined below.
N2gas cylinder: Standard nitrogen gas cylinder. High purity is not necessary. For
customers outside of North America a suitable regulator capable of outlet pressures
of at least 120 psi – 150 psi (~8 bar - ~10 bar) is ideal.
CO2gas cylinder: Proper function of the RM Synthesizer requires that CO2be
delivered in liquid form. A standard CO2gas cylinder will NOT work for this purpose.
Many companies can apply 2,000 psi helium head pressure to a cylinder to allow the
CO2to exit as a liquid. This requires the tank be equipped with an eductor or siphon
tube so liquid CO2will be drawn from the bottom of the tank. High purity is not
required. For customers outside North America a regulator capable of outlet
pressures of at least 1,800 psi (124 bar) is preferred. Lower outlet pressures are
possible, but it should not drop below the liquefaction pressure of CO2 (~850psi @
RT).
Alkane gas cylinder: Typically the propane and ethane gas cylinders used with the
RM Synthesizer do not have a regulator attached. The reason for this is the alkane
is generally loaded into the cylinder at or near the liquefaction pressure. So in most
cases the gas is withdrawn at maximum cylinder pressure hence no regulator is
needed. However, it is likely an adapter will be required mate the 1/16” tubing from
the RM Synthesizer to the cylinder outlet. Due to the variance in cylinder types
Daedalus does not attempt to supply suitable adapters. Companies such as High
Pressure Equipment Company (www.highpressure.com) can help identify a proper
adapter once the outlet specifications for the particular alkane tank are identified.

6
INSTRUMENT SITE CONSIDERATIONS
The operation of this instrument involves the use of high pressure
carbon dioxide and flammable gases. Quantities of these gases are
vented from the system after sample preparation. For the safety of the
user this instrument should be setup in an exhaust hood or other
suitable ventilated environment.
The setup instructions below assume that the syringe pump to be used with the RM
Synthesizer is the Daedalus Xtreme-10. The proposed arrangement of components
is merely a guide. Other configurations are possible, and may be necessary
depending on the space available. It is important to stress the necessity of using the
equipment in a ventilated space for the safety of the user.
The bench-top setup in Figure 1 assumes that the instrument in installed under an
appropriate exhaust hood. If that is not feasible, the instrument can be installed
inside a fume hood, however many fume hoods have a smaller depth than the length
of the Xtreme-10. This may require that the Xtreme-10 be placed towards the back
as shown in Figure 2. The Xtreme Controller would have to be placed outside the
hood, or mounted on top of the Xtreme Pump Box. Alternatively, the Xtreme-10
Figure 1: Possible bench-top setup

7
could be turned orthogonal to the placement in the figure with a portion protruding
outside the hood. If this configuration is selected, the Xtreme-10 should be placed
on the left side of the hood with the inlet / outlet side facing to the right hand side.
This places the internal tubing fully in the hood for optimal safety. The Xtreme
Controller could then be placed on top of the Xtreme Pump Box. Not shown are
nitrogen and carbon dioxide cylinders which would be outside the fume hood.
CONNECTION DETAILS
Once the instruments have been positioned the equipment should be connected
using the included 1/16” stainless steel tubing, the high pressure 15-AM1 glands,
and 15-2A1 sleeves. These steps should be followed when making a high pressure
connection:
i) Deburr the end of the tube section.
ii) Assemble the gland then sleeve onto the tube end.
iii) Insert the end of the tube into the fitting until it bottoms.
iv) Tighten the gland to 55 in·lb. A “bottoming out” or “dead stop” should be felt
when the connection is properly assembled.
Always use two wrenches when tightening fittings: one to tighten the
gland and one to prevent counter rotation of the fitting receptacle.
Failure to do so could break loose internal connections.
Make the following connections using high pressure tubing and fittings unless
otherwise specified:
Figure 2: Possible fume hood setup

8
1) Connect the OUTLET port of the Xtreme-10 to the HP ALKANE INLET port on
the back of the RM Synthesizer.
2) Connect the INLET port of the Xtreme-10 to the alkane gas cylinder.
3) Connect with high pressure the CO2INLET port on the RM Synthesizer to the
CO2gas cylinder regulator.
4) Connect the N2INLET port on the RM Synthesizer to the N2gas cylinder
regulator.
5) Connect a section of tubing to the WASTE port of the RM Synthesizer using a
high pressure fitting. Assemble the Cheminert CFL-1N gland and sleeve on the free
end. Feed this end through the small port of one of the three-port bottle caps until it
is at the bottom of the bottle. Tighten the Cheminert gland to secure the line. The
remaining ports of this bottle cap should be left open to allow gases to vent.
Figure 3: Cleaning manifold assembly diagram

9
6) Assemble the cleaning manifold according to the Figure 3 using the included parts
and connect to the RM Synthesizer as indicated.
7) The NMR cell is connected to the OUTLET/INLET valve on the RM Synthesizer
as indicated later in the instructions. This valve can also serve as the introduction
point for deuterated alkane in situations where the syringe pump is not fully loaded
with deuterated solvent.
(This section is intentionally blank)

10
THEORY OF OPERATION
The RM Synthesizer was designed to bring together all the necessary elements for
preparing reverse micelle samples in liquid alkanes at high pressures. One issue
with preparing samples in a vessel where the desired analysis cannot be performed
is the need to move the pressurized sample into a more appropriate container. In
the case of reverse micelle samples, the efficacy of the sample is dependent on the
pressure such that in moving the sample the pressure cannot dip below a certain
threshold without losing integrity of the construct.
There are a variety of methods that could be used. The first is to avoid the two
vessel system entirely; however, mixing in the high pressure NMR tube is not very
efficient and was discarded early in the development. Another method is to use a
high pressure gas to push that sample from one vessel into another. After
considering a variety of gases there are not many candidates that are immiscible
with liquid alkanes, readily obtainable, and do not require significant compression
cycles to bring the pressure of the gas up to the level required. Nitrogen is one of
the best candidates. However, for certain applications, the pressure required for the
transfer step increases the density of the nitrogen gas above that of the liquid alkane
such that the nitrogen is no longer pushing the sample; rather it replaces the sample
in the secondary chamber. The
method used by the RM Synthesizer is
to displace the sample, by way of a
piston, from the mixing chamber into
the NMR tube. The relative piston
position during preparation and
transfer is shown in Figure 4.
The force driving the piston
displacement is provided by the
expansion of a high pressure fluid
delivered by a secondary pressure
source. Again, there are a variety of
alternative methods that could be used to achieve this action. Rather than explain
why other methods are not used, this discussion will focus on the what RM
Synthesizer provides for this step. The liquid alkanes used in the preparation of
reverse micelles are highly compressible. Data from the website:
http://webbook.nist.gov/chemistry/ for liquid ethane shows that ethane undergoes a
decrease in volume of approximately 7% over the range of 4,000 – 7,000 psi. This
Figure 4: Piston position during operation

11
change in volume can be harnessed to rapidly move the piston when a reservoir at
high pressure is allowed to relax to a lower pressure. This process is rapid, and the
pressurizing fluid does not need to go through a transition from liquid to gas to
deliver the needed force.
This entire action could be provided solely by the syringe pump. However, the
syringe pump plays a role immediately after the actual transfer step by rapidly
returning the sample to the required encapsulation pressure. This will be discussed
later in the example protocols. The end result is the syringe pump has the role of
maintaining the reverse micelle sample pressure over being used to drive the piston
directly. In addition, and perhaps more importantly, more of the precious deuterated
alkanes would be wasted using it as the fluid for this step.
Instead the secondary pressure source is provided by an internal fluid reservoir or
gas booster. It turns out that carbon dioxide has nearly identical compressibility as
liquid ethane. Thus the reservoir can be filled with CO2and this fluid pressurized to
the required level using liquid ethane delivered by the syringe pump. A separator
piston in the reservoir keeps the fluids apart. Once the transfer steps are performed,
the CO2fluid can be used to push any deuterated alkane out of the reservoir
keeping the losses to an absolute minimum.
The piston displacement literally rams the sample into the waiting NMR tube.
Because it might be possible to deliver more pressure to the piston than the tube
can withstand the dimensions of the piston and length of the connection tube to the
NMR cell were selected such that the piston displaces less than the volume of the
NMR cell plus tubing. For most situations this is not strictly necessary. However, for
the small fraction of cases where this might be important, it is suggested this
approach be maintained.
Since the volume displaced is less than the volume of the NMR cell, additional
solvent molecules must be added to the mixing chamber fill this extra space. This is
again done by taking advantage of the compressibility of liquid ethane. The sample
in the mixing chamber is over pressurized just enough that when it is released, and
the piston pushes the sample into the NMR cell, the expanded fluid volume will fully
fill the volume of the NMR cell at the encapsulation pressure. The method for taking
all these details into account is described later in this manual when outlining
potential sample preparation protocols.

12
Figure 5: RM Synthesizer Operational Description

13
Figure 6: RM Synthesizer Flow Diagram

14
CONVENTIONS USED IN THIS MANUAL
When describing operations of this device the identification of the valves involved
will be made by listing the valve name that is stenciled on the instrument such as HP
ALKANE or PISTON BOOSTER valve. The same method will be used to identify
ports on the back of the instrument. Where it is prudent, the specific sequence of
valve actuation will be identified on the platform figure with indicators corresponding
to the step. Shown below is a typical example.
To transfer the sample from the mixing chamber to the sample tube perform the
following steps diagramed in Figure 7:
i) Open the OUTLET / INLET valve; wait for two seconds.
ii) Close the PISTON BOOSTER valve.
iii) Open the HP ALKANE valve to equalize the system pressure.
VALVE DESCRIPTIONS
Refer to Figure 5 and Figure 6 for pictorial representations of the valve connections
and how they control fluid flow.
OUTLET / INLET: This is the connection point for the reverse micelle NMR cell. The
transfer line that comes with the NMR cell should be used for this connection. In
cases where the syringe pump will not be fully loaded with deuterated alkane, this
valve can be used as an inlet port for the initial fill with deuterated solvents. The
ii
i
iii
Figure 7: Example valve actuation
progression

15
syringe pump would then use protonated solvents to pressurize the sample. Due to
the compressibility of ethane and propane, this will likely result is a sample that has
20-30% protonated solvent.
CO2INLET TO BOOSTER: This connects the CO2INLET port directly to the gas
booster. This valve allows the gas booster to be refilled with high pressure CO2.
VENT PISTON: This releases the pressure on the piston to the WASTE port. This
valve should not be opened with the PISTON BOOSTER open as this will release all
gas in the gas booster reservoir.
HP ALKANE TO BOOSTER: This connects the HP ALKANE INLET port to the
opposite side of the separator in the gas booster. This valve is opened when
changing the internal pressure of the gas booster or when releasing pressurized
alkane back into the syringe pump.
HP ALKANE: this connects the HP ALKANE INLET to the mixing chamber. This is
opened when preparing the reverse micelle samples.
PISTON BOOSTER: Opening this valve delivers the pressurized CO2from the gas
booster to the piston contained in the mixing chamber cap. This can be used both to
change the internal pressure of the mixing chamber without adding additional alkane
to the sample as well as more commonly for transferring the sample from the mixing
chamber into the NMR sample tube.
WASTE: Allows the contents of the mixing chamber to be flushed out to the
WASTE port. This is used for venting the chamber after the sample preparation as
well as for passing cleaning fluids out of the chamber.
N2FOR CLEANING: This connects the N2INLET port directly to the mixing
chamber. This supplies high pressure nitrogen gas for pushing the cleaning fluids
out of the mixing chamber through the WASTE port. This valve should not be
opened when the chamber is at a pressure above the nitrogen gas cylinder output.
CLEANING MANIFOLD: This provides a path for the selected cleaning fluid into the
chamber. This valve should only be opened when the chamber pressure is at
atmospheric otherwise it will cause a backflow into the cleaning manifold bottles.
Mixing chamber water ports: There are a series of channels cut into the mixing
chamber forming a continuous loop. The ends of this loop terminate at the two

16
brass barbed fittings on the right side of the mixing chamber. These can be
connected to a water bath to provide thermal regulation of the sample.
BACK PANEL CONNECTIONS
Shown in Figure 8 are the ports used to connect the system to the external fluid
sources required for operation of the RM Synthesizer.
HP ALKANE INLET: Connects to the outlet of the Xtreme-10 Syringe Pump. The
tubing should be 1 kbar rated.
WASTE: This port handles the outflow from the mixing chamber as well as the high
pressure gas from the piston. The tubing should be rated for high pressure, and the
end should be in a vessel that can tolerate organic solvents. It should be anchored
so it does not break loose when high pressure gas is vented.
CO2INLET: This is the high pressure carbon dioxide inlet. Standard CO2cylinders
are not able to deliver liquid CO2. Instead connect to a cylinder with an eductor tube
pressurized with helium to at least 1,800 psi for best performance.
N2INLET: This port is for connecting a standard nitrogen cylinder with an output of
125-150 psi. This inlet links to the mixing chamber as well as an internal regulator
rated to a maximum of 250 psi which delivers 10 psi gas to the LP N2INLET.
LP N2INLET: The output from this port is 10 psi nitrogen gas. Connect this to the
cleaning manifold pressurizing port. It is this gas pressure that promotes fluid flow
out of the manifold bottles. There is no valve between the N2INLET and LP N2
Figure 8: Back panel port connections

17
INLET so always have it connected or plugged to prevent discharging the nitrogen
cylinder.
CLEANING MANIFOLD: The outlet of the PEEK cross from Figure 3 should be
connected to this port. Solvents from the cleaning manifold flow from this port to the
mixing chamber.
FRONT PANEL CONTROL
POWER: Provides power for the lamp and mixing electronics. It also turns on a
venting fan inside the instrument. Even if the lamp and mixer are not required the
power should be turned on when in use to keep air circulating inside the instrument.
LAMP: This knob controls the intensity of the light source illuminating the mixing
chamber
MIX: This knob controls the sample stirring speed.
PREPARING THE INSTRUMENT FOR USE
The procedure described is the basic setup required for use of the instrument. It
assumes the Xtreme-10 Syringe Pump is being used as the pressure source.
(1) Fill the gas booster with 1,800 psi CO2by opening the CO2INLET TO
BOOSTER valve.
(2) Open the HP ALKANE TO BOOSTER valve while filling the gas booster to allow
the high pressure CO2to push the internal separator all the way to one end thus
pushing out any ethane present in the reservoir.
Figure 9: Front panel controls

18
(3) Close the HP ALKANE TO BOOSTER and CO2INLET TO BOOSTER valves.
The gas booster is now filled with CO2.
(4) Fill the syringe pump completely with liquid ethane. Follow the procedures in the
Xtreme manual for refilling the pump. To extract liquid from the ethane cylinder it
may be necessary to place the cylinder in warm water while filling the pump. It will
take time for the liquid to transfer. Depending on the temperature ethane liquefies
around 610 psi. See http://webbook.nist.gov/chemistry/ for detailed information
about the properties of liquid alkanes. Open the HP ALKANE TO BOOSTER to fill
this void as well.
(5) The nitrogen cylinder can be connected, but does not need to be open until the
cleanings steps. Set the cylinder pressure to between 125-150 psi.
At this point the system is ready for reverse micelle preparation work. The
remaining steps are provided as an example of how to load the syringe pump with
extra grams of ethane. This is optional, and does not need to be performed for
routine operation of the instrument. However, this operation might be useful if a
higher starting pressure is desired, or if the time between syringe pump recharges is
to be increased.
Only perform this procedure with the gas booster reservoir filled with
CO2to act as a brake for the internal separator. If the reservoir is
empty and subsequently filled entirely with alkane the piston would be
moved to the fully displaced position. Later additions of liquid CO2
may not be sufficient to push the separator back into position and as a
result the transfer step may not work as expected because of
insufficient distance for the piston to travel.
(6) With the syringe pump fully filled with liquid ethane and the pump INLET valve
closed, set the pump to pressurize to 7,000 psi. With the HP ALKANE TO
BOOSTER valve already open this will pressurize the gas booster to 7,000 psi.
Once complete proceed to the next step.
(7) Close the HP ALKANE TO BOOSTER and OUTLET valve on the pump and
fully refill the pump again with liquid ethane. Be sure to Close the INLET valve on
the pump after the refill step.