Files structure - United States Naval Academy
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NMR Pulse Spectrometer PS 15
Operating Manual for MS Windows
For: MS Windows software Winner v.1.2, Format: MS Word 2000
File: PS15 operating manual v1_2.doc
Last upgrade: 04December2003
***
by Jay H. Hank, PhD
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CONTENTS
1 introducing NMR and ps 15 1
2 iNSTALLATION 3
2.1 Introduction 3
2.2 Shipment check 3
2.3 Spectrometer location and environmental requirements 3
2.4 Electrical requirements 4
2.5 Computer requirements and software installation 5
2.5.1 Computer considerations 5
2.5.2 Software installation 5
2.6 Hardware connections. 6
2.6.1 Attaching the probehead 6
2.6.2 Unit connections 6
3 SPECTROMETER OPERATION 9
3.1 Spectrometer description 9
4 SOFTWARE description 13
4.1 Experimental setup 15
Magnetic field 16
Transmitter 19
Receiver 20
Data acquisition 22
Programmer 23
DC Level 29
Status bar 29
Menu Bar 30
4.2 Data acquisition 34
4.2.1 Acquired data display window 34
4.2.2 Extracted relaxation data display window 35
4.2.3 Experimental setup window 35
4.2.4 Parameter dialog window 35
4.2.5 Status line 37
4.2.6 Acquiring spectroscopy data. 38
4.2.7 Acquiring relaxometry data 39
4.2.8 Operations summary. 40
4.3 Processing page. 41
4.3.1 Spectroscopy data files 43
4.3.2 Relaxation data files 44
4.3.3 Summary of disk operations. 45
4.3.4 Processing spectroscopy data. 47
4.3.5 Processing relaxometry data. 52
5 Getting started 59
5.1 Introduction 59
5.2 Sample preparation and positioning 59
5.3 Executing the control program 61
5.4 A simple on-resonance one-pulse experiment with glycerin sample. 64
5.5 Preliminary setup 64
5.6 Final setup. 64
5.6.1 Data Acquisition adjustment 64
5.6.2 Receiver adjustment 65
5.6.3 Field adjustment 66
5.6.4 Pulse adjustment 67
5.6.5 Sample position 69
5.7 Acquiring FID 71
5.7.1 Viewing data and converting data from binary to text format 72
6 TROUBLE SHOOTING 73
6.1 Trouble shooting. 73
6.2 Magnetic field adjusting. 75
6.2.1 Switching to lock-off diagnostic mode. 76
6.2.2 Correcting magnetic field homogeneity. 77
6.2.3 Setting magnet I0 current. 79
7 SPECTROMETER SPECIFICATIONs 81
8 Appendix 83
8.1 Program directory structure. 83
8.2 Text data formats. 86
8.2.1 Spectroscopy data. 87
8.2.2 Relaxometry data. 89
8.3 Changing configuration file. 91
8.4 Samples 92
8.5 Electronic unit front panel 93
8.6 Electronic unit back panel. 94
8.7 Magnet and probehead front view. 95
8.8 Magnet and probehead side view. 96
9 Note to users of serial number 1 THROUGH 35 97
9.1 Electronic unit front panel 97
9.2 Electronic unit back panel 98
9.3 Magnet front view 99
9.4 Magnet side view 100
10 references 101
10.1 Papers: 101
10.2 Books: 101
10.3 Web references 102
10.4 Comments to versions 102
11 List of figures 103
12 Index 107
introducing NMR and ps 15
The postulate of Pauli in 1924 that certain nuclei posses a spin angular momentum led Gerlach and Stern to experimental confirmation that nuclei had magnetic moments. In 1939 Rabi first demonstrated resonance absorption of an oscillating electromagnetic field by molecules placed in a constant magnetic field. The first unsuccessful NMR experiment in solid state was performed in 1936 by Gorter. It was successfully done in 1946 independently by 2 groups Purcell at Harvard and Bloch at Stanford (Nobel Prize in 1952). Later in 1950 Hahn implemented an ingenious idea of replacing continuous wave excitation of polarized nuclei by pulse excitation. In 1951 Arnold went beyond the limits of magnet homogeneity and obtained the first high-resolution spectra discovering 1H chemical shifts. Hahn’s pulse spectroscopy idea matured in the 1960’s when technology allowed Anderson and Ernst the use of computers for Fourier Transformations (for his contribution to modern NMR Ernst received the Nobel Prize in 1991). This allowed one to change time domain to frequency domain in one keystroke.
The age of medical applications started in the early 1970’s after Lautertbur demonstrated the feasibility of using NMR for imaging. Liberated from the obsession of perfect magnetic field homogeneity he deliberately applied gradients to encode the spatial information into an NMR spectrum. This and Damadian’s discovery in 1971 about tissue contrast available through variation of nuclear relaxation times opened Pandora’s box for medical application.
Since its discovery, NMR has proved to be a versatile technique in basic research (Physics, Chemistry, Biochemistry). It found application in Geology (oil and ferrous compounds search), Agriculture and Food Industries (moisture contents and purity measurements), and in Archeology (tracing changes of the Earth’s magnetic field through the ages). Finally materializing under the MRI acronym (Magnetic Resonance Imaging; for “political” reasons the word “nuclear” was removed) Lauterbur’s idea on “ Image Formation by Induced Local Interactions” proved to be a perfect modality for clinical anatomical and functional imaging.
Tel-Atomic, Inc. now presents a desktop pulse NMR system, the PS-15, that combines all of the sophisticated features that mainframe spectrometers have including:
• Multiphase RF power pulses,
• Quadrature receiver,
• Three stage magnetic field stabilization (current, flux, and NMR lock on 19F),
• Intuitive software for experiment preparation, experimental data acquisition, storage and processing.
Although designated for teaching, the PS-15 hardware and software provides a convenient means for NMR spectroscopy as well as for relaxation experiments on 1H nuclei (protons) at a magnetic field of 350 mT and at frequency of 15 MHz.
There is also a category of instrumentation experiments involving magnetic field stabilization, RF pulse generation, quadrature detection, signal filtering, analog-to-digital conversion and signal accumulation that can be easily performed.
The purpose of this Operating Manual is to provide the user with comprehensive information about:
• Spectrometer installation,
• Spectrometer hardware,
• Spectrometer control program,
• Performing simple spectroscopy and relaxation experiment,
• Troubleshooting possible hardware and software problems.
Experiments that can be performed with the PS-15 are found in The ExperimentalLaboratory Manual.
iNSTALLATION
1 Introduction
The installation of the PS-15 spectrometer is very easy and requires only a flat and Philips screwdriver. Please read this chapter before attempting to connect the spectrometer.
2 Shipment check
After you have unpacked the instrument it is recommended that you keep the shipping cases so they may be used if the instrument should need to be returned for maintenance or repair.
Returning the instrument in anything other than the original case may result in damage not covered by warranty.
Check the contents of the shipment against the enclosed Product Checklist.
Inspect all parts for any signs of damage that may have occurred during shipment. Immediately report any visible damage or incomplete delivery to your distributor.
(Note:
Probehead and electronic unit covers are sealed with no removable labels. Please do not open. Warranty is void if seals are broken!
3 Spectrometer location and environmental requirements
The spectrometer should be placed on a solid table or bench, preferably wooden. Try to eliminate the presence of iron beams or any other ferrous components in the electromagnet proximity that can disturb its homogeneity. Avoid a vibrating environment: elevators, frequently used doors, etc. A clean, dust free, low humidity environment is recommended.
(Warning:
The magnet is protected by a process known as “bluing”. This is the same process by which gun barrels are protected. Therefore handle the magnet only by the handles since water or skin oils can cause corrosion to occur.
Do not expose the magnet to water or high humidity!!!
At least twice a year use gun oil or WD-40 to wipe the surface of the magnet. It is important to keep oil from getting into the magnet’s coils and the probehead therefore DO NOT SPRAY OIL OR WD-40 DIRECTLY ONTO THE MAGNET, rather saturate a piece of soft cloth or patch with the oil or WD-40 and wipe the magnet’s surface thoroughly with this.
Store the magnet in the box (in which it was shipped) in a low humidity environment.
4 Electrical requirements
Before you turn on the PS15, make sure that:
Figure 1. 115V label for USA market.
• The line voltage selector label matches the voltage mains supply. The label is located on the top right corner of control unit cover. 115 V label for USA market is shown in Figure 1.
• Ensure that AC power source meets the requirements specified in Table 1.
(Note:
Voltage selector is located inside the control unit and should be set by authorized personnel only.
Table 1. PS 15 power requirements.
Verify that the power cable is not damaged, and that the power source outlet provides a protective earth ground contact. The working fuse is located above the power cable receptacle on the PS15 back panel labeled 3 in Figure 2.
Figure 2. Electronic control unit back panel: 1) power entry module, 2) power cable receptacle, 3) fuse, 4) power switch.
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5 Computer requirements and software installation
1 Computer considerations
For proper operation, data storage and display, the spectrometer winner control program requires an IBM PC AT VGA or compatible computer. The program and factory created files occupy less than 2MB of hard drive total space. Average spectroscopy binary data files need only about 10 kb of space, but expand as much as 5 times when converted into text files. Average relaxation binary data files occupy about 100 kb, but collapse to 1 kb when amplitudes and corresponding delays are extracted for further relaxation time calculations. Processed spectra occupy about 25 kb. Exact numbers depend on number of data points acquired. Even if intensively used, the software generally needs only moderate space on the hard disk.
2 Software installation
To install the software, create a PS15 directory in the root directory of your “c:” hard drive and copy the winner file from the provided compact disk into it. Keep the directory structure as factory created. For more information about program files structure refer to Figure 62. After copy check files/directories properties. Make sure that attributes read-only box is unchecked.
6 Hardware connections.
General
Arrange the electromagnet, electronic unit and the computer on the desk, according to space availability and convenience. Remember that keyboard and monitor are the most used devices. As samples will be frequently replaced and repositioned in the probehead keep the magnet close to your hand and eyes.
1 Attaching the probehead
Remove protective nuts from the two metric M4 screws (keep nuts). Place the probehead in the electromagnet, sliding it gently between poles from the side where two tapped holes appear. Fix the Probehead in place using the Philips #2 screwdriver and M4 screws[1]. Avoid using excessive torque. The Probehead is the most fragile part of the spectrometer and requires special treatment when being attached or during transportation.
2 Unit connections
Connect the computer and electronic unit power supply cords to the same power line to avoid unwanted ground currents.
Connect the electronic unit, electromagnet and probehead according to the specification in Table 2 using the provided cables.
|Source |Destination |Description |
|Control unit |Magnet, Probe, Computer | |
|RS 232 |Computer COM1 or COM2 |9 pin D connector M/F |
|Magnet |Magnet on the front base |15 pin D connector M/M |
|Head |Probehead/ Intf |25 pin D connector M/M |
|TX |Probehead/ TX |BNC M/M |
|RX |Probehead/ RX |BNC M/M |
Table 2. Connections between electronic control unit electromagnet, and probehead
Notes:
• In Description column M denotes Male and F denotes Female,
• To establish reliable connection do not forget to secure all connectors with provided screws.
SPECTROMETER OPERATION
The Pulsed NMR technique combines the old fashioned precision of electromagnet mechanics and fine analog tuning of RF channels (transmit and receive) with modern, sophisticated digital methods of fast data acquisition and processing. The PS-15 spectrometer uniquely combines all these features to achieve high magnetic field homogeneity and stability, fast recovery after applying power pulses and high sensitivity.
1 Spectrometer description
Despite its internal complexity, the PS15 spectrometer can be divided into a few functional modules which may share some common elements. Looking at the spectrometer block diagram in Figure 3 we can distinguish the following:
Exciter
Generates a continuous wave signal with very stable frequency (sometimes called carrier frequency), provides necessary phase shift for reference signal in a phase sensitive quadrature detector, modulates CW into square RF pulses, and attenuates their amplitude. The pulse envelope must have rise and fall times short compared with pulses width.
Programmer
Generates certain pulse sequences, controls time duration of different events (length of pulses and delays), and selects required phase of pulses.
Transmitter or high power amplifier
Amplifies RF pulses to powerful bursts of power.
Probehead
Sits precisely between magnet poles and works as an antenna that generates a strong oscillating magnetic field to radiate the sample during RF pulses and thus can withstand relatively large voltages (during transmit period - TX). It quickly recovers and amplifies the weak nuclear signal following the pulses by a low-noise preamplifier that determines the overall spectrometer Signal-to-Noise ratio (during receive period - RX). The probehead also provides means for locking the magnetic field to the spectrometer carrier frequency.
Figure 3. PS 15 spectrometer block diagram.
Receiver
Further amplifies the nuclear signal at RF frequency, detects it, amplifies and filters the signal after detection. Following the filters are Analog-to-Digital Converters (ADC), that change analog signals into binary representation. After conversion, bits are stored in a memory buffer that holds the last data acquired.
Electromagnet
Provides very stable, constant magnetic field, that is very homogeneous within the sample volume. Homogeneity depends on the poles’ relative position, and can be modified by a set of several adjusting screws.
(Note:
This should only be attempted after consultation with the factory.
Electromagnet stabilizer
Regulates the current that flows through the main electromagnet coils. Additionally it receives “error” signals from the flux coil and from the lock sensor (19F NMR signal) and corrects the current that flows through the magnet correction coils to compensate for magnetic field short- and long-term instability.
Microprocessor controller
Supervises all processes and events that take place in the spectrometer. With the help of an internal program that resides in an EPROM, the microprocessor interprets commands from an operator and takes action. Some processes like magnetic field stabilization are done automatically, however, most of the processes require the operator’s participation via a dialog menu.
Computer
Runs the control program, displays and stores experimental results communicating with a microprocessor controller via bi-directional RS 232 bus.
SOFTWARE description
Introduction
The spectrometer operation is controlled by a package of dedicated software for user- friendly assistance during the preparation of an experiment, its final performance and later data processing. The software provides convenient means for acquisition of any form of nuclear signal related to NMR spectroscopy or relaxometry and its processing.
The software graphic interface consists of three main pages: Setup, Acquisition, and Processing. The user can toggle easily between aforementioned pages using a mouse or , , and function keys, respectively. However, from the Processing page a user can return only to the Setup page. Pages are organized in several windows accessible by a mouse click or other available function keys. There are additional Data display windows on each page.
The spectrometer can operate with and without NMR magnetic field stabilizer. Operation is determined in the Menu bar by selecting Spectrometer>lock-on or Spectrometer>lock-off. The NMR stabilizer provides excellent long-term stability of the magnet that compensates for thermal drift. This stability is necessary for experiments that require long times (for example multiple signal accumulation). With the NMR lock-off the user has the freedom to turn on/off the flux stabilizer that compensates for fast changes of the magnetic field. It is recommended only for diagnostic purposes like correcting magnet’s homogeneity (shimming) and adjustment of initial current (I0) of the basic magnet current stabilizer.
Regardless of the status of the magnetic field stabilizer (lock-on or lock-off) the experiment preparation is done in a Setup page and involves selection and adjustment of the following parameters or processes:
• magnetic field,
• signal detection,
• data acquisition, display and storage,
• receiver parameters,
• RF power attenuation,
• timing of pulse sequence.
Data obtained during any experiment that is run on the Setup page are shown continuously in real time in the data display window after the averaging is complete. Any change in Setup takes effect immediately on data the display. If multiple accumulations are conducted wait for one complete cycle to see an effect.
The final experiment and data storage is performed in the Acquisition page. This task requires the definition of the name of the destination binary file, the accumulation number, the variable delay file name if relaxation measurements take place, and any comment.
The data pconversion rocessing is performed in a Processing page and it allows the user the following file operations:
• loading any binary data files and vdisplaying iewing themit on the monitor,
• manipulating spectroscopy files and performing Fast Fourier Transform,
• processing spectra,
• converting spectroscopy binary files and storing them as text files,
• extracting certain data points from relaxation binary data files,
• fitting extracted relaxometry data points to calculate T1 by Inversion Recovery and Saturation, and T2 by CP and CPMG methods,and store them in a text file as two columns of time delay and corresponding signal amplitudes
• converting binary files and storing them as text files,.
Program can be terminated at any page, anytime by clicking on [pic] or, selecting File>Exit (additionally or by at Setup page).
1 Experimental setup
This general-purpose page appears when the program is first executed. It plays a key role in the spectrometer launch and during the preparation of the experiment.
Figure 4. Setup page G. A general view of Setup page.
Figure 4 illustrates the Setup page when an off-resonance one-pulse experiment was performed using 1P_X sequence. Besides Info, Menu, Tool and Status bars the SETUP page consists of a Data display window and seven Spectrometer setting windows:
• Magnetic Field
• Transmitter
• Receiver
• Data acquisition
• Programmer
• DC level
Magnetic field
Gives access to both the coarse change of the static magnetic field and to its fine adjustment, as well an access to the lock stabilizer activation as shown in Figure 5. Additional information on the locking conditions is also provided.
Figure 5. Magnetic field stabilizer controls.
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f0/B0
Range[2]:
frequency units - f0 fromf0 from 14,992.2 kHz tokHz to 15,043.2 kHz, 4.25 kHz step[3],
magnetic induction units - B0 from 352.1 mT to 353.3 mT, 0.1 mT step3.
The value of the magnetic field (in magnetic induction [mT][4] or in the frequency [kHz] units) that can be set by the lock stabilizer.
It can be changed around proton resonant magnetic field/frequency. When the value of f0/B0 is changed the program automatically starts to lock at the corresponding frequency. The default value is the field magnitude used in the last session that was stored in a configuration file after regular program termination.
(f0/(B0
Range:
frequency units - (F0, from, from - 2177 Hz to +2173 Hz, 4.2 Hz step[5],
magnetic induction units - (B0 fromB0 from -51.1 (T to +51.0 (T, 0.1 (T step5.
Provides fine adjustment of the static magnetic field without breaking the lock conditions.
Avoid fast changes which can confuse the lock stabilizer since it cannot react fast and therefore can loose the locking signal. This adjustment is a useful tool to reach on- or off-resonance conditions.
Fa
Shows the real resonance frequency of 1H nuclei at the locked field.
When lock is achieved an internal frequency counter measures the resonance frequency of 19F nuclei in a lock sample[6]. The processor recalculates the value taking into account the differences of 1H and 19F gyromagnetic ratios and displays it as resonance frequency of 1H nuclei. If the measured frequency significantly differs from the setting in f0/B0 box, the program considers lock as unsuccessful and starts locking procedure again. There may be a slight difference between both numbers due to some “rounding” effects during calculations and the fact that carrier frequency in 19F lock channel is purposely deviated (1 kHz deviation amplitude and, 125 Hz deviation frequency)[7].
(I0
Displays the percentage value of the entire magnetic field sweep after the NMR lock was achieved.
Extreme values (close to 0% and 100%) should be avoided to provide a safety margin necessary for corrections of magnetic field by the lock due to electromagnet’s thermal drift. The sweep during the locking procedure covers range of +/- 2,048 (T (512 (T x 8 screens) which is about 1% of the total magnetic field magnitude. If the initial electromagnet current I0 is properly adjusted the lock takes place close to the sweep center.
Lock
Activates or deactivates lock during the program initialization.
[Cleared] Keeps the locking procedure running in a loop and displays first derivative of CW 19F NMR signal when Lock option is cleared before the locking loop closes (see Figure 6). Used for an instant check of magnetic field homogeneity and overall performance of the lock. For proper operation first derivative should occupy about 30% of the data display window and should not have significant DC offset.
Figure 6. First derivative of NMR signal from 19F nuclei when Lock is cleared.
[pic]
[Checked] Default parameter that starts the locking procedure shortly after the control program was executed. Figure 7 shows deformed signal from Figure 6 due the reaction of the spin system on a magnetic field sweep perturbated by an acting lock.
[pic]
Figure 7. CW NMR signal from 19F in HBF4 sample after successful lock was achieved (when Lock option was checked).
Controls the power of the RF pulses by attenuation of the signal at transmitter’s input.
Figure 8. Transmitter attenuator controls.
Transmitter
[pic]
Attenuator main
Range: 0-31.5 dB, step 0.5 dB
Changes power of pulses simultaneously in all channels.
Attenuator Y
Range: 0, 1, 2, 4, 8
Changes power of pulses in Y channel only. Active only during T1( measurements (*.mrl sequence).
Receiver
Allows access for receiving and detection functions, and for RF power attenuation.
Figure 9. Receiver controls.
[pic]
Gain
Range: 0-60 dB, 1 dB step
The gain of receiver RF amplifier
Phase
Range: 0o-360o, 2o step
In phase quadrature detection the phase control of the reference signal.
If one channel option is active the phase should be set manually to achieve maximum signal after detection, either positive or negative.
Time C
Range: 1(s, 5(s, 30(s
Time constants of the low pass filter.
The filter limits the pass band after detection thus removing unwanted products of the detection process and decreasing noise. Filter significantly improves S/N noise ratio. However, short nuclear signals with a fast decay require a broader pass band, which corresponds to a shorter time constant. If the time constant is too long then fast transients in a signal become integrated and subtle details are lost. For solid-state use 1 (s, for liquid-like samples use 30 (s.
Acc
Range: 1-128
Number of accumulations.
The accumulation process improves signal-to-noise ratio (S/N). Assuming that there is predominantly thermal noise, with its average value around zero level, the S/N ratio increases as the root square from the number selected.
Detection
Range: (Phase, Amplitude)
Mode of the signal detection:
Phase- phase quadrature detection, usually used in real experiments.
Amplitude - amplitude detection (sometimes called diode detection).
Rarely used option due to diode detection nonlinear errors and requirements for high amplitudes of signals detected. Nuclear signal after amplitude detection is not affected by the receiver phase. Can be substituted by phase quadrature detection in a magnitude mode if necessary.
Provides commands to control acquisition parameters and to select quadrature detector channels shown in a data display window which can be stored in a binary file on the Acquisition page. Data from both quadrature detector channels, real I and imaginary Q, are simultaneously stored in a memory buffer, but only channels selected in this window will be later displayed and stored in the user’s defined file.
Data acquisition
[pic]
Figure 10. Data acquisition controls.
Dwell time
Range: 0.4, 1, 2, 10, 20, 40, 100, 200, 400 (s
Time between points sampling.
NOP
Range: 256, 512, 1024, 2048, 4096, 8192
Number Of Points acquired.
Dwell time DT and NOP determine the total acquisition time: Tacqu=(DT x NOP). More NOP require more storage space on the disk.
Channel I
Check to see and store data in I- real channel.
Channel Q
Check to see and store data in Q- imaginary channel.
I2 + Q2
Check to see and store data points magnitude. Magnitude value M of every point is calculated from formula: [pic]. Note that there are no negative values and there is no phase dependence.
Generally this window gives access to different factory created pulse sequences (see tables Table 3-7). After selecting the certain sequence, the Programmer provides the means to change sequence parameters (pulse width, delays, acquisition triggering) and to start or stop that sequence at any moment. The spectrometer generates some additional delays and pulses that help to protect the receiver from high power pulses and establish proper triggering for data acquisition. Figure 11 shows the case of three-pulse sequence: pulses P1, P2 and P3 separated by delays D1 and D2; sequence is repeated after period R- called repetition time.
[pic]
Programmer
Figure 11. Three pulse sequence.
Following is the description of the Programmer window for a specific one pulse (1P_X) sequence.
[pic]
Figure 12. Programmer dialog box with one-pulse sequence opened.
Method
Is used to open a directory with a list of different pulse sequences and to select one such sequence. Method in PS15 nomenclature refers to the experiment performed with a certain pulse sequence. Terms method and pulse sequence are somewhat interchangeable. Method refers to some experimental activity, whereas sequence indicates its complex, time dependent character. Generally any method is a series of events (Pn) separated by certain delays (Dn) between them. Events are usually RF pulses generated in the modulator (see Figure 2) by square pulses from the programmer or are other auxiliary pulses in a square wave form (internal triggering, delaying, etc).
Since the spectrometer can operate in spectroscopy and relaxometry mode all methods have been divided arbitrary in two categories: spectroscopy methods (stored in files with extension *.msp) and relaxometry methods (stored in files with extension *.mrl).
Action
To choose the method click on the rectangle next to method. After list of different methods pops in click on the method name.
Figure 13. Spectroscopy methods dialog box.
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Figure 14. Relaxometry methods dialog box.
[pic]
Factory created pulse sequences
The software package includes a set of the most popular NMR sequences. SThey pectroscopy methods (S) are stored in the S_mMtd whereas relaxometry method in R-mtd subdirectory. Tables below summarize all currently available sequences and their properties. Other sequences are available upon request. Note that due to space limitations the Description column uses a simplified convention explained later.
|ONE-PULSE |
|Name |Description |M |Comments |
|1P_Y |Y1 – R |S |One-pulse sequences are used to generate Free Induction Decays. RF |
| | | |signals in 1P_X, 1P-Y, and 1P-X sequences have different phase shifts |
| | | |relative to 1P_Y sequence; 90o, 180o, 270o, respectively. |
|1P_X |X1 – R |S | |
|1P_-Y |-Y1 – R |S | |
|1P_-X |-X1 – R |S | |
Table 3. One-pulse sequences.
|TWO-PULSE |
|Name |Description |M |Comments |
|2P_X_D |X1 – D1 – X2 – R |S |Useful to generate spin echo or to sample FID after certain time delay. |
| | | |In Acquisition uses delay from Setup page. |
|2P_X_VD |X1 – VD – X2 – R |R |Universal sequence to measure T1 or T2*. Requires Variable Time Delay |
| | | |file during the acquisition experiment. |
|HAHNECHO |X – D – 2*X – R |S |Simplified 2P_X_D. Second pulse is twice as long as first one is. For a |
| | | |brief generation of Hahn’s spin-echo. |
Table 4. Two-pulse sequences.
|THREE PULSE |
|Name |Description |M |Comments |
|3P_X_D |X1 – D1 – X2 – D2 – X3 - R|S |General use three-pulse sequence. |
|STIM_SE |X1 – D1 – X2 – VD – X3 – R |R |Stimulated Echo sequence. Frequently used in T1 measurements. During |
| | | |Acquisition Variable Time Delay file is required. |
Table 5. Three-pulse sequences.
|MULTI PULSE |
|Name |Description |M |Comments |
|CP_25 |X –[D/2 – |R |Carr-Purcell sequence to measure T2. Drastically reduces spin diffusion |
| |[X – D (25 times)] – R | |effect compared to simple Hahn’s spin-echo sequence. Generates 25 spin |
| | | |echoes. No VD required. |
|CPMG_25 |X – D/2 – |R |Carr-Purcell-Meiboom-Gill sequence to measure T2. Reduces spin diffusion|
| |[Y – D (25 times)] – R | |effect and cumulative effect of pulse length accuracy. Generates 25 |
| | | |spin-echoes. No VD required. |
|SOLID_SE |X1 – D – Y2 – R |S |So called Solid (State) Echo. Used to generate and acquire spin echo |
| | | |signals in solid like samples. |
|SAT | |R |Saturation method. |
Table 6. Multipulse sequences. Note that these sequences are too complex to describe them shortly. They are analyzed in detail in the LABORATORY EXPERIMENTAL MANUAL.
Column M describes the spectrometer mode method is used:
• S-Spectroscopy,
• R-Relaxometry.
In the Description column we used the convention that refers to the relative phase of pulses (Y=0o, Xo=90o, -Y=180o, -X=270o) and to its consecutive number in the sequence. For instance: X1 – D1 – X2 – R means that it is a chain of following events:
X1- pulse #1 with phase 90o (rotates magnetization along x’ axis)
D1- delay #1
X2- pulse #2 with phase 90o
R repetition; delay between two sequences
RF pulse
Radio frequency pulse that is characterized by:
• duration time (pulse width) –can be changed in the Programmer window,
• amplitude – can be changed in Transmitter window,
• phase – fixed; when using one-pulse sequences user can switch easily between different phases, selecting a certain method as shown in Table 3.
Action
To change pulse or delay time click on the corresponding rectangle with the pulse abbreviation (starts blinking) and move the bottom horizontal slider accordingly. You can change time with maximum available accuracy of 0.2(s clicking either on left (decrement) or right (increment) side of the slider.
Considerations
There is an additional acquisition delay between the end of the RF pulse and the beginning of data acquisition. You can change this delay according to experimental requirements. Usually the acquisition should be postponed by the spectrometer “dead time” that is the time between the end of the RF pulse and its complete decay as shown in Figure 15. During this time the receiver channel is “blind” due to ringing in the probehead coil. In the PS15, “dead time” is around 16-22 (s, depending on the power applied and quality factor Q of the resonant circuit loaded with the particular sample. Adjustment of acquisition delay is available through the rectangle right under repetition time R designator. If this produces some ambiguity note that acquisition delay time units are [(s] whereas repetition time units are [ms].
Figure 15. RF pulse and “dead time” that follows.
[pic]
Delay
This is the time that passes between the end of one pulse and the beginning of the next one. There is one specific delay called repetition time (R) that determines the repetition of the complete sequence. For proper sequence execution repetition time should be longer than acquisition time. (See timing of three-pulse sequence with associated data acquisition period in Figure 11). If there is an accumulation process running, then let nuclear spins relax before consecutives excitations. If TR=T1 magnetization return only to 63% of its equilibrium state. Keeping repetition time three times as long as T1 assures that the magnetization returns to 95% of its equilibrium state. If repetition time increases to five times the longitudinal relaxation time, spin relax to more than 99.9% of equilibrium value.
The spectrometer automatically generates some additional delays and pulses that help to protect the receiver from high power pulses and establishes proper triggering for data acquisition.
Trig
Allows one to select the beginning of data acquisition during a real experiment in the ACQUISITION page. The only acquisition triggering possible choice for one-pulse sequences is P1. In T1 measurements with Inversion Recovery trigger acquisition after the second RF pulse.
Action
Click on up/down barrows uttons next to the pulse box name to toggle between different pulses that compose the sequence.
Stop/Run
The radio button that activates the starts/stops pulse sequence. , Ddata acquisition follows the falling edge of triggering pulse. and display of the acquired Acquired data points are then transferred to computer and presented in the data display window. Display window shows last transmitted data and is refreshed after the current accumulation is completed. To confirm that the Programmer is working observe Programmer LED on the electronic unit’s front panel. It blinks after each RF pulse is generated. The data display window is refreshed when the accumulation process is completed.
Action
Click on Stop or Run radio button.
(Note:
It is recommended to Stop the programmer when returning to other programs.
Range: (+/- 125)
[pic]
Figure 16. DC level offset controls.
DC Level
DC offset of the NMR signal after detection.
Keep close to zero to avoid fast signal saturation during accumulation and problems with artifacts after performing Fourier Transform.
Action.
Status bar
Make acquisition time long enough to see the long tail that follows the signal. Then drag and move vertical sliders up/down to achieve right vertical position on a data display window.
Provides some additional information.
Figure 17. Status bar shortly after NMR lock is achieved.
[pic]
Marker on channel I – shows the channel that marker is bound to (real I channel).
t: and A: time in [(s] and amplitude in [arbitrary units] coordinates of data point indicated by marker
Lock: NMR lock status lock
• ON indicates that lock is turned on,
• locking indicates that locking process is in progress,
• sweep: -6[(T] indicates in magnetic field units the current position of the lock magnetic field sweep with regard to static magnetic field B0.
• 49.9% indicates the current percentage of total sweep range.
• Mode: Current mMode of spectrometer operation: Spectroscopy or Relaxometry.
Menu Bar
[pic]
Some functions in the menu bar are also available from the Tools bar. Use corresponding icon.
File
Used to perform disk operations and to exit the program.
Open method
To open new method from the list shown in a dialog box shown in Figure 13 and Figure 14.
Save method as
Used to save method under different name. Saves also timing of the recently used sequence.
Open setup [pic]
To load previously created setup.
Save setup [pic]
To save changes in recently used setup. Default standard.cfg can not be saved under the same name. Instead try Save As.
Save setup as
To save newly created setup under a new name. After renaming as standard.cfg it can be used as the default configuration file.
Exit
Terminates the work with the program. Saves timing of most recent sequence and updates spi.ini. Be sure that that method files and spi.ini are not write protected and that they are accessible through the correct paths in Tools>Preferences>File location.[8]
About
Contains information about the latest version of the software.
Spectrometer
To start the control program with or without NMR stabilizer.
lock-on
Turns on the NMR lock and starts the control program.
lock-off
Starts control program without NMR lock.
Mode
Directs access to spectroscopy or to relaxometry methods.
Spectroscopy
To acquire NMR signal in form of FID or spin echo.
Relaxometry
To perform relaxometry experiments that use variable time delay files or dedicated sequences like CPMG or CP.
Gamma
Future option
Task
To switch to other two pages.
Data acquisition [pic]
Directs the user to Data acquisition page.
Data processing [pic]
Directs the user to Data processing page.
Tools
Provides miscellaneous tools to organize setup page and directs access to different files.
Setup (zoom)
Produces whole screen data display window
Marker on channel I [pic]
Activates pointer on the real channel I of the quadrature detector.
Marker on channel Q [pic]
Activates pointer on the imaginary channel Q of the quadrature detector.
XY value on chart
Activates display of coordinates box on data display window with the marked point’s time and amplitude like: [pic].
Preferences
File Location
Determines paths of different directories used by the control program. Browse around using Preferences dialog box.
[pic]
Audio
Determines the location of audio files *.wav used to mark the experiment start, run and stop.
[pic]
Communication port
Select among one of four com ports. Be sure that the unit is connected to the right port.
[pic]
User’s Log
Allows time-stamped messages to be typed and added to spi.log file. Recommended for storing users’ comments.
Magnet stabilizer units
Click on mT or kHz to be displayed in Magnet stabilizer window.
[pic]
Note that system measures directly the frequency in [kHz] units not the field. When [mT] units are used new value is calculated with formula: [pic] and may be subjected to rounding error (see Figure 18).
Figure 18. Choosing magnet stabilizer units: [mT] or [kHz].
Display
Chose between Line or Discrete option for different representation of the signal in the data display window. If Discrete is selected chose among different shapes and sizes. Return to Line option by clicking on Restore line.
[pic]
2 Data acquisition
Used to perform experiments and to store data in a data file. This page is split into four windows and a status line as shown in Figure 19 below:
• Acquired data display window,
• Extracted relaxation data display window,
• Experimental setup window.
• Parameter dialog windowbox.
Figure 19. Acquisition page.
1 Acquired data display window
Displays in top most left corner of the Acquisition page current contents of the data buffer that holds consecutively accumulated data points. Accumulated signals are automatically normalized to fit the data display window size. Unlike the Data display window in the Setup page this window is refreshed at each single data acquisition.
2 Extracted relaxation data display window
Used in relaxation experiments to display the amplitude of the signal at the data pointer position for different delay times. Data pointer position must be set earlier on the Setup page. Horizontal axis is time delay, vertical axis is amplitude. This window is located on the bottom left corner (Figure 23) and provides helpful information for estimating the required delay time span in VTD file.
3 Experimental setup window
The window contains information on parameters established in the SETUP page. With the exception of the accumulation number they are transferred to Acquisition page intact.
4 Parameter dialog windowbox
Bottom dialog wbox indow that provides access to the following changeable items:
File - File name
Type the file name for the acquired binary data file. Program automatically adds the extension dta and stores the file in Data directory after experiment is completed.
Acc - number of accumulations (1-65,536)
Select the number of accumulations needed to get the required S/N ratio.
[pic]
Comment
Type any comment you need to be included into data file. Maximum 52 characters are accepted. If you click on the white field next to Comment the full comment window opens.
[pic]
VTD – Variable Time Delay
In relaxation measurement experiments, select the proper Variable Time Delay file. The file contains column of delay times in milliseconds stored as a plain text. Note that spectroscopy experiments do not require a VTD array, thus during spectroscopy experiments this box remains inactive. See for available VTD files by clicking on the field next to VTD. When Load VTD dialog box opens click on file name.
Figure 20. VTD directory.
[pic]
There is a list of factory prepared delays that can be used to measure T1 by Inversion Recovery method in rubber, glycerin, and paramagnetic ion doped water and in ethanol.
|File name |Time delays [ms] |Use |
|t1_16_r |0.3, 0.5, 0.75, 1, 2, 4, 8, 16, 32, 50, 75, 100, 150, 175, 200, 250 |T1 in rubber |
|t1_16_g |1,2,4,8,16,32,50,75,100,150,200,250,300,350,400, 500 |T1 in glycerin |
|t1_16_w |5, 8, 12, 16, 25, 32, 50, 75, 100, 150, 200, 300, 400, 500, 600, 700 |T1 in water |
|t1_16_e |100, 150, 175, 200, 250, 500, 1000, 2000, 3000, 4000, 6000, 8000, 12000, 12000, 16000, |T1 in ethanol |
| |24000, 32000 | |
|vd_user |1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16 |to create user’s array |
Table 7. Factory prepared VTD files that can be used in T1 measuremets by Inversion Recovery method.
VTD files can be viewed/edited or created from scratch on this page by selecting Tools>VTD>View VTD table /Edit. Once Edit is selected a new list can be created by New, an existing list can be loaded by Load. After editing, perform Sort to arrange lines in ascending numbers and save the file by Save or Save As. If you want to abandon changes, exit the editor by Close. Delays in relaxation measurements will be called during the experiment in the order in which they were placed on the list.
Figure 21. Time delay editor.
[pic]
5 Status line
Accumulation:
Shows current accumulation number and total number of accumulations.
VTD number:
Not used in Spectroscopy - [pic],
In Relaxometry mode shows current delay time being applied in the sequence - [pic],
Experiment:
Shows current status of experiment
waiting - [pic]
running - [pic]
completed - [pic]
Last data saved in:
shows the name of the file used to save recently acquired data - [pic].
6 Acquiring spectroscopy data.
To acquire spectroscopic data
• Type file name (File field).
• Type or select number of accumulations (Acc field).
• Type comment (Comment field).
• Start acquiring by clicking on [pic]. To stop data acuisitionacquisition click on [pic].
Figure 22. Acquisition page when spectroscopic data are acquired.
• After data acquisition is completed check status of Last data saved in: if data were saved under declared name and extension *.dsp (Figure 22).
[pic]
7 Acquiring relaxometry data
• type file name (File field),
• select number of accumulations (Acc filed); declare at least 8 since for certain delays, the nuclear signal will be very week,
• type comment (Comment field)
• select time delay file if required by method (VTD field),
• start acquiring,
• if points in in the relaxometry window are not scattered and at least 3-4 points reach maximum, stop the experiment. If points are scattered check on the Setup page to assure the triggering pulse was selected correctly (for Inversion Recovery it is 2nd pulse), check if data pointer is placed shortly after “dead time” usually 50(s is safe. If points do not reach maximum modify times in VTD and start experiment again.
• after data acquisition is complete check Last data saved in: in Status line if data were saved under declared name and with extension .drl.
[pic]
Figure 23. Acquisition page during the relaxation experiment.
8 Operations summary.
Executing the experiment
To start the experiment click [pic]on the Tool bar or select Experiment>Start from menu bar. Data starts to appear in the data window and if relaxation measurements are performed extracted points appear in the relaxometry window. You can stop the experiment by clicking on [pic] on the Tool bar or by selecting Experiment>Stop from menu bar[9]. If audio options were chosen then the selected sound follows.
Saving data.
After the experiment is completed data are stored automatically in the data directory under name declared in File field. If the File field is empty data can be stored manually by selecting Files>Save As and typing file name in the Save data to dialog box (Figure 24). If data were not saved there will be a warning of unsaved data before terminating job on Acquisition page. There are also standard warnings before attempting of overwriting existing file.
Figure 24. Saving data manually.
[pic]
Terminating work on Acquisition page.
To end working on Acquisition page and go to Setup or Processing pages click on [pic] button on Tools bar, Select Task>Exp.Setup/Data processing or hit F5/F7 function key.
3 Processing page.
This page allows one to:
• Load a binary data file from the disk and display file contents on the data display.
• Manipulate spectroscopy data (*.dsp) without saving changes: left/right shift, line broadening, Fast Fourier Transform.
• Extract points from relaxometry data (*.drl).
• Analyze spectra after FFT: determining line width, peak amplitude, and integral value.
• Export original and unchanged data as text for further processing with independent software: Origin, Matlab, Mathematica, Excel, etc. Default destination folder is also C:/Ps15/Dataout
• Calculate T1 using extracted points from relaxometry data generated by an inversion recovery (IR) and saturation methods.
• Calculate T2 using extracted points from relaxometry data generated by CP and CPMG.
• Save and Save As processed spectroscopy and relaxometry data. Default destination folder is C:/Ps15/Dataout.
• Export processed binary data files as text for further processing with independent software.: Origin, Matlab, Mathematica, Excel, etc. Default destination folder is also C:/Ps15/Dataout
According to the spectrometer mode selected, data files are divided into two categories: spectroscopy data files and relaxation data files. They are distinguishable by extension *.dsp and *.drl, respectively. They are stored in the same data directory.
Processing page consists of two windows:
Acquired data window with associated tool bar and experimental setup list - used to load and to present binary data.
[pic]
Figure 25. Processing page.
Processed data window with associated tool bar and processing parameters list - data from acquired data window appear here.
There is also a menu bar and a status bar common for both windows.
The way acquired and processed data are presented can be changed in Tools>Display. Select display window, either Acquisition (Acqu) or Processing (Proc) and select Line or Discrete.
[pic]
In Discrete mode open Style to choose among different shapes. Default mode is Line and it can be restored easily by clicking on Restore Line.
[pic]
1 Spectroscopy data files
n sample time coordinate = (n-1) x Dwell Time
They contain discrete data points (point number and corresponding amplitude) of the nuclear signal taken in a certain time period that begins with Trig and ends after the acquisition time passes (which is: Dwell Time x Number of Points). Knowing the Dwell Time and sample number n one can calculate time of any data point that appears. For instance first data points is associated to 0 in time scale.
Later we can refer to such an elementary signal as a spectroscopic signal. Data in spectroscopy data files can be used for further Fourier Transform to produce an NMR spectrum. The experiment that generates a spectroscopic signal is called a one-dimensional (1D) experiment as data are collected only in one domain of time, that is the time that runs during the appearance of NMR signal.
Spectroscopy data files are stored automatically in the data directory with default extension *.dsp.
2 Relaxation data files
The structure of relaxation data files is mere complex dependsand depends on the method applied. If T2 measurements with CP or CPMG methods were performed the file looks like an ordinary spectroscopy file, but contains as many spin echoes, as there were 180o pulses applied. This file can be displayed instantaneously on one screen. However, if the sequence that required Variable Delay array file was applied, as happens during all T1 measurements, or during T2 measurements by simple Hahn sequence, the data file contains as many spectroscopic signals as numbers of delays used. At once you can display only one spectroscopic signal that corresponds to a certain delay time. Data from relaxation measurements may illustrate a “quasi” two-dimensional experiment (2D) as data are collected in two domains of time; that is time that runs during appearance of the NMR signal and the delay time.
Relaxation data files are stored automatically in the data directory with default extension *.drl.
3 Summary of disk operations.
Processing of any experimental data starts with loading raw files and ends with storing processed data. Note that you can not manipulate original data sets and save them under the same name.
Load
To load any type of binary data: select File>Acq Data>Load Data from Menu bar or click on [pic] icon. Default source folder is C:/Ps15/Data. Choose from *.dsp or *.drl files in the dialog box that opens, see Figure 26 below.
[pic]
Figure 26. Dialog box for loading binary files.
Export
To export experimental data as ASCII select File>Acq Data>Export Data or just click on [pic] icon. Default destination folder is C:/Ps15/Dat. File is stored automatically with new extension *.txt.
To export processed data as ASCII select File>Proc Data>Export Data. or just click on [pic] icon. Default destination folder is C:/Ps15/Dataout. File is stored automatically with new extension *.txt.
Figure 27. Opening files with processed previously data.
[pic]
Open
Opens a file with previously saved processed data. Select File>Proc Data>Open or click on [pic] icon (Figure 27).
Save
Saves a file with processed data. Select File>Proc Data>Save or click on [pic] icon. File is stored automatically with new extensions: *.psp for spectroscopy, *.prl for relaxometry.
Save As
Save file with processed data under new name. Select File>Proc Data>Save As and type new file name.
4 Processing spectroscopy data.
The ultimate purpose for processing spectroscopy data is to obtain a Fourier Transform of acquired FIDs. Practically it means to go from the time domain of the FID to the frequency domain of the spectra.
After loading FID it is achieved in two steps: manipulating with FID and performing Fast Fourier Transform.
Manipulating FID
RS/LS- [pic]
Right/Left data Shifting by one data point to remove unwanted oscillations from the beginning of FID that appear due to “dead time”. In the case of left shift rmissing emoved points are replaced by zeroes.
LB - [pic]
Define line broadening for EM routine.
EM - [pic]
Multiplication of data points by an exponential function (Exponential Multiplication) that reduces noise, but broadens transformed spectrum.
BC
Removes any DC offset present in FIDs. It is performed automatically during executing of FFT.
FT - [pic]
Perform Fast Fourier Transform
Figure 28. One-pulse sequence details on graphics after clicking Tools>View Sequence.
Details about Method are visible by pointing on related line in the Setup Parameter list or by clicking on Tools>View Sequence.
[pic]
Manipulating spectrum
Horizontal Zoom
Left-click on the HZ icon [pic] to activate zooming routine. Right-click to mark the beginning of zooming area. Release button and move curser to the end of zooming. Right-click again to perform expansion of selected part of the spectrum.
Vertical Zoom
Left-click on VZ icon [pic] to expand spectrum in vertical direction.
Unzoom
Left-click on UZ icon [pic] to return to original spectrum size after FFT.
Phase correction
After performing FFT on FID the obtained spectrum is more than likely not in the pure absorption mode as shown in Figure 29.
[pic]
Figure 29. NMR spectrum from FID in glycerin (Figure 25) soon after FFT was performed.
Such distorted spectrum requires the correction of the phase. Processing program provides tools to do the so calledso-called zero order phase correction thatwhich is enough for one broad NMR line that is obtained with the PS 15 magnet[10].
The phase correction can be performed simply by clicking at up/down buttons [pic] in the Tool bar and force the whole spectrum to flip above the zero line and make it symmetrical (see Figure 30).
Figure 30. Spectrum after proper phase correction.
[pic]
Another way of phase correction is to define a numerical value for the correction by clicking on [pic] and typing the correction angle vale. To recalculate and perform the correction click on the [pic] icon. This method is convenient to repeat phase correction with certain values. Note that PA variable remembers last value used in phase correction, regardless of the method chosen.
Line width at half maximum
After phase correction click on LW [pic] icon to execute line width calculations. Line width is calculated by interpolation as seen in the Figure 31. Data points have been emphasized by Tools>Display>Proc>Discrete Style to make them more visible.
[pic]
Figure 31. Calculation of line width at spectrum half maximum. Discrete points presentation is used to show interpolation.
Peak picking
The routine returns spectrum’s peak position [pic] (F-frequency in [Hz], A-amplitude in [arbitrary units]). Left-click on PP [pic] icon to complete the routine.
Figure 32. Spectrum after executing peak picking routine.
[pic]
Spectrum Integration
The routine integrates part of displayed spectrum.
Figure 33. Integration of the spectrum.
[pic]
Procedure
1. Expand region of spectrum to be integrated by Horizontal Zoom (HZ) and Vertical Expansion (VE).
2. Start spectrum integration routine by left-clicking on I [pic].
3. Continue with Automatic Integration AI- [pic] that defines arbitrary integration limits near spectrum ends.
4. Modify manually left and right integration limits by left-clicking on LC/RC [pic][pic] icons and moving vertical cursors to the desired positions. Clicking on left/right side of the cursor moves it precisely by one point left/right.
5. Correct spectrum zero line offset with Spectrum base line Correction by left-clicking SC [pic] up/down buttons if spectrum base line is below or above zero level. Otherwise the constant offset accumulates and becomes significant if integration limits are far apart.
6. On right Processing Param windows Absolute Integral (AI) value appears. This value can be calibrated to any arbitrary number. Left-click on Integral Calibration- IC and in dialog box type new value of integral. Last calibrated integral will be later used as reference for Integral Normalization (IN) [pic]. You may need to normalize current integral to any other integral (like comparison of signal intensities to estimate relative concentration of hydrogen atoms). To do normalization click on [pic] and current integral will be normalized to last calibration value. Normalized value IN1 of absolute integral AI1 is defined by formula:
[pic]
-were AI0 is absolute value of integrals of spectrum used for calibration and IC0 is its calibration value. Of course normalization of last calibrated spectrum returns the same value. Processing parameters list carries also the name of the file used for calibration (IC file in Figure 33).
7. Finish integration by left-clicking on End of Integration EI [pic] button.
Table 8. Processing spectroscopy. Summary of Integration routines.
Table 9. Processing spectroscopy. Summary of general routines.
Summary of different routines available at Processing page for spectroscopy.
| |Function |Icon |
|I |start Integration |[pic] |
|AI |Automatic Integration |[pic] |
|LC |manual integration Left limit Correction |[pic] |
|RC |manual Integration Right limit Correction |[pic] |
|IC |Integration Calibration |[pic] |
|IN |Integration Normalization |[pic] |
|SC |Spectrum base line Correction up/down |[pic] |
|EI |End of Integration |[pic] |
| |Routine |Icon |
|HZ |Horizontal Zoom |[pic] |
|VE |Vertical Expansion |[pic] |
|UZ |Undo Zoom |[pic] |
|I |Integrate spectrum |[pic] |
|P0 |up/down by 1o – Zero order Phase correction[11] |[pic] |
|PA |define Phase correction for PC |[pic] |
|PC |Phase Correction; makes phase correction with parameters defined in PA |[pic] |
|LW |Line Width; returns line width at spectrum half maximum |[pic] |
|PP |Pick Peak; returns peak value |[pic] |
5 Processing relaxometry data.
The Processing page additionally allows one to extract data points for relaxation calculations and perform calculations of T1 by inversion recovery and saturation method and T2 by the CP and CPMG Methods.
Data extracting for T1 calculations.
Generally relaxation data are obtained by acquiring FIDs for different delays. Subsequent extraction of FID amplitudes for each delay time is required. Extraction of points should be done from the time domain where the FID signal is not affected by “dead time” and other artifacts.
Procedure
1. Load data,
2. Move the pointer at approximately 100 (s position.
3. Using [pic] buttons check every FID to be sure that pointer covers “clean” area not affected by RF disturbance.
Figure 34. Extracting data points for T1 calculations.
4. Change position of the pointer if necessary. To avoid loosing signal intensity try to keep pointer as close to zero as possible. Important for short FIDs!
[pic]
5. Click on [pic] (Set Mark) to lock pointer at a certain time.
6. Click on [pic] (Extract) to perform extraction. Extracted points appear immediately on the bottom processed data display window.
Figure 35. Viewing extracted amplitudes and time delays.
8. You may look at extracted points and corresponding time delays by clicking on Tools>View Extract and Tools>View VTD (see Figure 35).
9. If you are satisfied save or/and export extracted data, if not erase data by [pic] (Clear), change the position of the pointer and perform the data extracting procedure again.
Calculating T1 by IR[12] routine.
The program can perform one exponential fit to experimental data acquired by Inversion Recovery method. After extracted data points are shown click on [pic] (T1 by IR) to perform fit. Figure 36 illustrates T1 measurements in glycerin at room temperature: T1 = 86.3 ms, standard deviation = 1.7 ms. The equilibrium magnetization M0= 105 [au] used for this fit was calculated from last three points.
[pic]
Figure 36. One exponential fit for experimental data obtained by IR method in glycerin.
Figure 37. Viewing data points.
User can view fit as well as data points in the table simultaneously. Open View Extracted Data Points from Tools. Once the data box appears click on a certain point that will be visible on left plot in green. Note that last three points are not visible on the plot as they are used for M0 calculations.
[pic]
Calculating T1 obtained by Saturation method[13].
Load and extract data using the same method as for Inversion recovery. For calculating left-click on Sat [pic] icon.
[pic]
Figure 38. Extracted data points and their fit for T1 measurements by Saturation method in rubber.
Extracting data and calculating T2 by Carr-Purcell and Carr-Purcell-Meiboom-Gill method.
Carr Purcell and its modification Carr Purcell MaiboomMeiboom Gill method of calculating T2 time requires extracting echoes amplitudes from the train of decaying echoes. Follow the procedure below.
Procedure
Figure 39. View the echo train in the CPMG method. Note the FID at the beginning of the train and the sharp spikes between spin-echoes that correspond to RF pulses position. These RF spikes do not count as echoes!
1. Load data (see Figure 39).
[pic]
2. Move pointer on the top of last visible echo in the echo train and click on Select last point icon [pic].
3. Mark echoes by clicking on [pic]. When Mark Echoes dialog box appears type the number of echoes you selected (Figure 40).
Figure 40. Echoes number selection.
[pic]
4. Extract echoes amplitudes and corresponding times by clicking on the Extract [pic] button. Locations of selected echoes will be covered with blue markers and extracted points appear in the bottom window as shown in Figure 41.
Figure 41. Processing page after extracting data from CPMG experiment.
[pic]
For calculation of T2 click on the CP or CPMG buttons [pic] depending on the method that was used.
[pic]
Figure 42. Fitting CPMG data.
Getting started
1 Introduction
In this chapter the user will learn how to deal with samples, how to execute the control program, how to turn on the spectrometer and how to complete a simple one-pulse pulse NMR experiment in on-resonance conditions.
2 Sample preparation and positioning
Description
The NMR signal originates from a sample located between poles of the electromagnet. To avoid magnet contamination and possible field homogeneity degradation due to corrosion of iron alloy, the poles use only glass vials to keep liquid samples isolated. Solid samples like rubber, acrylic or wood can be placed directly in sample holder. They should be cylindrically shaped of no more than 5 mm OD and minimum 40 mm length.
Background
Figure 43. Proper sample tube placement inside the probehead; all dimensions are in mm.
The spectrometer probehead incorporates an ID=5.5 mm sample holder that safely accepts standard OD=5 mm NMR tubes. We recommend glass NMR tubes from WILMAD[14]. The important dimensions of the sample holder design areis shown in Figure 43. Use the rubber O-ring to establish the proper position of the sample and to hold it in the probehead. When inserted into the probehead the o-ring should sit firmly on the Teflon support (white plastic-like collar at the probehead top), and the center of the sample should be in the area of the most homogeneous constant magnetic field and oscillating RF field. This area is called magnet isocenter. In this particular design the center of the RF coil is about 35 mm from the top edge of the Teflon support. As the RF coil is only 10 mm long use a small amount of compound to make a sample. As a rule of thumb the sample length should not exceed 10 mm, preferably 7-8 mm. For higher resolution studies only small samples of 4-5 mm length are recommended, but expect the Signal-to-Noise to drop dramatically. As dimensions slightly vary from probehead to probehead be prepared to individually adjust the sample position by observing the NMR signal.
Procedure
Slide the rubber O-ring about 38 mm from the bottom of the sample tube. You can use either a ruler or the transparent acrylic tubing (with marks marks in the center corresponding to top and bottom of RF coil), which is provided.
Carefully put the tube into the probehead. Do not use force thus avoiding damage of the delicate tube. If tube breaks turn off the spectrometer and remove broken glass pushing it all the way over through the way using a piece of wood or other material that will not harm the softthe soft Teflon sample holder. Dry the holder if the brokenthe broken tube carried glycerin. Water or alcohol will evaporate.
Considerations
For a first test use a glycerin[15] sample that produces a very strong signal and is characterized by a relatively short relaxation time. This allows rapidly repeating repetition ofrepetition of the experiment and tothe watching of cchanges of the NMR signal due to experimental setup variations in real time. When a small amount of glycerin is used fast accumulation can compensate for a week signal.
If you have problems in obtaining an NMR signal the first time with minute samples use one that almost fills almost whole the tube to be sure if covers the area inside the RF coil.
Figure 44. Sample positioning with acrylic adjustment tube.
3 Executing the control program
We assume that control program Wwinner has been installed and all elements of the spectrometer’s hardware have been connected properly following the guides given in pages 5 and 6. Also glycerin sample is properly positioned inside the sample holder.
Procedure
1. Turn on the electronic control unit (black switch 4 inon the back panel, onof Figure 2). Wait 10-15 minutes for thermal stabilization of the quartz generator and of the electromagnet. There will be further thermal drift of both, but not very dramatic[16] This is easily compensated by NMR stabilization.
2. Turn on the computer. Start the control program by clicking on the yellow-greenish [pic] link on the computer desktop or on the same icon in the c:\ps15\winner directory.
3. User’s Assistant (1) will guide you to three different pages. To shorten the process you can click on links in User’s Assistant (1)s (in violet color) or click OK to enter a the Setup page without starting the spectrometer.
Figure 45. User's Assistant options after program starts.
[pic]
10. If you are running the program for first time we recommend tothat you simply click OKclick OK on the User’sthe User’s Assistant (1) message, and enter to the Setupthe Setup page and firstthen checkthen check the file locations by Tools>Preferences>File locations. The Ffactory created initialization file spi.ini provides the directory paths as shown in Figure 46. If for some reason configuration is different follow Changing Configuration in Appendix chapter 8.3.
11. Check if the spectrometer operates in the spectroscopy mode by markingselecting Spectroscopy in the Modethe Mode .tab.
[pic]
Figure 46. Factory created directory paths.
12. To start the control program operating in a research mode (in the which is basic mode for teaching) mode select Spectrometer>lock-on. (The lock-off mode has a special use described elsewhere in chapter 6.2).
13. If there is no communication between the computer and the electronic unit anunit an error message appears.
[pic]
If this message appears check to assure:
• the unit is powered (red LED on right side of from panel is on),
• serial port connectors are securely connected and locked,
• in Tools>Preferences>Communication Port thatPort that the correct com port has been chosen.is correct assignment of communication port.
If necessary turn on the unit, reconnect RS 232 cable and lock its connectors, make correct port assignment (if cable is connected to serial port #1 chose COM1, etc).
14. If the electronic unit works and the connection through RS 232 port has been established the NMR stabilizer starts its locking procedure as described on page 18. The program first activates an automatic zeroing of the DC offset in the lock channel, the flux stabilization is then turned on and finally the NMR stabilization starts (NMR lock, or just lock). It takes 2-4 minutes to find the NMR signal from 19F sample and to close the feedback loop around this signal to get a stable lock. During locking, the magnetic field sweep is visible and the lock status line shows LOCK: locking [pic]. Note that locking is done regardless of whether or not a sample is present in the probehead because the spectrometer uses its own internal miniature sample of HBF4 solution for this purpose.
[pic]
Figure 47. Setup page after successful lock.
15. When the locking procedure is successfully completed the status line shows LOCK: ON (with values of the field sweep where locking loop has been successful closed in [(T] and in [%]). The Programmer radio-button Run is automatically checked and the data window is refreshed after data has been acquired from spectrometer memory buffer as shown on Figure 47.
Figure 48. Electronic unit front panel after locking and when programmer is pulsing.
[pic][pic]On the electronic unit front panel the green LED labeled, as STABILIZER ON is active and the Programmer red LED blinks. The two STABILIZER LEVEL LEDs that indicate DC offset should be off (see Figure 48). +/- DC offset compensation is done automatically and should remain unchanged. There is a momentshort of sudden blinking ofblinking of DC offset diodes when the sweep reaches the locking position.
At this point the appearance of the pulsing programmer with an FID shown in the data display window means the spectrometer is operating properly. Of course the FID signal may look more or less on- or off-resonance, but the overall picture should be close to one shown in Figure 47).
4 A simple on-resonance one-pulse experiment with glycerin sample.
Objectives:
• selection of one-pulse sequence,
• adjustment of vital experimental parameters to get on-resonance conditions,
• performing prepared experiment and data saving,
• retrieving data from file; display and conversion to text format.
5 Preliminary setup
After a successful lock the control program starts running the last used sequence. Regardless of current settings modify the Setup page according to the following list.
• CheckThe if spectrometer is in Spectroscopy mode (look at the status line), if theif the mode is Relaxometry go to Mode>Spectroscopy in in the menu bar,
• If one-pulse sequence is not selected click on the box next to method in Programmer windows. From From the list of sequences chose 1P_X. You can also load the method from File>Open method.
6 Final setup.
There is only a small chance that you will get satisfying factory results instantly. More likely you will get a weeak off-resonance signal which is convenient for preliminary adjustment of Data acquisition and Receiver adjustment. If accidentally you are on-resonance increase or decrease Magnet stabilizer>(f0/(B0 slightly to see several oscillations onf a FID signal. Then follow the step-by-step instructions and watch the data display.
1 Data Acquisition adjustment
Description
This will be a first place to adjust. You dDecide which one of the quadrature channels areto be displayedbe displayed and stored and what will bewill be the time scale of recorded signals. . Signals of interest should fit the data display in a time domain with somean additional “noise tail” beyond it to determine the proper zero DC level base. Manipulate the acquisition time (NOP x Dwell Time). SA short dwell time is required for fast decaying signals in solid-like samples.
Background
The analog signals from two channels of the quadrature detector is digitized by two fast 8 bit analog-to-digital converters running with a maximum conversion rate of 0.1(s. After conversion, the signals’ digital representation is stored in a memory buffer. Only data from selected channels will be later transferred to the computer for display on the monitor and for further storage on the hard drive. The transferring program ignores data points that did not match the Dwell Time parameter. For instance if the Dwell Time is 0.4 (s only each 4th point is transferred, if Dwell Time is 20 (s only every 200th point is transferred.
Recommended settings
1. Dwell Time = 20 (s.
2. NOP (number of points) = 1024
3. Check only Channel I. For simplicity only a signal from one channel will be acquired.
Related subjects
Quadrature detection, analog-digital conversion, dwell time, acquisition time, Fourier Transform DC level base.
2 Receiver adjustment
Description
Receiver adjustment involves selecting Phase Detection, change of DC Level, RF amplifier Gain and Phase of the reference signal, and the number of accumulations (Acc) to get the best signal-to-noise in reasonable time.
Procedure
1. CheckSelect the Phasethe Phase Detection radio button.
2. When working with glycerin sample remember to set the Time Constant of the RC filter to 5 or 30 (s (5 (s recommended). For solid-like samples (rubber, wood, acrylic) use 1 (s.
3. Change the DC Level to compensate or any DC offset. The base level (the noise floor provides a good base) should be in the middle of the data display.
4. Change Gain to achieve a maximum signal on the screen. Apply some safety margin to avoid further signal cut-off, particularly at its beginning,
5. If necessary decrease the gain in order to fit a complete signal on the Data display.
6. At this stage do not modify Phase.
Warning
When other parameters of an experiment are changed always check to assure that the signal amplitude does not exceed +/- 128 range. This will avoid signal clipping after conversion into digital form.
Related topics
RF signal amplification, detection, DC offset, time constant, signal accumulation, signal-to-noise.
3 Field adjustment
Description
On-resonance conditions require precise matching of the spectrometer carrier frequency fc with the precession frequency f0 of nuclear spins [pic]. This is achieved when the nuclear signal shown on the data display, after phase detection, has no oscillations due to beats between carrier modulated FID and reference signal. After executing the program and locking, the data display window will most likely show off-resonance FID more or less like the one shown in Figure 49.
[pic]
Figure 49. Off resonance FID from glycerin.
Background
Since the carrier frequency produced by a highly stable quartz generator is fixed, you can manipulate only with with the frequency of precessing spinsion frequency. This is done by changing the magnetic field magnitude B0 as itwhich determines the precession frequency according to the Larmor equation:
[pic]
Procedure
1. First match both frequencies using (f0/(B0 function in the Magnetic field window. It covers a range from - 2177 Hz to +2173 Hz (or from -51.1 (T to +51.0 (T) in 1024 steps. With up/down keys change (f0/(B0 (increase or decrease) to see the decrease of the frequency of oscillations and final appearance of smooth, exponentially decaying free induction signal.
2. If (f0/(B0 function does not produce enough offset to meet on-resonance conditions change radically the magnetic field magnitude by changing the f0/B0 parameter. This significantly increases or decreases the electromagnet’s current thus changing the magnetic field coarsely by an equivalent of about 4.25 kHz/0.1 mT. Highlight f0/B0 and increase or decrease its value by one unit. Note that any change of f0/B0 causes automatic adjustment of the lock stabilizer to the new magnetic field value so you have wait until lock is done..
3. After locking at new magnetic field, attempt to reach fine on-resonance conditions again by (f0/(B0. Repeat 1steps 1 and 2 several times to reach satisfactory resonance conditions as illustrated in Figure 50.
[pic]
Figure 50. On resonance FID from glycerin.
4. In Receiver windows adjust Phase to get signal as strong as possible.
Warning
Avoid (f0/(B0 extreme settings. This can lead to lock mechanism failure and large field corrections will be required since the NMR lock requires some headroom to properly lock.
Related topics
On- and off-resonance conditions, electromagnets, magnetic field stabilizers.
4 Pulse adjustment
Description
In the pulse NMR experiment, the RF pulse tips the nuclear macroscopic magnetization from its equilibrium position along the B0 field towards the direction that depends on the pulse phase and to the position that depends on the pulse length and the magnitude of the oscillating magnetic field B1. Following the RF pulse is the detection period. Only macroscopic magnetization components that precess in a detection plane (that is the plane parallel to the solenoid axis) induce the signal, which is recorded during detection.
Background
Generally an RF pulse rotates the magnetization by the angle [pic]. Where B1 is the magnitude of the magnetic component of the RF pulse; tp is the pulse duration time, and ( is the gyromagnetic ratio. In NMR spectroscopy popular jargon there are (/2 pulses or 90o pulses, ( or 180o pulses, and other pulses that refer to certain tip angles.
Figure 51. Tipping nuclear macroscopic magnetization by RF pulses
As B1 depends on the square root of pulse power P incident to the sample circuit[17], changing the pulse power will change pulse length and provide additional means to rotate the nuclear magnetization more or less. From the point of view of the maximum signal-to-noise ratio the (/2 pulse is the best choice since after a (/2 pulse the whole magnetization vector is projected on the detection plane thus giving the maximum signal intensity (Figure 51b). A long pulse rotates magnetization M too much and its y component can reach even negative values –m as shown in Figure 51c.
[pic]
An experimental situation corresponding to this case is illustrated in Figure 52.
[pic]
Figure 52. Effect of a too long RF pulse.
Procedure
Set programmer for fast pulsing at repetition time TR=500 ms. Use maximum pulse power from the transmitter by setting the attenuator in the Transmitter>Attenuator main to zero and, having selected the 1P_X sequence, you have to adjust only the pulse length to get the pulse that rotates the nuclear magnetization by approximately (/2. This is achieved by a discrete increase of pulse length from the minimum available (0.4(s) and finding pulse lengths such that the free induction decay signal reaches its first maximum. This maximum is rather flat so change the pulse length back and forth a few times to find the optimum position. For your convenience place the data pointer at the beginning of the FID and follow the amplitude indicator A: which shows values as the pulse length is changed. If the signal reaches maximum close to 128 units decrease Gain again. Avoid clipping!
5 Sample position
Description
Experiments with liquid-like samples frequently require fine adjustment of the sample position. There are two geometrical factors that influence the FID signal and can be changed by a user:
• Ssample size.
• Sample position relative to RF coil.
To fulfill strict on-resonance conditions the whole sample must be placed inside the most homogeneous part of RF generated by the coil. The PS 15 coil consists of 18 turns of a total of 10 mm length and a 5 mm inside diameter. The most homogeneous part of the field is inside the coil center and consequently the sample must be located inside this area.
The following procedure will help to optimize the sample position tso that the strongest nuclear signal is achieved.
[pic]
Figure 53. FID signal when sample is not placed in the center of the coil.
Procedure
1. Slide the rubber o-ring closer to the tube cap,
2. Continuously running the 1P_X sequence slowly moveslide sample up and down about 1 mm at a time. Watch indications of the data pointer,
3. With thea fine point marker, mark the position of the sample where the maximum signal was seen,
4. Position the rubber o-ring on the mark,
5. Place sample back in the probehead,
6. Check if approximately the same signal amplitude is achieved. If not repeat procedure several times.
When properly adjusted, on-resonance free induction decay from glycerin will look like the data display in Figure 54. This nice NMR signal has been captured from glycerin sample of the volume of only 0.07 cc!
[pic]
Figure 54. On resonance FID from glycerin sample after final adjustments.
Once all elements of the experiment have been refined you can store the setup by File>Save Setup As for later use. Give this setup a unique name so you can recognize it easily and use for further relaxation times measurements.
7 Acquiring FID
Description
To perform a final experiment of storing an FID in a binary data file go to the Acquisition page. The experiment will use parameters established in the Setup page which are displayed in the Exp Setup window at the upper right corner of this page.
Procedure
Fill linesEnter information in the type-in Pparameter dbox in the bottom right corner ialog window as shown on the right. Click on the Start [pic] button. This to activate pulsing of the programmer. The most left box in the status line shows the number of accumulations to go. When completed, the averaged signal is displayed in the data display window and is automatically stored on the hard drive in the Data directory with a declared file name and with default extension dta. Judge visually if S/N ratio is sufficient. If necessary repeat with more accumulations to improve S/N. Remember that S/N ratio increases with square root of the number of accumulations.
Figure 55. Accumulated FID from protons in glycerin.
[pic]
1 Viewing data and converting data from binary to text format
To view the experiment experiment, load data on the Processing page by File>Acq>Load Data. After loading the binary data acquired with one-pulse sequence the Processing page will look as shown below.
[pic]
Figure 56. On-resonance FID from glycerin viewed on Processing page.
The PS15 software creates binary files in its own densely packed format. The user can convert them to a widely accepted text format and process this data later. The experimental data viewed in data display window can be saved in a text format by File>Acq Data>Export Data. This operation converts data from binary to text format and stores them under the same name but with a txt extension in the Dataout folder. See Appendix chapter 8.2 to learn about format of text files.
TROUBLE SHOOTING
Please contact your distributor if the results you obtained are not within specifications, do not satisfy you, or if the instrument is not working at all. Please be advised that despite its simple look the PS15 is quite a complex electronic and mechanical device.
1 Trouble shooting.
|Spectrometer does not turn on |
|Power line |Check if there is 115V AC and if power cord is properly attached to the unit. |
|Fuse |Check fuse with resistance meter. Replace if broken. |
|“Device not Ready” error message |
|Powering spectrometer |Check if unit is turned on. |
|RS 232 connection broken |Check connections and tighten locking screws. |
|Incorrect COM port assignment |From Setup>Preferences>Communication Ports change port assignment. |
|NMR Lock does not lock |
|No lock’s DC level compensation |If after 3-6 minutes after program executing any of Level diodes is still on there is no |
| |automatic DC offset compensation in NMR Lock channel. Contact distributor. |
|No constant magnetic field |Use a piece of iron (key, paper clip, etc) to determine the presence of magnetic field. Check |
| |connection between magnet and unit. |
|Electromagnet homogeneity |Check electromagnet homogeneity (see p.77). Contact distributor. |
|Wrong electromagnet I0 current. |Changeeck I0 settings (see p. 79). Contact distributor. |
|Weak or no NMR signal with one-pulse sequence |
|Sample position |Use bigger sample. Reposition the sample. |
|TX and RX cable connections |Check coaxial cables and their connections. Avoid crossing RX and TX cables. |
|Transmitter failure |Use 20 dB attenuator and an oscilloscope to check the presence of RF pulses at the transmitter|
| |output (TX). |
|Receiver/detector |If there are no traces of signal. |
|Probe circuit and preamplifier failure |No change of the noise amplitude after Signal (RX) cable disconnection/connection. |
|On-resonance conditions beyond specification |
|I0 offset |Change f0/B0 in Magnetic field window on the Setup page in both directions. If on-resonance |
| |conditions still unavailable do manual I0 (see p.79). Contact distributor. |
|Short term instability of FID and spin-echo signals |
|Flux stabilization is not working. |Amplitude of NMR signal oscillates. This is particularly visible n the spin-echo signal. Flux |
| |stabilization is not working. Contact distributor. |
|Irregular FID and spin-echo signal, see Figure 53 |
|Electromagnet homogeneity |Check electromagnet homogeneity (see p.77). Contact distributor. |
|Sample size |Use smaller sample to achieve better homogeneity over the sample (Hlock-off. A new setup page appears and the programmer will start the pulsing of the 1_P sequence.
• Use the settings on the screen capture that is attached to the shipment of your unit (Figure 3. Ser #xx FID from glycerin in lock-off mode).
• You can also load the factory created setup ser ## lock-off.cfg for this unit and manipulate the Receiver gain to obtain an off-resonance picture shown in the Figure 57.
(Note: Consult your distributor before manipulating with magnet alignment and current.
Figure 57. Spectrometer operating in lock-off mode.
[pic]
2 Correcting magnetic field homogeneity.
To achieve best experimental results the magnetic field should be very uniform within the sample volume. Any change in position of the magnet yoke or poles geometry dramatically affects homogeneity of the magnetic field. A similar unwanted effect can be expected if the magnet is located near any ferrous structure like iron construction beams, magnetic steel desk, etc. Magnetic field inhomogeneity contributes to a faster decay of nuclear magnetization which causes a so called inhomogeneous broadening of the NMR absorption line.
Figure 58. Magnet side plate. A is a M10x1 screw that holds the pole. A, C and D are three pairs of six alignment screws, E are for M4 screws that hold the magnet’s solenoid frame, F are four M6 screws that join vertical bars with side plates.
Compensation of field inhomogeneity can be done by painstaking adjustment of three pairs of correcting screws (M8x0.75 fine thread, B, C and D in Figure 58) on the magnet side plates[18]. When turned clockwise each of six screws can push slightly against the corresponding part of the “floating” iron pole that hangs on a center screw (M10x1). The small spring washer between both poles and side yokes gives some freedom to the minute movement of the pole in practically all directions thus changing their relative position as shown in Figure 59.
Theoretically the best homogeneity is achieved with a parallel orientation of both faces of the poles. The experimental objective of this procedure is to obtain an off-resonance signal from glycerin that is as long as possible.
Procedure.
• Activate only one observation channel. If you want to watch the real component of magnetization check Channel I in Data acquisition windows.
• Manipulating with (B0 in in theMagnetthe Magnet stabilizer to reach off-resonance conditions to seeso that at least a dozen of FID oscillations are visible.
• Adjust Receiver gain to see the beginning of the FID within the +/- 128 limits.
• Avoid simultaneous alignment of left and right pole. Tighten the central screw of the unused pole. This will to stabilizeto stabilize its position.
• Chose leither the left or right pole correction screws. Using the included 6 mm hex-Allen socket wrench try to tighten one screw of the B, C, D pairs (turn wrench clockwise).
• If there is no room to move first screw release its counterpart one across the center M10 (turn wrench counter-clockwise). Do not use high torque!
• Watch changes of FID on the monitor. For proper NMR lock operation the FID should not disappear into the noise before the 3 ms mark. Usually a decay of 6-10 ms can easily be achieved as in Figure 57.
• If If the FID is still too short or its envelope shows irregular or no exponential decay, then change positions of other two pair of screws.
• Sometimes the central M10 screw is tighten too much providing no room for pole movement. You may release it by turning wrench counter-clockwise by about 10o.
• When the long FID is achieved complete the procedure by slightly tightening any screws that remain loose.
[pic]
Figure 59. Aligning the left pole. Bottom screw pushes pole upward against top screw that must be released to make room for pole movement. The center screw holds the pole through spring washer. If more room is needed release center screw turning it counter-clockwise no more than 10o. Note that size of separating washers and movement of the pole has been exaggerated for better illustration.
3 Setting magnet I0 current.
The I0 current is the main contribution to the current that produces a polarizing magnetic field B0. Other contributions (from flux and NMR lock) are just small corrections to keep the field at stable conditions. It is of utmost importance to set the I0 current at a value that will generate a B0 field within the margin of flux and NMR lock operation.
Procedure.
With the programmer pulsing:
• Change (B0=0,
• Change Dwell Time=0.4(s,
[pic]
Figure 60. On resonance FID for short dwell time of 0.4(s is only partially visible.
• Put a flat screwdriver into the I0 set slot on the rear panel (item 12 in Figure 65on Figure) and slowly rotate the 10-turn potentiometer clock and counter-clockwise to achieve on-resonance conditions (Figure 60),
• Increase the Dwell Time to 10 (s and make final adjustments.
Figure 61. On resonance FID after proper adjustment of I0 current.
Since the flux and NMR stabilizations are off, you will experience FID instability but the final picture should look more or less like the Figure 61.
[pic]
You may enjoy blessing stability of magnetic field with flux and NMR lock active by By activating stabilization Fbyusing ile>Spectrometer>lock-on. yYou may now enjoy the blessing of a stable magnetic field!.
SPECTROMETER SPECIFICATIONs
|Mode |pulse NMR (1H) |
|Operational Frequency |15 MHz |
|Frequency Stability |( 1 PPM/ 24h |
|Magnetic Field Source | |
| |- magnetic field magnitude |350 mT |
| |- gap |10.5 mm |
| |- pole diameter |60 mm |
| |- homogeneity |( 10 (T/ sample volume |
| |- field stability (NMR stabilizer) |( 0.1 (T/24hrs |
|Programmer | |
| |- output channels |10 |
| |- number of pulses |2048 |
| |- minimum pulse increment |200 ns |
| |- maximum time interval |24 h |
| |- measurement sequences |factory and user created |
|RF Square Pulse Modulator | |
| |- RF channels |Y, X, -Y, -X |
|RF Transmitter | |
| |- pulse power |( 15 W ((/2 ( 3.0 (s) |
| |- maximum pulse width |20 ms |
|RF Probehead | |
| |- solenoid coil dimensions |ID= 5.8 mm; L= 10 mm |
| |- recover (dead) time |< 22 (s |
|Receiver | |
| |- gain |60 dB (1 dB step) |
| |- detection |amplitude/ phase-sensitive, quadrature |
| |- low pass filter band |300 kHz; 100 kHz, 30 kHz |
| |- DC offset converter |+/- 50 % |
|A/D Converter | |
| |- type |flash |
| |- channels |2 |
| |- resolution |8 bit |
| |- dwell time |0.4 – 400 (s |
| |- number of samples |256-8192 |
|Weight and dimensions WxDxH | |
| |- electronic unit |6.3 kg, 47x26.3 x11 cm |
| |- probehead |0.8 kg, 12x12x2.3 cm |
| |- electromagnet |21 kg, 21x13x18 cm |
|Power Consumption |110V/220 V; 50/60 Hz; 70 W |
|Communication Port |two way RS 232C |
|Computer Required |IBM PC AT VGA color or compatible |
|Software |MS Windows operated |
Appendix
1 Program directory structure.
The program consists of the main winner directory and six additional subdirectories.
Winner main directory:
• spi.exe - the executable file.
• spi.ini - initialization file. This contains information about Preferences and is updated every time a user exits the program. If there is no spi.ini thespi.ini the program starts with some default parameters and recreates a new spi.ini when the program is terminated. It is highly recommended to check Tools>Preferences before starting spectrometer with lock-on or lock-off and select correct options. When program starts it first checks the COM port number declared in spi.ini, establishes connection and then looks for the location of configuration file standard.cfg.
• spi.log - spectrometer log file. User can place date stamped permanent notes to this file by File>Log.
Subdirectories:
• cfg - contains setup files that carry information about spectrometer settings (except pulse sequence timing, that which is stored in *.msp and *.mrl methodtd files). The standard.cfg file is the default configuration file that is loaded after theafter the program starts. Path to cfg folder is in spi.ini file. If program does not find standard.cfg file it uses some default parameters. User has to recreate parameters for standard.cfg before program is terminated.
Users can create their own setups with specific settings, store them by File>Save Setup As under new a name and later use these setups to change program settings. If any setup created this way is renamed as standard.cfg it will be used at the next program initialization. There are few factoryfew factory prepared setups.
- ser## T1 by IR.cfg (where mod## is the unit serial number), that can be used for T1 measurements by the Inversion Recovery method.
- ser## lock-off.cfg, for magnet adjustment.
• r_mtd contains relaxometry pulse sequences, see Figure 14. Each pulse sequence file carries information about the pulse’s length and phase. Timing of all pulses can be changed on the Setup page. When terminated the program stores timings in currently used *.method file. AwWhen the lock is active the program calls the pulse sequence name stored in standard.cfg file.
• s_mtd contains spectroscopy pulse sequences[19], see Figure 13.
• vtd contains files with a list of variable time delays that are used in relaxometry measurements. These files can be created and edited on the Acquisition page by entering dedicated editor in Tools>View VTD.
• data contains data files. Binary read only files are used for automatic experimental data storage. Binary data can be exported in a text format on a Processing page.
• dataout contains files with processed data on a Processing page. They are read/write files in binary or if exported in text format.
[pic]
Figure 62 Winner program directories.
2 Text data formats.
To reduce occupied space data files are stored in Winner’s own binary format. User ‘s can convert binary format to ASCII format on athe Processingthe Processing page and use this format to do calculations with own in other software or popular packages available at the market likeas: Mathematica, Matlab, Origin, Excel, etc.
Experimental data (from the top window) are stored in ain a data subdirectory under the same name but with new *.txt extension. Perform File>Acq Data>Export Txt on Processing page.
Processed data (from bottom window) are stored in dataout subdirectory under the same name but with *.txt extension. Perform File>Proc Data>Export Txt on Processing page.
Regardless of the type file type (experimental, processed, spectroscopy, relaxometry) each text file consists of three elements: Header, Data block and Footer, each separated by an empty line.
1 Spectroscopy data.
Spectroscopy experimental data
Spectroscopy experimental data files carry digitized FID or spin-echo signals.
Header: Acquired Data
-Contains units for horizontal [ms] and vertical axis [a.u.]
Data block:
-Contains three columns (two columns only if one channel for data acquisition was selected) with data point sampling time, real component amplitude (I) and imaginary component amplitude (Q). Number of data rows corresponds to number of points acquired (NOP).
Footer:
- Contains all relevant information about experimental setup.
Acquired Data
Horizontal [ms], Vertical [a.u.]
0.000 458 521
0.010 371 587
0.020 296 629
0.030 202 650
0.040 125 675
-------- -------- --------
-------- -------- --------
-------- -------- --------
10.190 6 -5
10.200 13 4
10.210 6 -4
10.220 14 1
10.230 14 1
Experiment parameters
Mode : Spectroscopy
B0 : 15,000.3 kHz
Delta B0 : -569.8 Hz
Attenuator main : 0.0 dB
Gain : 41 dB
Phase : 180°
Detection : P
Time const : 5 µs
Dwell time : 10.0 us
NOP : 1024
Channel : I & Q
Method : 1P_X
Trig : P1
No of accumulation : 8
Comment : off resonance FID from glycerin at room temperature
Table 10. .Example of experimental data acquired in spectroscopy modespectroscopy mode (FID) stored in text format.
Spectroscopy processed data
Spectroscopy processed data files carry image of Fourier Transformation of corresponding experimental data.
Header: Processed Data
- Contains units for horizontal [kHz] and vertical [a.u.] axis
Data block:
-Contains two columns with spectrum coordinates in rows (total equal of NOP): frequency [kHz] and amplitude [a.u.].
Footer:
-Contains all relevant information about experimental and processing parameters.
Processed Data
Horizontal [kHz], Vertical [a.u.]
-8.594 0
-8.496 0
-------- --------
-------- --------
-------- --------
12.891 -0
12.988 1
Experiment parameters
Mode : Spectroscopy
B0 : 15,000.3 kHz
Delta B0 : -569.8 Hz
Attenuator main : 0.0 dB
Gain : 41 dB
Phase : 180°
Detection : P
Time const : 5 µs
Dwell time : 10.0 us
NOP : 1024
Channel : I & Q
Method : 1P_X
Trig : P1
No of accumulation : 8
Comment : off resonance FID from glycerin at room temperature
Processing parameters
LB = 50 Hz
PA = 309 °
AI = 1,415
IL = -6.45 kHz/+10.84 kHz
NI = 100.0
IC file: off-res FID glyc
CI = 100
Table 11. Example of processed data acquired in spectrosopyspectroscopy mode (NMR spectrum after FFT of FID signal) stored in text format.
2 Relaxometry data.
Relaxometry experimental data
Header: Acquired Data
- Contains labels for horizontal t [ms] and vertical Mz [a.u.] axis.
Data block:
-Contains series of FIDs acquired for each delay time and organized in two columns with delay times and corresponding amplitudes.
Footer:
- Contains all relevant information about experimental setup
Table 12. Example of experimental data acquired in relaxometry mode (series of FID signals taken for different delay times during T1 measurements in glycerin by the Inversion Recovery method) stored in text format.
Relaxometry processed data
Header: Processed Data
- Contains labels for horizontal t [ms] and vertical Mz [a.u.] axis.
Data block:
-Contains two columns with delay times and corresponding amplitudes. Number of data rows is determined by number of delay times in VTD file.
Footer:
-Contains all relevant information about experimental and processing parameters.
Processed Data
Horizontal t[ms], Vertical Mz[a.u]
1.000 -74
2.000 -72
4.000 -66
-------- --------
-------- --------
350.000 106
400.000 107
500.000 107
Experiment parameters
Mode : Relaxometry
B0 : 15,000.3 kHz
Delta B0 : +1,067.3 Hz
Attenuator main : 0.0 dB
Gain : 43 dB
Phase : 140°
Detection : P
Time const : 5 µs
Dwell time : 10.0 us
NOP : 1024
Channel : I
Method : 2P_X_VD
Trig : P2
No of accumulation : 16
Number of FIDs (Echoes): 16
X : 10
t : 100.0 us
VTD File : T1_16g.ttb
Comment : T1 in glycerin by IR
Processing parameters
T1 by IR
ln((M0-M)/2M0)=-t/T1
T1 =48.5 [ms]
SD =1.0 [ms]
M0 =107.0 a.u.
Table 13. Example of processed data acquired in relaxometry mode (extracted data points from Inversion Recovery experiment) and stored in text format.
3 Changing configuration file.
Follow instructions in the case there is no standard.cfg file in cfg subdirectory or you want to change parameters in existing standard.cfg setup file.
1. Start Winner program.
2. Start spectrometer by Spectrometer> lock-on.
3. Modify elements of the Setup page that you want to appear when the program starts.
4. Save setup by File>Save As with new name (new.cfg).
5. Exit program
6. Rename standard.cfg as standard.oldstandard. old, delete or move to another directory.
7. Rename previously saved setup new.cfg as standard.cfg.
8. Start program again and check if these changes you introducedintroduced appear on athe Setupthe Setup page.
If a new *.cfg is not renamed, it can later it can be calledused for fast Setup modification by selecting File>Open Setup.
4 Samples
We recommend the use of 5 mm glass tubes for samples. Torch seal liquid-like samples to avoid evaporation. Label samples to avoid further ambiguity and confusion.
Figure 63. Suggested sample size for PS 15 spectrometer: a) liquid like samples, b) solid-like samples.
5 Electronic unit front panel
Figure 64. PS-15 NMR spectrometer. Electronic unit front panel.
[pic]
1. Power ON.
2. Programmer operating indicator, blinks red when sequence is pulsing.
3. NMR lock stabilizer DC offset compensation indicator.
4. NMR lock stabilizer ON.
6 Electronic unit back panel.
[pic]
Figure 65. PS 15 spectrometer. Electronic unit back panel.
1. Power entry module.
2. Power cable receptacle.
3. Fuse.
4. Power switch
5. TX 1:10. Transmitter RF pulses monitor output; BNC. Can be used with an oscilloscope.
6. TX – to probehead. Transmitter RF pulses main output; BNC.
7. Programmer. RF pulses envelope monitor output. TTL level; BNC.
8. RX- from probehead. Nuclear induction signal input (to the receiver); BNC.
9. Magnet. Electromagnet power supply output (to main coils and flux coils) /input (correction coils); 15 pin D-subminiature connector.
10. Probehead. Input/output to probehead; 25 pin D-subminiature connector.
11. RS 232. PC serial port input/output; 9 pin D-subminiature connector
12. – I0 Set +. Electromagnet I0 current offset.
8 Magnet and probehead front view.
[pic]
Figure 66. PS-15 Spectrometer. Electromagnet and probehead front view.
1. Probehead.
2. RX- to receiver. Nuclear induction signal output (to the receiver); BNC.
3. TX- from transmitter. RF pulses input (from the transmitter); BNC
4. Probehead interface input/output; 25 pin D-subminiature.
5. Probe locking screw.
6. Electromagnet handle.
7. Electromagnet base.
8. Sample.
9. Magnet rubber foot.
10. Magnet yoke.
11. Electromagnet coils (main coil, flux coil, correction coil) input/output, 5 pin D-subminiature.
12. Electromagnet poles.
9 Magnet and probehead side view.
[pic]
1. Probehead.
2. RX- to receiver. Nuclear induction signal output (to the receiver); BNC.
3. TX- from transmitter. RF pulses input (from the transmitter); BNC
Figure 67. PS-15 Spectrometer. Electromagnet and probehead side view.
4. Into. Probehead interface input/output; 25 pin D-subminiature.
5. Probe locking screw.
6. Electromagnet handle.
7. Electromagnet base.
8. Sample.
9. Electromagnet rubber foot.
10. Electromagnet side plate.
11. Electromagnet shimming screw.
12. Electromagnet pole central screw.
Note to users of serial number 1 THROUGH 35
Users of PS15 spectrometer of serial number from 1 through 35 please note:
• slight cosmetic differences
• absence of Programmer and TX1:10 outputs on the rear panel,
• absence of Programmer indicator on the front panel,
• three shimming screws on the magnet.
These changes do not affect other features of the instrument.
1 Electronic unit front panel
Figure 68. PS-15 spectrometer. Electronic unit front panel
[pic]
1. Power ON
2. Lock stabilizer DC offset compensation indicator
3. Lock stabilizer ON
2 Electronic unit back panel
Figure 69. PS-15 Spectrometer. Electronic unit back panel.
[pic]
1. Power entry module
2. Power cable receptacle
3. Fuse
4. Power switch
5. 220V/115V voltage selector label
6. RF pulses output; BNC
7. Electromagnet power supply output (main coils, flux coils )/input (correction coils); 15 pin D-subminiature connector
8. Probehead connector; 25 pin D-subminiature connector
9. Electromagnet current offset
10. PC serial port connector; 9 pin D-subminiature connector
11. Receiver input; BNC
3 Magnet front view
Figure 70. PS-15 Spectrometer. Electromagnet front view.
[pic]
1. Probehead
2. RF pulses input (from the transmitter); BNC
3. Nuclear induction signal output (to the receiver); BNC
4. Probehead interface connector; 25 pin D-subminiature
5. Probe locking screw
6. Electromagnet left pole and solenoid
7. Electromagnet right pole and solenoid
8. Electromagnet PCB cover
9. Sample
10. Electromagnet coils (main coil, flux coil, correction coil)
4 Magnet side view
Figure 71. PS-15 Spectrometer. Electromagnet side view.
[pic]
1. Probehead
2. RF pulses input (from the transmitter)
3. Nuclear induction signal output (to the receiver)
4. Probehead interface (NMR lock control, probe power supply)
5. Probe locking screw
6. Electromagnet handle
7. Electromagnet
8. Electromagnet pole central screw
9. Electromagnet pole side screws; shimming
references
1 Papers:
1. Edward Mills Purcell, H. C. Torrey and R. V. Pound
Resonance Absorption by Nuclear Magnetic Moments in Solids
Physical Review, 69, 37-38 (1946)
2. F. Bloch, W. W. Hansen and M. E. Packard
Nuclear Induction
Physical Review 69, 127- (1946)
3. E. L. Hahn
Spin-Echoes
Physical Review, 80, 580-594 (1950)
4. H. Y. Carr and E. M. Purcell
Physical Review, 94, 630- (1954)
5. S. Meiboom and D. Gill
Modified Spin-Echo Method for Measuring Nuclear Relaxation Times
Review of Scientific Instruments, 29, 688- (1958)
6. Robert R. Ernst and W. A. Anderson
Application of Fourier Transform Spectroscopy to Magnetic Resonance
Review of Scientific Instruments, 37, 93- (1966)
2 Books:
1. Thomas C. Farrar, Edwin D. Becker
Pulse and Fourier Transform NMR. Introduction to Theory and Methods.
Academic Press, New York, 1971
2. Ray Freeman
A Handbook of Nuclear Magnetic Resonance
Longman Scientific & Technical, UK, 1988
3. Eichii Fukushima and S. B. W. Roeder
Experimental Pulse NMR. Nuts and Bolts Approach.
Addison-Wesley, Reading, Massachusetts, 1981
4. Richard R. Ernst, Geoffrey Bodenhausen and Alexander Wokaun
Principles of Nuclear magnetic Resonance in One and Two dimensions
Clarendon Press, Oxford, UK 1987
3 Web references
1. Joseph P. Hornak
The Basics of NMR
2. W. Faulkner
Basic MR Principles
3. Henry Rzepa
NMR Spectroscopy. Principles and Application.
Six second year lectures given at Imperial College
4. Marc Bria, Pierre Watkin, Yves Plancke
2D NMR Spectroscopy. Or an Help for the Structural Determination of Chemical Molecules
5. There is a German web page with gigantic list of different links related to NMR we strongly recommend to visit:
4 Comments to versions
This book was printed on: Friday, December 05, 2003
v1.2
date: 12/04/03
file name: PS15 operating manual v1_2.doc
Pages reformatted for two-page printing. Minor typing errors corrected.
List of figures
Figure 1. 115V label for USA market. 4
Figure 2. Electronic control unit back panel: 1) power entry module, 2) power cable receptacle, 3) fuse, 4) power switch. 5
Figure 3. PS 15 spectrometer block diagram. 10
Figure 4. General view of Setup page. 15
Figure 5. Magnetic field stabilizer controls. 16
Figure 6. First derivative of NMR signal from 19F nuclei when Lock is cleared. 18
Figure 7. CW NMR signal from 19F in HBF4 sample after successful lock was achieved (when Lock option was checked). 18
Figure 8. Transmitter attenuator controls. 19
Figure 9. Receiver controls. 20
Figure 10. Data acquisition controls. 22
Figure 11. Three pulse sequence. 23
Figure 12. Programmer dialog box with one-pulse sequence opened. 23
Figure 13. Spectroscopy methods dialog box. 24
Figure 14. Relaxometry methods dialog box. 24
Figure 15. RF pulse and “dead time” that follows. 27
Figure 16. DC level offset controls. 29
Figure 17. Status bar shortly after NMR lock is achieved. 29
Figure 18. Choosing magnet stabilizer units: [mT] or [kHz]. 33
Figure 19. Acquisition page. 34
Figure 20. VTD directory. 36
Figure 21. Time delay editor. 37
Figure 22. Acquisition page when spectroscopic data are acquired. 38
Figure 23. Acquisition page during the relaxation experiment. 39
Figure 24. Saving data manually. 40
Figure 25. Processing page. 42
Figure 26. Dialog box for loading binary files. 45
Figure 27. Opening files with processed previously data. 45
Figure 28. One-pulse sequence details on graphics after clicking Tools>View Sequence. 47
Figure 29. NMR spectrum from FID in glycerin (Figure 25) soon after FFT was performed. 48
Figure 30. Spectrum after proper phase correction. 48
Figure 31. Calculation of line width at spectrum half maximum. Discrete points presentation is used to show interpolation. 49
Figure 32. Spectrum after executing peak picking routine. 49
Figure 33. Integration of the spectrum. 50
Figure 34. Extracting data points for T1 calculations. 52
Figure 35. Viewing extracted amplitudes and time delays. 53
Figure 36. One exponential fit for experimental data obtained by IR method in glycerin. 54
Figure 37. Viewing data points. 54
Figure 38. Extracted data points and their fit for T1 measurements by Saturation method in rubber. 55
Figure 39. View the echo train in the CPMG method. Note the FID at the beginning of the train and the sharp spikes between spin-echoes that correspond to RF pulses position. These RF spikes do not count as echoes! 56
Figure 40. Echoes number selection. 56
Figure 41. Processing page after extracting data from CPMG experiment. 57
Figure 42. Fitting CPMG data. 57
Figure 43. Proper sample tube placement inside the probehead; all dimensions are in mm. 59
Figure 44. Sample positioning with acrylic adjustment tube. 60
Figure 45. User's Assistant options after program starts. 61
Figure 46. Factory created directory paths. 62
Figure 47. Setup page after successful lock. 63
Figure 48. Electronic unit front panel after locking and when programmer is pulsing. 63
Figure 49. Off resonance FID from glycerin. 66
Figure 50. On resonance FID from glycerin. 67
Figure 51. Tipping nuclear macroscopic magnetization by RF pulses 68
Figure 52. Effect of a too long RF pulse. 68
Figure 53. FID signal when sample is not placed in the center of the coil. 69
Figure 54. On resonance FID from glycerin sample after final adjustments. 70
Figure 55. Accumulated FID from protons in glycerin. 71
Figure 56. On-resonance FID from glycerin viewed on Processing page. 72
Figure 57. Spectrometer operating in lock-off mode. 76
Figure 58. Magnet side plate. A is a M10x1 screw that holds the pole. A, C and D are three pairs of six alignment screws, E are M4 screws that hold the magnet’s solenoid frame, F are four M6 screws that join vertical bars with side plates. 77
Figure 59. Aligning the left pole. Bottom screw pushes pole upward against top screw that must be released to make room for pole movement. The center screw holds the pole through spring washer. If more room is needed release center screw turning it counter-clockwise no more than 10o. Note that size of separating washers and movement of the pole has been exaggerated for better illustration. 78
Figure 60. On resonance FID for short dwell time of 0.4(s is only partially visible. 79
Figure 61. On resonance FID after proper adjustment of I0 current. 79
Figure 62 Winner program directories. 85
Figure 63. Suggested sample size for PS 15 spectrometer: a) liquid like samples, b) solid-like samples. 92
Figure 64. PS-15 NMR spectrometer. Electronic unit front panel. 93
Figure 65. PS 15 spectrometer. Electronic unit back panel. 94
Figure 66. PS-15 Spectrometer. Electromagnet and probehead front view. 95
Figure 67. PS-15 Spectrometer. Electromagnet and probehead side view. 96
Figure 68. PS-15 spectrometer. Electronic unit front panel 97
Figure 69. PS-15 Spectrometer. Electronic unit back panel. 98
Figure 70. PS-15 Spectrometer. Electromagnet front view. 99
Figure 71. PS-15 Spectrometer. Electromagnet side view. 100
Index
1
19F, 4, 13, 18, 19, 62
1H, 4, 17, 18, 81
A
Acq. no, 36
acquisition, 14, 26, 27, 29, 35, 36, 71
delay, 28
triggering, 24, 29
ACQUISITION data
acquired data, 35
added parameter, 35
experimental setup, 35
extracted relaxation data, 35
acrylic, 59, 60, 65
acrylic tubing, 60
Anderson W.A., 4, 100
Arnold J.T., 4
B
B0, 17, 18, 66, 67
Becker E.D., 100
binary data file, 15, 36
Bloch F., 4, 100
block diagram, 11
Bodenhausen G., 100
Bria M., 101
C
Carr H.Y., 100
Carr-Purcell method of T2 measurements, 27, 57
Carr-Purcell-Meiboom-Gill method of T2 measurements, 27, 57
cfg setup configuration directory, 31, 74, 76, 82, 90
comment, 36
computer, 8, 10, 13, 81
requirements, 8
configuration file
changing, 90
connections, 9, 73
converting data, 72
CP, 45
CPMG, 45
D
Damadian R., 4
data, 14, 45
acquired data display window, 35
directory, 71
display window, 14, 23, 35, 65, 66, 71
display window of extracted relaxometry points, 36
extracting for T1, 53
extracting for T2, 57
pointer, 69, 70
data experimental data directory, 36, 83
dataout processed data directory, 83, 85
DC level, 16, 64, 65, 73
dead time, 28, 40, 48, 53
directory structure, 82
display window, 35
drl binary relaxation data, 42, 45, 46
dsp binary spectroscopy data, 39, 42, 44, 46
dwell time, 44, 64, 65, 79
E
electrical requirements, 7
electromagnet, 73, 74, 93, 94, 95
description, 13
Electromagnet, 97, 98, 99
electromagnet stabilixer
description, 13
electronic unit
back panel, 93
front panel, 92
Ernst R.R., 4, 100
exciter
description, 11
exit the program, 15, 31, 90
Export save data in text format, 42, 46, 72, 85
F
f0/B0, 73
factory created pulse sequences, 26
Farrar T.C., 100
Fast Fourier Transform, 42, 48, 49, 87
Faulkner W., 101
FID, 26, 32, 48, 49, 53, 57, 64, 66, 67, 69, 70, 71, 72, 74, 76, 77, 78, 79, 86, 87, 88
file
name for experimental data, 36
Freeman R., 100
Fukushima E., 100
fuse, 8, 73
G
Gerlach W., 4
Gill D., 100
glycerin, 37, 60, 65, 70
glycerol, 60
Gorter C.J., 4
H
Hahn E.L., 4, 100
Hahn sequence, 45
Hahn spin echo, 27
Hansen W.W., 100
Hornak J.P, 101
I
IBM PC AT VGA, 8, 81
integration of spectrum, procedure, 51
Inversion Recovery method of spin-lattice relaxation measurement, 15, 29, 37, 40, 55, 82, 88, 89
L
Lautertbur P.C., 4
level
DC level compensation for NMR lock, 73
Load
experimental binary data file, 42, 46, 72
relaxometry binary data file, 53, 56, 57
VTD file, 37, 38
lock, 62, 63, 73
Lock, 96
M
macroscopic magnetization, 60, 67, 68
magnet
front view, 94
side view, 95
magnetic field, 4, 5, 11, 13, 14, 17, 18, 19, 30, 59, 60, 61, 62, 66, 67, 73, 75, 77, 79, 80, 81
correcting homogenity, 77
lock, 19, 30
on-resonance adjustment, 66
setting magnet I0 current, 79
manipulating
FID, 48
spectrum, 48
Meiboom S., 100
method, 24, 27, 28, 45
microprocessor controller
description, 13
P
Packard M.E., 100
Pauli W., 4
Philips screwdriver, 6, 9
Plancke Y., 101
power switch, 8
prl processed relaxometry data, 47
probehead, 9, 10, 11, 28, 59, 60, 62, 70, 81, 93, 94, 95
description, 11
Probehead, 97, 98, 99
processing, 14, 15, 72
PROCESSING FID, 48
EM Exponential Multiplication, 48
FFT Fast Fourier Transform, 48
LB define Line Broadening, 48
R/L Right/Left data shifting, 48
PROCESSING relaxometry data
calculating T1 from Inversion Recovery experiment, 55
calculating T1 from Saturation experiment, 56
calculating T2 from CP or CPMG experiment, 58
extraction data for T1, 53, 54
extraction data for T2, 57
PROCESSING spectrum, 48
AI Absolute Integral, 51
AI Automatic Integration, 51
HZ Horizontal Zoom, 48
I spectrum Integration, 51
IN Integral Normalization, 51
LC/RC Left/Right integration limits, 51
LW Line Width at half maximum, 50
P0 zero order phase correction, 49
SC Spectrum zero line Correction, 51
VZ Vertical Zoom, 48
product checklist, 6
programmer
description, 11
Programmer, 81
psp processed spectroscopy data, 47
Pulse adjustment, 67
pulse sequence, 14, 24, 27, 29, 64, 72, 73
1P_X, 16, 24, 26, 64, 69, 70, 86, 87
1P_Y, 26
1P_-Y, 26
2P_X_D, 26
2P_X_VD, 26, 89
3P_X_D, 27
CP_25, 27
CPMG_25, 27
HAHNECHO, 26
SAT, 27
SOLID_SE, 27
STIM_SE, 27
Purcell E.M., 4, 100
R
r_mtd relaxometry methods directory, 82, 83
Rabi I.I., 4
receiver, 65, 73, 81
description, 13
gain, 86, 87, 89
Receiver, 97
relaxation binary data files, 15, 42
Roeder S.B.W., 100
RS 232, 10, 13, 62, 73
rubber, 37, 59, 60, 65, 69, 70
Rzepa H., 101
S
s_mtd spectroscopy methods directory, 83
sample position, 69
sample preparation, 59
Saturation method of spin-lattice relaxation measurement, 56
Save As
save acquired data with a new name, 41
save processed data with a new name, 42
save Setup with a new name, 31, 47, 90
save VTD with a new name, 38
setup, 14, 15, 16, 26, 32, 35, 36, 40, 41, 48, 61, 63, 64, 70, 71, 73, 82, 90
SETUP
DC Level, 30, 65
SETUP Data acquisition, 23
Dwell Time, 23
I2 + Q2, 23
imaginary channel - Q, 23
NOP - Number of Points acquired - NOP, 23
real channel - I, 23
SETUP Magnetic field, 17
f0/B0, 17
Fa, 18
lock, 19
Δf0/ΔB0, 17
ΔI0, 18
SETUP Menu
File, 31
Mode, 32
Spectrometer, 31
Task, 32
Tools, 32
SETUP Preferences, 33
Audio, 33
Communication port, 33
File location, 33
Magnet stabilizer units, 33
SETUP Programmer, 24
Acquisition delay, 29
Acquisition triggering, 29
Method, 24
RF pulse, 28
Stop/Run, 29
SETUP Receiver, 21, 65
Amplitude detection, 22
Gain, 21, 65, 69
Number of accumulations, 21
Phase control, 21, 65
Phase quadrature detection, 22
Time Constant, 21
SETUP Transmitter, 20
Attenuator main, 20
Attenuator Y, 20
shipment check, 6
Signal-to-Noise, 11, 59
software installation, 8
spectrometer
description, 11
installation, 5
location, 6
operation, 11
specifications, 81
spectroscopy binary data files, 15
, 15
spectroscopy data files, 42, 44
spin-echo, 26, 27, 32, 74, 86
stabilizer level, 63
stabilizer on, 63
standard.cfg, 74
Stern O., 4
T
T1, 15, 20, 26, 27, 29, 37, 42, 45, 53, 55, 56, 82, 88, 89
T2, 15, 26, 27, 42, 45, 53, 57
Teflon support, 59
text data format
relaxometry, 88
spectroscopy, 86
Torrey H.C., 100
transmitter
description, 11
trouble shooting
list, 73
troubles, 73
txt experimental or processed data in text format, 46, 85
U
user, 5, 14, 15, 17, 28, 37, 59, 81
V
viewing data, 72
voltage selector 115/220 V, 7
voltage selector label, 7
VTD (Variable Time Delay), 37, 38, 40, 45, 83, 89
VTD file
t1_16_e, 37
t1_16_g, 37
t1_16_r, 37
t1_16_w, 37
vd_user, 37
W
Watkin P., 101
WILMAD, 59
Wokaun A., 100
wood, 59, 65
-----------------------
[1] Instead of M4 screws, units with a serial number #28 and above use permanently attached locks with knurled knobs.
[2] For center frequency f0 =15,000.7 kHz/ B0=352.3 mT. It may vary by hundreds of Hz from model to model, depending on final tuning of the magnet stabilizer.
[3] In 12 steps.
[4] [pic]0; where ( is as gyromagnetic ratio for 1H nucleus.
[5] In 1024 steps, 10 bit DAC.
[6] Sealed solution of HBF4 is used for lock stabilization.
[7] Due to locking sample aging process the difference between fo and Fa may become wider. Consult manufacturer for instructions if it reaches 0.4 kHz.
[8] To change file attributes right-click on file then left-click on Properties and in General clear read-only box.
[9] Function key aficionados can use F1 and F2 for Start and Stop.
[10] Due to small size of the PS 15 magnet and the lack of shimming coils all spectra are inhomogeneously broadened to about 250 Hz. Exact value of broadening depends on magnet adjustment.
[11] Because of strong inhomogeneous broadening of spectra acquired with PS15 electromagnet First Order phase correction was not implemented.
[12] For detail on Inversion Recovery Method refer to ELABORATORYXPERIMENTAL MANUAL.
[13] For details about Saturation Method refer to LABORATORY EXPERIMENTAL MANUAL.
[14] WILMAD/Lab Glass, PO Box 688, 1002 Harding Highway, Buena, NJ 08310-0688, USA, tel. 856-697-3000, for order 800-220-5171, , cs@. We suggest 5 mm student NMR tube: borosilicate WG-5mm Thrift
[15] Chemical name glycerol; C3H8O3. It contains relatively many protons that build strong macroscopic magnetization when polarized by the constant magnetic field.
[16] Generally magnetic field will decrease when temperature of the magnet yoke increases due to decrease of the permeability of alnico alloy.
[17] B1 ( 3(PQ/fV)1/2, Q [pic], where Q is quality factor of the sample circuit, P is the pulse power in watts, V is sample volume, f is operating frequency in MHz.
[18] Bigger magnets are equipped with additional correcting coils called shimming coils. They are connected to independent power supplies and can change geometry of the magnetic field to the desired shape by turning potentiometers knobs rather than screws.
[19] See above info about r_mtd.
-----------------------
|Nominal |AC Line Power |AC Line Power |Fuse |
|Setting |Voltage [V] |Frequency [Hz] |[A] |
|115 V |100 – 122 |45-100 |2 |
|220 V |200-230 |45-100 |1 |
[pic]
Info bar
Menu bar
Tool bar
Data display window
Spectrometer
setting windows
Status bar
[pic]
Acquired Data
Horizontal [ms], Vertical [a.u.]
VD = 1.000 [ms]
0.000 -1148
-------- --------
10.230 -8
---------------------------------
---------------------------------
VD = 500.000 [ms]
0. 1739
-------- --------
10.230 4
Experiment parameters
Mode : Relaxometry
B0 : 15,000.3 kHz
Delta B0 : +1,067.3 Hz
Attenuator main : 0.0 dB
Gain : 43 dB
Phase : 140°
Detection : P
Time const : 5 µs
Dwell time : 10.0 us
NOP : 1024
Channel : I
Method : 2P_X_VD
Trig : P2
No of accumulation : 16
Number of FIDs (Echoes): 16
VTD File : T1_16g.ttb
Comment : T1 in glycerin by IR
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[pic]
[pic]
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