picoSpin-45 User's Manual - Cole
Contents
1. If non zero applies an exponential appodization to the data specified in Hertz This parameter only effects the displayed phase and not the phase of saved data Max plot points The maximum number of points to plot to the browser If fewer points are specified than the number of acquisition points then the script will attempt to decimate the time and spectral data down to a number of points which does not exceed this number If greater than the number of acquisition points are specified then the script will plot the number of acquisition points to the browser The purpose of this parameter is to decrease the load on the operating system This may improve the ability of the operating system to keep up with the user specified T request This parameter does not effect the number of points saved to the data files Max time to plot The maximum time to plot for the time series data in the browser This param eter is useful when the user wants a long acquisition time but wants to have a zoomed in look at the beginning of the FID This parameter does not effect the number of points saved to the data files Min freq to plot The minimum frequency to plot for the spectral data in the browser This parameter is useful when the user only wants to look at a limited range of the acquired spectrum This parameter does not effect the number of points saved to the data files Max freq to plot The maximum frequency to plot for the spectral data in2. If you suspect you are looking at a ghost increase and then decrease the transmitter frequency by 4 kHz to see if the signal amplitude increases in either case Once your FID and spectrum look similar to the screen shot above set max iterations to 100 Max plot points to 200 Min freq to plot to 500 Max freq to plot to 500 and click on Start to start the autoShim script The changed plot settings will make the display less smooth but they also reduce load on the server because fewer points have to be sent to the web browser This makes it possible to view live plots while the shimming algorithm is operating picoSpin Quick Start picospin 45 AP y Tx Frequency MHz 100000 increments 1storder increments 2nd order max iterations targetrms Channel Pulse width Acq pts zero filling Bandwidth Post filter atten Rx recovery time T1 recovery time phase correction Exp apod rate Max plot points Max time to plot Min freq to plot Max freq to plot SS jj i i O 1000000 ms kHz us s degrees Hz ms Hz Hz Hz magnitude spectrum peak height 22375 iteration 9 best 41189 worst 18809 rms 6966 7 Run Name autoShim QuickStart Script autoShim setting shims 0 09843 0 22957 0 33305 0 02801 0 21439 0 02640 0 22640 0 01481 0 00000 Shims QuickStart processing complete waiting 2 591780 s before sequence repeat Figure 3 9 autoShim screen during shimming The screen shot above shows the
3. samples injected from the front panel of the instrument and channel B is for the internal reference Scans The number of times to run the single pulse acquisition sequence If a certain target SNR is desired it is probably easiest to run with the small number of scans at first to estimate the SNR per scan then recall the SNR scales as the square root of the number of scans Pulse width The duration of the RF pulse in microseconds Acq pts The number of points to acquire during an acquisition The acquisition time is this number divided by the specified bandwidth Bandwidth The bandwidth of the receiver channel This number determines the dwell time of the data acquisition It is the rate in kHz at which the digitizer samples the signal Post filter atten The attenuation setting of the filter electronics For a further description see the hardware section Rx recovery time The time between the end of the pulse and the beginning of acquisition to wait for the receiver electronics to recover from ring down T1 recovery time The requested T recovery time between experiments Since this is imple mented at the script level the parameter is non deterministic 36 Chapter 5 Experiment Scripts picoSpin 45 User s Manual Release 0 8 0 32 phase correction The amount of phase correction to apply to the FID in degrees This parameter only effects the displayed phase and not the phase of saved data Exp apod rate
4. tion can be made using the magnet temperature coefficient which is roughly 35 kHz C A more accurate value of the temperature coefficient can be found in a shim file for the magnet If nothing is known about the magnet search from 46 0 MHz down to 43 5 MHz The settings shown are appropriate for a system that is already roughly shimmed as will be the case for a new unit If you are looking for the signal in a unit that is unshimmed or poorly shimmed for example if the shim settings have been lost or a new cartridge has just been installed refer to more detailed documentation on the search script Press the Start button to start the script At first the time and frequency domain plots will show noise but when the signal is found the plots will appear similar to the screen shot and the script will stop Note the information that appears in the message pane at the bottom of the window When the signal is found it may take a few minutes the last frequency shown in the messages is the center frequency of the final spectrum plot The frequency of the signal can be found by adding this frequency to the signal offset frequency seen in the spectrum plot 4 kHz in this case An accuracy of 1 kHz is sufficient for initial set up of the other scripts 3 6 Auto Shimming The resolution of an NMR spectrometer depends upon how uniform the magnetic field is over the sample volume Since the proton Larmor frequency is directly proportional to the field
5. Contact us to discuss other materials for special applications How do I remove a sample Just flush the capillary with either a clean solvent or your next sample 7 3 Chemical Applications What kind of samples can I measure Any proton containing liquid not too viscous for injection into a 0 3 mm ID capillary can be used Will the signal I am looking for be strong enough to see Good question It is always a good idea to estimate the signal to noise ratio SNR before you get started with unfamiliar samples The exact SNR depends on many things including the magnet shim and the way data is recorded and analyzed However you can usually make an adequate estimate like this The picoSpin 45 single shot SNR for pure water is about 300 and the concentration of water molecules in pure water is 55 moles liter Since the SNR is directly proportional to concentration you can scale from this case to estimate your SNR You should also include a factor for the weight of the line relative to the weight of the water line The weight is the number of protons per molecule contributing to the line times the line s normalized intensity within a multiplet if it is not a singlet For example a water singlet has a weight of 2 a CH3 singlet has a weight of 3 and one line in a CH3 doublet has a weight of 1 5 Let s say your molecule has a concentration of 0 55 moles liter and you want to estimate the SNR of one line in a CH doublet That
6. be aware of setting the number of FT pts appropriately live plot Plots data to the browser for each scan acquired Unchecking this parameter may improve the ability of the operating system to keep up with the user s requested Ti JCAMP sum If align add data is set this parameter determines whether a JCAMP DX file of the aligned and added data is saved for the run JCAMP ind Whether to write individual JCAMP DX files for each scan for processing with the user s analysis software 5 2 autoShim The picoSpin 45 contains a set of eight shim coils for improving the field homogeneity plus a ninth coil to apply a uniform z field These coils are contained in the user re placeable cartridge which is included in the unit The cartridge implements the following magnetic field gradients zeroeth order e Bo first order e y e y ez second order e zx zy xy 5 2 autoShim 31 picoSpin 45 User s Manual Release 0 8 0 32 e 7 e x y The orientation of the coordinate system is such that y is coaxial with the capillary x is parallel to the ground and z is vertical Due to very slight differences between magnets shim cartridges and shim electronics different hardware components need different shim parameters Although these harmon ics can be set with the shim drop down of the browser interface this script attempts to automate the task To do this it implements the Nelder Mead optimization algorithm to find the
7. in the factory test report to verify that 42 0 C was used as the set point when the unit was shimmed and tested at the factory If a different temperture was used enter it instead The optimal shim settings are somewhat temperature dependent so the initial shim will be better if the original temperature can be used The three plots on the temperature page display the magnet temperature the ambient or case temperature and a number proportional to the magnet heater current These plots help the user monitor the magnet temperature and check that the set point and other controller settings are suitable After start up it may take from 20 minutes to 2 hours for the magnet to stabilize at the set point depending on the starting temperature of the magnet When the magnet temperature reaches the set point and stabilizes the heater current will be between 0 and its maximum value of 65535 If the ambient temperature is too low the current will saturate at 65535 and a lower set point has to be used If the ambient temperature is too high the heater current will be at 0 and a higher set point is needed 3 3 Magnet Temperature Control 11 picoSpin 45 User s Manual Release 0 8 0 32 3 4 Injecting a Sample While the magnet is stabilizing you can inject a sample into the spectrometer For initial shimming we need a sample that will generate a strong singlet Water is the usual choice but if there is some reason why you prefer not to put water int
8. o A AA RA 37 TAG gee oe Re ke cs Re AR a GR Ss SE 38 Data Analysis 2 428444482244 2448 44 hb odie EE ae RAS 38 CHAPTER ONE WELCOME Welcome to the User s Manual for the picoSpin 45 NMR spectrometer This document is available on the support page of the picoSpin web site in both HTML and pdf formats There is also an HTML version installed on your picoSpin 45 spectrometer Make sure the version number of the documentation you are viewing is the same as the installed software version on your picoSpin 45 spectrometer Version 0 8 is the first released version of the picoSpin software It includes an embedded web server that allows users to control the spectrometer from a web browser anywhere on their local network The server also provides live preview of time and frequency domain data selection and control of experiment scripts data storage and download interfaces to the shim and temperature control hardware and a software update function Experiment scripts included in version 0 8 support spectroscopy with complete control of experimen tal parameters automatic shimming and signal search These scripts support most of the anticipated applications of the picoSpin 45 Version 0 9 will provide enhancements to the browser interface and additional experi ment scripts including T inversion recovery and nutation curves With the release of version 1 0 we will provide documentation and new functionality that will allow users to write
9. search script is used to find the Larmor frequency of the sample It is often used when a new cartridge has been installed in the spectrometer or the temperature set point of the magnet has been changed The pulse sequence this script loads to the NMR Engine is the same as what the onePulse script uses The difference is that instead the script steps the transmission frequency before running the sequence and checks the spectrum for a resonance which passes a user specified signal to noise SNR criterion The SNR is calculated by taking the peak magnitude and dividing by the standard deviation of the points in a user specified window of the real part of the spectrum No checking is done to see whether the peak itself is in that window so the frequency step size should be chosen to be less than the acquisition bandwidth and probably greater than the frequency width of the noise window While the script is running the LCD indicates that a search is being run and the current frequency which is being probed In situations where the signal is very strong it may be possible that the SNR criterion is passed for an aliased signal This might be the case if already good shims are being used Therefore when a search stops because a signal was found it maybe worthwhile to use the onePulse script with transmission frequencies which push the signal off of the left or right side of the acquisition bandwidth to see that the signal is reduced in amplitude or vanishes a
10. strength a resolution or line width of 50 ppb parts per billion requires that the field strength be uniform to 50 ppb across the sample This is a very demanding require ment In all modern NMR spectrometers the magnetic field is adjusted for uniformity by adjusting currents in shim coils within the magnet The picoSpin 45 has 8 shim coils 3 that create linear gradients and 5 that create quadratically varying fields There is also a 9th coil for generating a uniform field The shim settings can be examined on the Run page by clicking on the shims button just to the left of the orange navigation links in the upper right corner of the page Saved shim settings files can be examined by clicking on their names on the Files page New picoSpin 45 spectrometers are shimmed at the factory before shipment However during shipment and storage inevitable temperature cycling of the magnet will degrade the shim somewhat To obtain the best possible resolution it is necessary to readjust the shim currents after the unit has been switched on and the magnet temperature has sta bilized If the unit is then left on and the magnet temperature remains constant only occasional and minor reshimming will be necessary There is no need to reshim when the 16 Chapter 3 Quick Start picoSpin 45 User s Manual Release 0 8 0 32 samples are changed and the magnet will tend to become more stable over time More substantial reshimming will be needed if the unit is
11. switched off for a time or if the mag net temperature set point is changed The most complete reshimming is necessary when a cartridge is changed Consult the autoShim script documentation for more information Go to the Files page choose the autoShim QuickStart saved run and click on use these values at Run You will see a page with settings similar to those shown in the screen shot below The plots will remain blank until the script is started lt picoSpin X Quick Start picoSpin 45 X we v Tx Frequency 45 034 MHz 1000000 increments 1st order 0 005 increments 2nd order 0 02 max iterations o target rms 1 Channel B Pulse width 35 us Acq pts 1000 a zero filling 8000 Bandwidth 4 kHz Post filter atten 10 Rx recovery time 500 us T1 recovery time 8 s phase correction 90 degrees Exp apod rate 0 Hz Max plot points 1000 a Max time to plot 250 ms Hz Min freq to plot 2000 Hz Max freq to plot 2000 Hz magnitude Y setting shims 0 09453 0 22737 0 33220 0 04361 0 22213 0 02794 0 22947 0 03041 0 00000 A A sequencer start time 0 989941 s Run Name gt oe spectrum peak height 20512 Shim QuickStart script autoShim completed successfully Figure 3 8 autoShim screen before shimming In the first field Tx Frequency transmitter frequency enter a value that you know to be within 1 kHz of the correct Larmor frequency Check that the max iterations setting is zero This setting determi
12. the browser This parameter is useful when the user only wants to look at a limited range of the acquired spectrum This parameter does not effect the number of points saved to the data files live plot Plots data to the browser for each scan acquired Unchecking this parameter may improve the ability of the operating system to keep up with the user s requested Ti magnitude 5 3 search 37 picoSpin 45 User s Manual Release 0 8 0 32 Whether to plot the complex spectral magnitude along with the real part of the spectrum 38 Chapter 5 Experiment Scripts CHAPTER SIX HARDWARE DESCRIPTION The picoSpin 45 NMR spectrometer is a complete pulsed fourier transform liquid phase proton NMR spectrometer in a shoebox sized package It includes a capillary cartridge a permanent magnet radio frequency transmitters and receivers digital data acquisition and signal processing a programmable pulse sequencer and a web server user interface In most respects the picoSpin 45 hardware components have functions similar to the components of a conventional superconducting magnet NMR spectrometer Apart from drastically lower cost and size the main differences are that the magnet is permanent rather than superconducting and the sample is delivered by flow into a capillary rather than by inserting a glass NMR tube Operation is much simpler than for conventional spectrometers because there is no need to handle cryogens or other utiliti
13. their own experiment scripts and pulse sequences 1 1 Getting Started If you are new to the picoSpin 45 and want to get started right away go to the Quick Start You may also want to browse the picoSpin Frequently Asked Questions and view the full Contents For technical support contact picoSpin using this form If you are unfamiliar with the basics of NMR or you need a refresher go to NMR Spectroscopy picoSpin 45 User s Manual Release 0 8 0 32 1 2 Software Updates The picoSpin software system is updated regularly picoSpin customers may register here to recieve e mail notification of software updates as soon as they are available A link for downloading the update files will be provided Instructions for installing updates can be found on the spectrometer s Settings page 2 Chapter 1 Welcome CHAPTER TWO NMR SPECTROSCOPY Readers of the picoSpin 45 User s Manual should be familar with the basics of pulsed NMR spectroscopy of liquids An introduction to this subject can be found in any college level organic chemistry textbook There are also several excellent on line resources avail able 2 1 References The Basics of NMR by Josef P Hornak Almost every section of this excellent text will be helpful to users of the picoSpin 45 The only sections that are not directly relevant are these carbon 13 superconducting magnets solid state microscopy field cycling The NMR section of The Virtual Textbook of Org
14. will be 300 0 55 55 1 5 2 2 25 You can increase the single shot SNR by aver aging many scans The SNR increases as the square root of the number of scans so if you average 100 scans you can enhance the SNR by a factor of 10 We use the spectroscopist s definition of SNR which is the peak height of the line divided by the RMS of the baseline How long does it take to get a spectrum This can vary widely For a high concentration sample of a simple molecule you can get very useful information from a single shot acquired in less than a second One the other hand if you are looking for a low SNR line and your 7 3 Chemical Applications 43 picoSpin 45 User s Manual Release 0 8 0 32 sample has a long T relaxation time you may want to collect data for many minutes or even several hours See previous question to learn how to estimate the SNR Can I detect other nuclei besides hydrogen A special version of the picoSpin 45 is available for fluorine The electronics can be adapted for any frequency but the SNR will not be adequate for most applications with nuclei other than hydrogen and fluorine Carbon 13 satillites can be seen on proton spectra in favorable cases Do I need to use deuterated solvents Not in most cases Deuterium is not used by the picoSpin 45 to provide a lock signal and receiver saturation is also not a problem even with a pure water sample You might want to use a deuterated solvent if
15. E picospin picoSpin 45 User s Manual Release 0 8 0 32 picoSpin LLC July 07 2011 Welcome 1 1I Ei Started oa esea daaa oo a OH SHOES OEE SES HEE HH Hed 4 1 1 2 Sottware Updates y ade deeds ERA 2 NMR Spectroscopy 3 A AR 3 Quick Start 5 Sl What sinth BOK eos ts he a iaaa ED ee dd a 5 3 2 Ethernet CONNECTION y aw dto he wh we ha eca s KER EME OS KS 7 3 3 Magnet Temperature Control socia dada A A AA 8 34 Injecting a Sample gt ces ses saa siik gia CREED EES da e A 9 as Finding the Signal 6 s i ecu doa araa dy ec eaa eh eS 10 36 Aut ShiMMiNg r as e a eana ena a eee d a ed de 8 12 Of Your First Spectr o a aa iea a e a e e e BE gt 4 15 System Operation 19 4 1 Web Browser Interface aooaa a a a e a 19 12 Sample Handling lt e 23 5 4 a ad aeai d aa Aoa a dhe hee ha i 19 AD SAIMONE e de Soa e aa A A AA EA 19 44 Changing the Gartridge sesse sses 4 ee 4 aane aane gis airia des s 19 Experiment Scripts 21 A A 22 52 o sr se O a 25 Dae Sear s a or a ae he EA 28 Hardware Description 33 Od Manele cd mes nen atadta OM KEK g i II 33 6 2 Capillary Carias de qu aca dde ha ed aa eo A 33 6 3 RF and Data Acquisition Electronics ARA A 34 64 Shi Systemi se sa geint tant edi PEK i A A EGE S 34 Go OPENS AA E A G A 34 CONTENTS 7 Frequently Asked Questions 35 Tok Tal 7 4 pes General Questions s sieste i i adei e i i AREA 35 Sample Handling 32 ria A RR A 36 Chemical Applications isi dhe dk eee
16. about 2 5 Hz or 55 ppb 2 5 Hz divided by 45 MHz This is below the specified line width of 100 ppb More careful measurements of the line width can be made using data from the onePulse script which is discussed next 3 6 Auto Shimming 19 picoSpin 45 User s Manual Release 0 8 0 32 picoSpin 6 Quick Start picoSpin 45 ar y Tx Frequency 45 0342 MHz increments 1st order 0 005 increments 2nd order 0 02 max iterations 0 target rms 1 Channel A some Pulse width 35 us aioe Acq pts 2000 zero filling 8000 ms Bandwidth 4 kHz oes Post filter atten 10 PEA Rx recovery time 500 us T1 recovery time 8 s phase correction 110 degrees 10000 Exp apod rate 0 Hz Max plot points 2000 a i y Max time to plot 500 ms Hz Min freq to plot 00 Hz Max freq to plot 50 Hz magnitude rodri Run Name autoShim QuickStart script autoShim completed successfully Script autoShim Figure 3 11 autoShim zoomed in 3 7 Your First Spectrum For your first attempt at spectroscopy pick a simple molecule without labile protons Ethyl acetate is a good choice Following the instructions on Injecting a Sample fill the cartridge capillary with the sample fluid In most cases the new sample can be used to flush out a previous one although one should keep in mind the possiblity of reactions or precipitation where the two fluids mix In cases of concern a compatible solvent can be used to flush the previous s
17. ample Go to the Files page choose the onePulse QuickStart saved run and click on use these values at Run You will see a page with settings similar to those shown in the screen shot below As before the plots will remain blank until the script is started Set the transmitter frequency to the known Larmor frequency Scans to 1 Min freq to plot to 2000 Max freq to plot to 2000 and the other settings as shown in the screen shot Click the Run button and examine the plots Make adjustments to phase correction and the plot limits until the spectrum looks similar to the screen shot With a neat sample you will be able to see the main spectral features from a single FID In this case we see a CH singlet a CH triplet and a CH quadraplet The spectrum is plotted backwards relative to the usual NMR convention where higher frequencies appear to the left Once you are happy with the settings set Scans to 25 Max plot points to 300 and click on the Run button Plotting fewer points reduces the load on the server so that live plots can be viewed during the run without extending the desired T recovery time The plot 20 Chapter 3 Quick Start picoSpin 45 User s Manual Release 0 8 0 32 lt picoSpin Quick Start picoSpin 45 X we v Tx Frequency 45 0340 MHz ad Channel A 1500000 Scans 1 1000000 Pulse width 35 us 500000 Acq pts 3000 Bandwidth 4 kHz meneen Post filter atten PY 0000 Rx recovery time 500 us me 2 T1 rec
18. an do them all automatically and perform many other useful processing steps including multiplet analysis peak integration and global spectral decomposition 3 7 Your First Spectrum 21 picoSpin 45 User s Manual Release 0 8 0 32 M MestReNova Document 1 Mi File Edit View Processing Analysis Advanced Stack Predict Annotate Scripts Documents Help Oy s SPASE Aye 9 e mreng v gt Ra a aw gt 4 a y Mm Yom E 4 4 ot x j el 4 Figure 3 13 Ethyl acetate in MNova 22 Chapter 3 Quick Start picoSpin 45 User s Manual Release 0 8 0 32 We hope this Quick Start guide has been useful If you have encoutered any difficulties please contact us using this form or consult the full documentation Contents 3 7 Your First Spectrum 23 picoSpin 45 User s Manual Release 0 8 0 32 24 Chapter 3 Quick Start CHAPTER FOUR SYSTEM OPERATION 4 1 Web Browser Interface 4 2 Sample Handling This section is in preparation 4 3 Shimming This section is in preparation 4 4 Changing the Cartridge This section is in preparation 25 picoSpin 45 User s Manual Release 0 8 0 32 26 Chapter 4 System Operation CHAPTER FIVE EXPERIMENT SCRIPTS All experiments on the picoSpin 45 spectrometer are implemented by means of several factory defined scripts The scripts run on a Linux based operating system and are re sponsible for loadin
19. anic Chemistry by William Reusch The basics in just a few pages The NMR section of the On line Learning Center for Organic Chemistry by Francis A Carey Another brief introduction picoSpin 45 User s Manual Release 0 8 0 32 4 Chapter 2 NMR Spectroscopy CHAPTER THREE QUICK START The picoSpin 45 NMR spectrometer is a complete 45 MHz pulsed Fourier transform liquid phase proton NMR spectrometer in a shoebox sized package It includes a capil lary cartridge a permanent magnet with temperature controller and shim system radio frequency transmitters and receivers digital data acquisition and signal processing a programmable pulse sequencer and a web server user interface In most respects the picoSpin 45 hardware components have functions similar to the components of a conventional superconducting magnet NMR spectrometer Apart from drastically lower cost and size the main differences are that the magnet is permanent rather than superconducting and the sample is delivered by flow through a capillary rather than by inserting a glass NMR tube Operation is greatly simplified because there is no need to handle cryogens or other utilities tuning and shimming are not required when samples are changed and there is no software installation required to set up the system Users can produce high resolution spectra with a new unit a few hours after the shipping package is opened In normal operation samples can be injected into t
20. autoShim script while it is running The script uses the Nelder Mead simplex algorithm to find shim settings that optimize the peak height of the magnitude spectrum With the settings shown the script will reach 100 interations and stop after about 30 minutes The execution time is not deterministic because the simplex algorithm uses a variable number of evaluations of the spectrum peak height for each interation When the script stops it will enter the best shim settings found into the shim 18 Chapter 3 Quick Start picoSpin 45 User s Manual Release 0 8 0 32 fields on the Run page These can be examined by clicking on the shims button near the top of the page The autoShim script does not save the shims to a file when it completes unless a name has been entered in the Shims Name field When autoShim completes save the shims by typing a name into the Shims Name field and clicking on the Save button The new shim file will then appear on the Files page lt picoSpin X 9 Quick Start picoSpin 45 X ar bd Tx Frequency 45 034 MHz increments 1st order 0 005 increments 2nd order 0 02 max iterations 0 targetrms 1 Channel A Pulse width 35 us 1000000 Acq pts 1000 o 50 100 ae 150 zero filling 8000 Bandwidth 4 kHz Post filter atten 10 Rx recovery time 500 us T1 recovery time 8 s phase correction 90 degrees Exp apod rate 0 Hz Max plot points 1000 f Max time to plot 250 ms l i i Hz Min freq to p
21. ct the computer to the spectrometer using the provided Ethernet cable Configure the Ethernet port on the computer so that it can communicate with the default IP address To do this you must set the IP address of the computer to another address on the same sub net For example you could set the sub net mask to 255 255 255 0 and the IP address to 192 168 42 10 The details of setting up Ethernet ports and network adapters on different computers vary widely Consult your computer s documentation or your IP support staff if you need help Once the port has been set up type http 192 168 42 31 into the address field of your browser to see the welcome screen shown above After the welcome screen has been displayed for a moment it will be replaced by the Run page which is used to enter experiment parameters start experiments and monitor their progress The orange text links at the upper right of the page are used to navigate between pages Go to the Settings page and click on About This pS45 to find the current installed software version If the installed software version is not the same as the docu mentation you are reading go to the picoSpin web site and get the documentation for the software version you are using Do not click on the System Update link at this time We recommend that you do not update the software on a new unit until after you have ver ified correct operation by following the steps in the Quick Start guide This will re
22. duce confusion if it becomes necessary to communicate with picoSpin support staff because you will be using the same software version that was used to generate the factory test report 3 3 Magnet Temperature Control The permanent magnet in the picoSpin 45 has a magnetization temperature coefficient of about 700 ppm C As a consequence the stabilty of the instrument depends upon high resolution control of the magnet temperature The controller can stabilize the magnet temperature to better than one milli degree over a period of several hours and to higher accuracy over shorter times Click on the Temperature link at the upper right to go to the temperature controller page Also click on the Controller button near the top of the page to display the temperature con 10 Chapter 3 Quick Start picoSpin 45 User s Manual Release 0 8 0 32 troller settings The screen shot below shows the temperature page after the temperature is fully stabilized e Quick Start picoSpin 45 picoSpin x P y pico Sp in Temperature controller Run Files Temperature Settings Magnet set point 42 0 P 10 2 heater on y setpoint 42 0 1 0 02 closed loop on output Submit MA Magnet 41 999994 C EN HA Ambient 28 904626 C Figure 3 4 Temperature screen Adjust the temperature controller settings to P 10 2 I 0 02 heater on closed loop on set point 42 0 C and click the Submit button Check the shim settings
23. e front panel is used to monitor the status of the instrument 6 Chapter 3 Quick Start picoSpin 45 User s Manual Release 0 8 0 32 E picoSpin ETHERNET POWER IN O Y ur Figure 3 2 Rear panel 3 1 What s in the Box 7 picoSpin 45 User s Manual Release 0 8 0 32 On the rear panel you will see an Ethernet connector an auxilliary output connector a power input connector and an on off switch The auxilliary output is intended for controlling external hardware such ongas valves The test report includes the spectrometer and cartridge serial numbers the shipped soft ware version the shim settings that were used for factory tests a screen shot of the free induction decay signal of water and a screen shot showing a measurement of the signal to noise ratio 3 2 Ethernet Connection The first step is to establish communication with the spectrometer using a computer and a standard web browser We recommend Mozilla s free Firefox web browser for best compatiblity with our software Any type of computer with an Ethernet port can be used There are two options for making the initial connection through a LAN local area network with the IP address of the spectrometer assigned by the LAN or by a direct connection between the spectrometer and your computer without using any network Connection through a LAN is more convenient in most cases However if you do not have a LAN do not have access to an open Et
24. e upper left corner of the temperature plot Next go to the Files page This page provides access to previously saved experiment runs together with their settings and data It also allows you to select shim settings files and experiment scripts The screen shot above shows the Files page as it appears in a new unit The three groups of orange links down the left column are labeled Run Data Shims and Scripts In the screen shot the link search QuickStart has been selected This is the name of a run that was saved in the unit at the factory When this link is selected the settings for this run appear at the center of the screen The Last Run link stores the settings of the most recent run The Current shims link stores the shims currently set on the Run page The QuickStart shims were saved for this unit at the factory The Default shims will be used in future versions of the software The three scripts available in the Scripts group are autoShim for finding optimal shim settings onePulse for 1D spectroscopy and search for finding the Larmor frequency Scripts with default settings can be accessed through these links More often scripts are selected by choosing a previous run in the Run Data group To make sure you are using the shims saved at the factory click on the QuickStart shims and then click on use these shims at Run You will be transferred to the Run page Go back to the Files page and click on the search QuickStart saved run Th
25. en click on use these values at Run You will return to the Run page with settings similar to those shown in the screen shot below the data plots will be empty until the script is started 3 5 Finding the Signal 13 picoSpin 45 User s Manual Release 0 8 0 32 picoSpin Run Data Shims Scripts Files Last Run autoShim QuickStart onePulse QuickStart search QuickStart Current Default QuickStart autoShim onePulse search search QuickStart search run values Start Frequency Stop Frequency Frequency Step SNR noise window start noise window end Channel Pulse width Acq pts Bandwidth Post filter atten Rx recovery time Tl recovery time phase correction Exp apod rate Max plot points Max time to plot Min freq to plot Max freq to plot live plot magnitude Run Files Temperature Settings Use these values at Run 44 372 MHz 44 172 MHz 10 kHz a iu 6000 Hz 1000 Hz Uk N o 20 kHz co o c a 0 degrees 0 Hz al el 4 1000 ms 10000 Hz 10000 Hz 3 Las Figure 3 6 Files screen 14 Chapter 3 Quick Start 7 6 2011 11 02 pm picoSpin 45 User s Manual Release 0 8 0 32 E picoSpin Run search Run Name Start Frequency 44 372 MHz Stop Frequency 44 172 MHz Frequency Step 10 sne 10 noise window start 6000 noise window end 1000 Channel A Pulse width 30 Acq pts 200 Bandwidth 20 Postfi
26. es tuning and shimming are not required when samples are changed and there is no software installa tion required to set up the system Users can produce high resolution spectra with a new unit less than two hours after the shipping package is opened In normal operation sam ples can be injected into the system and spectroscopic data can be obtained in less than 10 minutes The primary disadvantage of the picoSpin 45 relative to a conventional spectrometer is that it is less sensitive and concequently samples must be at higher concentration This is an unavoidable trade off for an instrument that costs 10 to 100 times less than a super conducting spectrometer 6 1 Magnet This section in preparation 6 2 Capillary Cartridge This section in preparation 39 picoSpin 45 User s Manual Release 0 8 0 32 6 3 RF and Data Acquisition Electronics This section in preparation 6 4 Shim System This section in preparation 6 5 Specifications This section in preparation 40 Chapter 6 Hardware Description CHAPTER SEVEN FREQUENTLY ASKED QUESTIONS 7 1 General Questions Is the picoSpin 45 spectrometer really the world s first miniature NMR spectrometer Haven t desktop NMR machines been around for years In a proton NMR spectrum lines are typically separated by a few parts per million ppm To qualify as a true spectrometer an NMR system must have resolution well below 1 ppm The picoSpin 45 s resolution is bette
27. g pulse sequences to the NMR Engine retrieving data from the NMR Engine and sending the data to the embedded web server for plotting to a browser win dow Optionally the scripts may do a range of other tasks such as communicate with the shim controller the temperature controller or the LCD display There are three scripts distributed with this version of the spectrometer software They are called onePulse autoShim and search Of the three only the onePulse script is used to acquire data The search and autoShim scripts are used to find the Larmor frequency of the sample and improve the line shape respectively NMR pulse sequences require events to occur at precisely defined times however the scripts are not running on a real time operating system so the timing of the script s actions are not deterministic Therefore the script compiles pulse sequences to be sent to the NMR Engine board which can execute actions in a deterministic fashion The NMR Engine however has limited memory and limited computing power so some less time critical experiment operations are performed on the OS hardware For instance with the autoShim script the user may want to re excite the sample at a time before the spins have had chance to complete their longitudinal relaxation in order to speed up the shimming process However the script must first get the data from the NMR Engine to be analyzed and perhaps plot it to the browser The more data there is to deal wi
28. he system and spectroscopic data can be obtained in less than 10 minutes This Quick Start assumes that the user is setting up a newly received instrument It will also be helpful to a user who is becoming familiar with a unit that has already been set up for operation In this case it will be possible to skip many of the steps If the unit is already set up to communicate with a web browser temperature stabilized shimmed adequately and the Larmor frequency is known skip to Injecting a Sample and then read Your First Spectrum 3 1 What s in the Box Inside the shipping box you will find the following items e picoSpin 45 spectrometer e 12 V modular power supply e power cord picoSpin 45 User s Manual Release 0 8 0 32 e Ethernet cable e accessory packet e factory test report E picoopin PICOSPIN 4S Figure 3 1 Front panels The fluid sub panel mounted on the left side of the front panel with four thumb screws is a part of the replacable capillary cartridge Do not remove the cartridge at this time When a cartridge is replaced the unit has to be shimmed It is better to gain some experi ence with the unit and with shimming before replacing a cartridge The unit is delivered with the inlet and outlet fittings covered with protective tape You will notice that the inlet fitting has a double nut A stainless steel frit filter is held in place by the smaller outer nut The LCD display on the upper right of th
29. hernet port on your LAN or if your LAN cannot assign IP addresses using DHCP dynamic host configuration protocol then you should use a direct connection Connect the power cord to the power module and connect the multi pin connector from the power module to the power input connector on the rear panel The multi pin connec tor has a threaded collar that should be tightened by hand to secure the connector to the rear panel Check that the rear panel power switch is in the off down position and plug the power cord into an AC power source Connecting through a LAN Connect the the unit to an available Ethernet port on your LAN using the Ethernet cable provided or a longer cable if necessary Switch on the unit while watching the front panel LCD display After about one minute an IP address should appear on the front panel This address has been assigned by your LAN using DHCP See below if the address displayed is 192 168 42 31 Point a web browser at the address and you will see the welcome screen shown below For example if the address displayed is 192 168 2 12 type http 192 168 2 12 into the address field of the browser Automatic assignment of the IP address by the LAN will only be successful if the unit is switched on after it has been connected to an active Ethernet port on your LAN and then only if your LAN has DHCP capability If the unit is not assigned an IP address by DHCP it will display a factory default IP address
30. l time between acquisitions is not deterministic which should be kept in mind In general the fluctuation in time due to processing overhead can be as much as 2 3 seconds depending on the processor load If the actual start of the next sequence exceeds the specified target T recovery time a statement in the message window will indicate processing extended repetition delay by x seconds If the specified T recovery time is long enough for the script to start the next acquisition sequence in the recommended time a statement indicating processing complete waiting x s before sequence repeat will be shown in the message window When multiple scans are acquired the user has the choice to save the data from each pulse separately or to have the data added together Although the temperature controller in the spectrometer keeps the magnet very stable to achieve the best resolution the instrument is capable of it is necessary to align the data before subsequent spectra are added With the onePulse script when spectra are added the data is always aligned before adding Loading this sequence into one channel also writes to the other channel to put the other channel in receive mode As described in the hardware section this prevents interaction between the channel electronics which affects receiver noise 28 Chapter 5 Experiment Scripts picoSpin 45 User s Manual Release 0 8 0 32 5 1 1 parameters Tx Frequency The RF transmitter field frequenc
31. ll together If the signal gets larger instead then the original frequency window had an aliased signal 5 3 1 parameters Start Frequency The frequency in MHz at which to begin the search Stop Frequency The frequency in MHz for the search to stop Frequency Step The size of the frequency steps in kHz to take during the search Negative or positive values are allowed appropriate to starting and stopping frequencies to scan either up or down in frequency SNR The signal to noise ratio at which the search will consider that it has found a resonance When this condition is passed the search stops and the message window reports the SNR and frequency of the largest peak magnitude found noise window start 5 3 search 35 picoSpin 45 User s Manual Release 0 8 0 32 The relative frequency with respect to the transmitter frequency to use for the lower limit of the noise window in the estimation of SNR Due to the discrete nature of the spectrum the actual frequency boundary may differ The message window will indicate the actual frequency used noise window end The relative frequency with respect to the transmitter frequency to use for the upper limit of the noise window in the estimation of SNR Due to the discrete nature of the spectrum the actual frequency boundary may differ The message window will indicate the actual frequency used Channel The channel where the pulse sequence should be loaded Channel A is for user
32. lot 2000 Hz Max freq to plot 2000 Hz magnitude g setting shims 0 09753 0 22737 0 33220 0 04361 0 22213 0 02794 0 22947 0 03041 0 00000 sequencer start time 0 950583 s spectrum peak height 46198 script autoShim completed successfully Run Name autoShim QuickStart Script autoShim Shims QuickStart Figure 3 10 autoShim screen after shimming Once the shims have been saved go to the Run page and set max iterations back to 0 Max plot points back to 1000 and click on Start again An example of the resulting FID is shown in the screen shot above The shim you achieve may be better or worse than is shown To check that the shim you have achieved yields a line width that meets specifications run autoShim with max iterations set to zero and the vales of Min freq to plot and Max freq to plot adjusted to show a small region around the peak as shown in the screen shot above Note that the Magnitude check box is not checked With this setting the real part of the spectrum is displayed rather than the magnitude and it will be necessary to adjust the value in the phase correction field The phase should be adjusted so that the line in the spectrum is everywhere positive and roughly symmetrical about the peak The Magnitude checkbox must be unchecked because the line width of a magnitude spectrum is much greater than the line width of the real part In the screen shot we see that the full width at half maximum FWHM of the line is
33. lteratten 8 Rx recovery time 80 us T1 recovery time 8 s phase correction fo degrees Exp apod rate fo Max plot points 400 Max time to plot 1000 Min freq to plot 10000 Max freq to plot 10000 live plot magnitude Sl kHz Hz Hz us kHz Hz shims Run Files Temperature Settings 100000 50000 50000 100000 ms 40000 30000 20000 10000 10000 20000 10000 7500 5000 2500 o 2500 5000 7500 setting frequency 44 282000 get data from NMR engine done processing FID done biggest peak magnitude 56459 at 9100 Hz SNR 89 32 signal passed SNR criterion plotting data done search finished script search completed successfully stdev of noise window 6000 Hz 1000 Hz 51 pts RunName LastRun F Script search 632 1 Figure 3 7 Search script screen 3 5 Finding the Signal 15 picoSpin 45 User s Manual Release 0 8 0 32 The first two settings are the start and stop frequencies for the signal search and the third setting is the step size which is negative in this case so that the search will move down wards from the start frequency to the stop frequency Start and stop frequencies appropri ate for your magnet may be different When a previous Larmor frequency for a particular magnet and temperature is known it is sufficient to search 100 kHz around the last known frequency If the last known frequency was at a different temperature a correc
34. nes the maximum number of interations that the autoShim script will perform while attempting to improve the shim When it is set to zero only a single FID free induction decay will be generated with the starting shim values This can be used to check that all the settings are suitable for automatic shimming to proceed Press the Start button After a few moments you should see plots similar to those in the screen shot The upper plot shows the first 250 ms of the FID while the lower plot shows the magnitude of the spectrum Fourier transform of the FID If the peak in the spectrum is not within about 300 Hz of the transmitter frequency 0 Hz on the plot adjust the transmitter frequency and click on Run again Your starting shim may be better or worse than is shown here Better shim corresponds to a slower decay of the FID and a stronger peak in the spectrum while poor shim cor 3 6 Auto Shimming 17 picoSpin 45 User s Manual Release 0 8 0 32 responds to a FID that decays more quickly and a spectrum with a broader and weaker peak Note that the initial amplitude of the FID upper plot in the screen shot above is about 500 000 If the FID you are looking at has a much smaller initial amplitude you may be looking at a ghost signal A ghost is a strong signal that is outside of the acquisition bandwidth 4 kHz in this case It can appear as a weak signal within the bandwidth because of finite rejection of the signal processing filters
35. ng of the FID This parameter does not effect the number of points saved to the data files Min freq to plot The minimum frequency to plot for the spectral data in the browser This parameter is useful when the user only wants to look at a limited range of the acquired spectrum This parameter does not effect the number of points saved to the data files Max freq to plot The maximum frequency to plot for the spectral data in the browser This parameter is useful when the user only wants to look at a limited range of the acquired spectrum This parameter does not effect the number of points saved to the data files FT pts The number of Fourier transform points to use when aligning data by cross correlation Generally the greater the number of points the better the aligning routine performs but the longer the processing time is required which may affect the Ty request Using a value which is the nearest power of 2 greater than four times the number of acquisition points works well for most cases For 30 Chapter 5 Experiment Scripts picoSpin 45 User s Manual Release 0 8 0 32 example if 1000 points are acquired per scan then setting this to 4096 would produce a good alignment align add data Whether to align and add the data that is acquired The alignment routine per forms a cross correlation between the current scan and the aligned sum of the previous scans before adding the two together When setting this parameter also
36. o the cartridge you can use acetone instead The sample fluid should be free of particulates that could clog the inlet filter Otherwise there are no critical purity requirements Figure 3 5 Fill tube Inside the accessory packet you will find the following items e 2 plugs for the inlet and outlet fittings e Fill and drain tubes e Blunt 30 needle e 1 ml polypropylene syringe The fill and drain tubes have PEEK ferrules and stainless nuts for attachment to the front panel inlet and outlet fittings The syringe and 30 needle is used to inject sample fluid into the fill tube Remove the protective tape on the inlet and outlet fittings and screw the fill and drain tubes into the fittings The drain is the one with the longer piece of tubing You can direct the drain tube into a small bottle if you wish It is sufficient to finger tighten the stainless nuts Draw a few hundred microliters of fluid into the polypropylene syringe and fit the 30 blunt needle to the syringe Hold the syringe with the needle upwards tap it with a finger and eject any bubbles Next insert the needle into the tubing connected to the inlet fitting and inject fluid into the cartridge until you see it flowing out of the outlet The only concern with this process is that you might inject a bubble into the cartridge If a bubble is left at the center of the cartridge where the RF coil is located there will be no signal Any time you fail to find an expected signal it is g
37. of 192 168 42 31 In most cases you will not be able to communicate through your LAN to this address because LANs are configured so they can only communicate with a sub set of all IP addresses For example your LAN might only allow communication between IP addresses of the form 8 Chapter 3 Quick Start picoSpin 45 User s Manual Release 0 8 0 32 Quick Start picoSpin 45 picoSpin picospin Welcome to picoSpin miniature NMR spectrometers Copyright 2011 picospin com All Rights Reserved Transferring data from 192 168 42 31 Figure 3 3 Welcome screen 3 2 Ethernet Connection 9 picoSpin 45 User s Manual Release 0 8 0 32 192 168 2 xx where xx is a number between 0 and 255 If you see the default IP address and you are sure that your LAN does support DHCP try using the same cable to connect another device to the LAN Ethernet port you have chosen to make sure it is active If you are unable to connect to the spectrometer through your LAN make a direct connection as descibed below Direct Connection The computer must have an available Ethernet port with a working network adapter If you are unsure if the Ethernet port is working try using it to connect to a network Turn the spectrometer power switch on before connecting it to the computer with the Ethernet cable After about a minute the front panel LCD display will show the factory default IP address of 192 168 42 31 Now conne
38. ood to keep in mind that it could be because of a bubble 12 Chapter 3 Quick Start picoSpin 45 User s Manual Release 0 8 0 32 Remove the fill and drain tubes and plug the inlet and outlet fittings with the two PEEK plugs from the accessory package These should be tightened lightly with your fingers to seal the ports When the spectrometer is in continuous use it is sufficient to plug just the inlet fitting and leave the drain in the outlet fitting However it is bad practice to leave the instrument like this for long periods because the sample will evaporate and may leave solid residue in the cartridge Cartridges will last longest if they are left filled with clean solvent and with both ports plugged 3 5 Finding the Signal The first step towards making an NMR spectrum is locating the proton Larmor frequency According to specifications the picoSpin 45 proton Larmor frequency is 45 1 MHz Pro ton NMR is normally done in bandwidths of only a few kHz so the Larmor frequency has to be known to much higher accuracy than the specification The exact Larmor frequency varies from magnet to magnet as a function of the magnet set point temperature as a function of shim settings and it may also be influenced by external applied fields Before we look for the signal go to the Temperature page and check that the magnet tem perature has stabilized to within a few milli degrees of the set point The current tem perature can be found in th
39. over from ring down T1 recovery time The requested T recovery time between experiments Since this is imple mented at the script level the parameter is non deterministic 5 1 onePulse 29 picoSpin 45 User s Manual Release 0 8 0 32 phase correction The amount of phase correction to apply to the FID in degrees This parameter only effects the displayed phase and not the phase of saved data Exp apod rate If non zero applies an exponential appodization to the data specified in Hertz This parameter only effects the displayed phase and not the phase of saved data Max plot points The maximum number of points to plot to the browser If fewer points are specified than the number of acquisition points then the script will attempt to decimate the time and spectral data down to a number of points which does not exceed this number If greater than the number of acquisition points are specified then the script will plot the number of acquisition points to the browser The purpose of this parameter is to decrease the load on the operating system This may improve the ability of the operating system to keep up with the user specified T request This parameter does not effect the number of points saved to the data files Max time to plot The maximum time to plot for the time series data in the browser This param eter is useful when the user wants a long acquisition time but wants to have a zoomed in look at the beginni
40. overy time 8 s phase correction 105 degrees Exp apod rate 0 Hz Max plot points 1000 50000 Max time to plot 750 ms i Min freq to plot 0 Hz Max freq to plot 400 Hz FT pts 4 z align add data g Hz live plot g JCAMP sum g JCAMP ind Start scan A get data from NMR engine done Run Name onePulse QuickStart processing FID done Script onePulse experiment completed script onePulse completed successfully Figure 3 12 onePulse script with ethyl acetate settings have no effect on the data that is recorded After the run finishes about 3 min utes go to the files page and click on Last Run The list of files written will appear near the bottom of the page Click on the file id avg jdx which contains the averaged FID data from the 25 scans in JCAMP DX format Download the file to your computer Every picoSpin 45 comes with a one year free license to the MNova NMR data analysis package from Mestrelab Research MNova is a powerful package that makes all common NMR analysis tasks fast and easy To learn the basics of MNova download the manual from the Mestrelab site and read the first 5 sections of Chapter VIII Processing Basics The screen shot above shows the result of processing the fid avg jdx file in MNova as follows e open the JCAMP file e set zero filling to 32 000 e apodization 0 3 Hz exponential e adjust phasing e zoom axes e reference the methyl singlet to 2 0 ppm These steps were done manually but MNova c
41. pulse sequences and experiment scripts 7 2 Sample Handling How do I inject a sample The spectrometer has an inlet connector and an outlet connector on the front panel The fluid path between them is a capillary with an ID of about 0 3 mm and a total volume of about 20 microliters Our standard stainless steel 1 32 panel fittings are part numbers VICI ZBU 5 for the outlet and VICI ZBUFR 5F for the inlet available from VICI The inlet fitting has a replaceable 2 micron frit filter VICI 2FR1 10 also available in other materials and sizes You can connect to these fittings in many ways If you would like to inject your sample from a syringe we suggest the VICI VISE5FPK syringe port PEEK To close off the inlet and outlet you can use VICI ZP 5FPK plugs PEEK You can also connect 0 030 OD microbore PTFE tubing Cole Parmer part EW 06417 11 to these fittings using a grooved PEEK ferrule VICI ZGR 5PK 10 A 30 syringe needle can be used to inject fluids into this PTFE tubing 42 Chapter 7 Frequently Asked Questions picoSpin 45 User s Manual Release 0 8 0 32 What materials are in contact with the sample fluid Our standard cartridges use microbore PTFE capillary and a short section of quartz glass capillary at the location of the RF coil The front panel fittings are stainless steel with a stainless still frit filter on the inlet PEEK ferrules are used to connect the microbore PTFE capillary to the front panel fittings
42. r than 0 1 ppm or 100 ppb parts per billion Before the picoSpin 45 all commercial miniature NMR machines had resolution that was too poor for them to qualify as spectrometers They could be used to analyze NMR relaxation times but they were not spectrometers in the sense usually meant in NMR So yes the picoSpin 45 really is the world s first miniature NMR spectrometer How does it work The picoSpin 45 is in most respects a conventional Fourier transform pro ton NMR spectrometer It has all of the usual NMR spectrometer components including a magnet shim coils programmable pulse sequencer RF transmit ter solenoid RF coil low noise receiver and digital data acquisition system What is different is just that everything is so small Instead of a large and ex pensive superconducting magnet we use a fist sized room temperature per manent magnet The electronic circuits are all miniaturized using techniques similar to those used in cell phones The sample fluid is confined to a small capillary with an inside diameter of about 0 3 mm How stable is the picoSpin 45 Can I use averaging to improve the signal to noise ratio The system is stabilized by a magnet temperature controller and by software techniques If the sample itself behaves in a time independent way any num ber of single shots can be averaged together to improve SNR Can I look at flowing samples 41 picoSpin 45 User s Manual Release 0 8 0 32 Yes but
43. resonance s Larmor frequency and signal strength which are used by the script Bandwidth The bandwidth of the receiver channel This number determines the dwell time of the data acquisition It is the rate in kHz at which the digitizer samples the signal Post filter atten The attenuation setting of the filter electronics For a further description see the hardware section Rx recovery time The time between the end of the pulse and the beginning of acquisition to wait for the receiver electronics to recover from ring down T1 recovery time 5 2 autoShim 33 picoSpin 45 User s Manual Release 0 8 0 32 The requested T recovery time between experiments Since this is imple mented at the script level the parameter is non deterministic phase correction The amount of phase correction to apply to the FID in degrees This parameter only effects the displayed phase and not the phase of saved data Exp apod rate If non zero applies an exponential appodization to the data specified in Hertz This parameter only effects the displayed phase and not the phase of saved data Max plot points The maximum number of points to plot to the browser If fewer points are specified than the number of acquisition points then the script will attempt to decimate the time and spectral data down to a number of points which does not exceed this number If greater than the number of acquisition points are specified then the script
44. set of harmonic values which maximize the quality of the peak The size of the steps that the algorithm starts off with we refer to as increments To re duce the complexity of the user interface it is only necessary to specify the size of the increments to use for all the first order shims and the size of the increments to use for the second order shims If either of these are zero that set of shims will be excluded from the optimization While the script is running the message window indicates the shim values that are being tried by the optimization algorithm and the LCD displays the number of times the pulse sequence has been run on the first line and the best value for the quality of the peak on the second line The script also keeps a log file of all the shim values tried the associated quality value and the frequency of that peak When the script stops either because it has reached the maximum number of iterations specified it has passed the convergence criterion or the run has been aborted the best values of the shims found will be kept and will appear in the shim drop down of the browser interface 5 2 1 parameters Tx Frequency The RF transmitter field frequency specified in MHz This frequency corre sponds to the 0 or center frequency of the spectral plot For example if this is specified as 45 0 and a peak in the spectral plot appears at 2000 Hz then the actual peak frequency is 45 002 Mhz If this field is subsequently se
45. spectroscopic resolution will suffer unless the sample is stationary during the NMR data acquisition For most applications either the inlet port or the outlet port should be closed during data acquisition and there should be a small fluid volume between the closed valve or plug and the port Other wise thermal expansion of the fluid can cause flow Why does the picoSpin 45 have a capillary cartridge When reasonable precautions are observed problems with clogging and con tamination of the capillary can be avoided However accidents do occur and when they do it is a great advantage to be able to replace the capillary in the field Cartridge changes only take a few minutes The unit should be re shimmed whenever the cartridge is changed What experiments can I do other than 1 D spectroscopy The picoSpin 45 contains a general purpose programmable pulse sequencer with 20 ns time resolution The sequencer controlled RF oscillator has 32 bit frequency resolution 8 bit phase resolution and 8 bit attenuator resolution The main channel pulse program can contain up to 1024 instructions With these capabilities essentially any proton NMR experiment is possible includ ing spin echo T measurements and T inversion recovery The first released version of the picoSpin software Version 0 80 supports 1D spectroscopy only Can I write my own pulse sequences When version 1 0 of the software is released users will be able to write their own
46. t to 45 002 then the peak will appear to occur at the 0 frequency of the spectral plot increments 1st order The starting step size to use for the first order shims in the Nelder Mead method increments 2nd order The starting step size to use for the second order shims in the Nelder Mead method 32 Chapter 5 Experiment Scripts picoSpin 45 User s Manual Release 0 8 0 32 max iterations The maximum number of times the Nelder Mead algorithm should evaluate the simplex during the search This is a number that is less than the number of times the sequence is run which is not the number indicated on the LCD display target rms The criteria for convergence of the auto shimming algorithm When the algo rithm reaches this value the script stops and reports the best shims found in the order shown at the beginning of the description of this script Channel The channel where the pulse sequence should be loaded Channel A is for user samples injected from the front panel of the instrument and channel B is for the internal reference Pulse width The duration of the RF pulse in microseconds Acq pts The number of points to acquire during an acquisition The acquisition time is this number divided by the specified bandwidth zero filling The number of points to use for zero filling of the time series data Increas ing this number beyond the number of acquisition points provides a quick improvement in the estimate of a
47. th the longer the script takes to process it In addition if other processes request the attention of the OS s processor it may not be possible to run the next sequence at the rate the user requested In the case of the autoShim script the next sequence might start at a delayed time giving the spin system more time to relax and the subsequent signal will then be larger which will give the shim optimization algorithm a falsely better value Therefore when running this series of scripts please keep in mind that the T entry is implemented at the OS level and therefore might not be adhered to It is safest to wait for the system to fully relax if time permits 27 picoSpin 45 User s Manual Release 0 8 0 32 5 1 onePulse The onePulse script is the experiment which will most often be used in daily use for col lecting and analyzing data It implements a single pulse acquisition sequence as shown in the figure below Pulse Rx Recovery Width Time Acq Pts Bandwidth Figure 5 1 onePulse pulse sequence The sequence transmits a single pulse waits for a relaxation time then begins recording data If better SNR is desired it is possible to repeat the sequence a user specified number of times In this situation there is a target time before the next sequence is started to wait for T relaxation Since this target time is implemented at the script level instead of in the sequence loaded to the NMR Engine on a non RTOS system the actua
48. will plot the number of acquisition points to the browser The purpose of this parameter is to decrease the load on the operating system This may improve the ability of the operating system to keep up with the user specified T request This parameter does not effect the number of points saved to the data files Max time to plot The maximum time to plot for the time series data in the browser This param eter is useful when the user wants a long acquisition time but wants to have a zoomed in look at the beginning of the FID This parameter does not effect the number of points saved to the data files Min freq to plot The minimum frequency to plot for the spectral data in the browser This parameter is useful when the user only wants to look at a limited range of the acquired spectrum This parameter does not effect the number of points saved to the data files Max freq to plot The maximum frequency to plot for the spectral data in the browser This parameter is useful when the user only wants to look at a limited range of the acquired spectrum This parameter does not effect the number of points saved to the data files magnitude If set uses the spectral magnitude in the optimization routine instead of just the real part of the signal This avoids having to worry about changes of phase when using large shim search increments 34 Chapter 5 Experiment Scripts picoSpin 45 User s Manual Release 0 8 0 32 5 3 search The
49. y specified in MHz This frequency corre sponds to the 0 or center frequency of the spectral plot For example if this is specified as 45 0 and a peak in the spectral plot appears at 2000 Hz then the actual peak frequency is 45 002 Mhz If this field is subsequently set to 45 002 then the peak will appear to occur at the 0 frequency of the spectral plot Channel The channel where the pulse sequence should be loaded Channel A is for user samples injected from the front panel of the instrument and channel B is for the internal reference Scans The number of times to run the single pulse acquisition sequence If a certain target SNR is desired it is probably easiest to run with the small number of scans at first to estimate the SNR per scan then recall the SNR scales as the square root of the number of scans Pulse width The duration of the RF pulse in microseconds Acq pts The number of points to acquire during an acquisition The acquisition time is this number divided by the specified bandwidth Bandwidth The bandwidth of the receiver channel This number determines the dwell time of the data acquisition It is the rate in kHz at which the digitizer samples the signal Post filter atten The attenuation setting of the filter electronics For a further description see the hardware section Rx recovery time The time between the end of the pulse and the beginning of acquisition to wait for the receiver electronics to rec
50. you find that a solvent proton signal overlaps strongly with an important solute signal 7 4 Installation Where can I install a picoSpin spectrometer There are no special facilities or environmental requirements You can place a picoSpin spectrometer in any indoor location where a person would be comfortable AC magnetic fields generated by nearby utility power that are stronger than 1 mgauss amplitude will cause small side bands to appear on spectra In unusual cases where this is a problem the unit can be oriented so that the AC field vector is perpendicular to the magnet s field Will a picoSpin technician install the unit in my lab We can do this for a fee but it is not generally necessary Set up and operation of the picoSpin 45 is far simpler than for conventional NMR spectrometers In most cases customers with only a little knowledge of NMR have no problem installing the system 7 5 Data Analysis How do I analyze my data The picoSpin 45 generates data in the industry standard JCAMP DX format Any NMR data analysis package that can read this format may be used to an alyze your data A one year license to MNova NMR software from Mestrelab Research is included with each picoSpin spectrometer 44 Chapter 7 Frequently Asked Questions
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