Glossary

This sections explains some of the terms used in the instruction material. Entries are in alphabetical order. Click on the letter or number to go to the section you need.

A B C D E F G H I J K L M
N O P Q R S T U V W X Y Z
0 1 2 3 4 5 6 7 8 9

A

aglycon Non-reducing carbohydrates contain an aglycon such as methyl, octyl or octyl-ester. The latter two are hydrophobic aglycons allowing certain filtration techniques to separate them from by-products.
APT Attached Proton Test. A one-dimensional 13C experiment whereby peaks originating from C and CH2 are of opposite sign than those from CH and CH3. In cases where there is a solvent peak, C and CH2 signals are on the same side as the solvent whereas CH and CH3 are on the opposite side of the solvent signal.
archiving data Archiving of data is the permanent transfer of data from a hard disk to removable media such as tapes or CDs. The d600 data station has a tape drive with 4 GB capacity that allows this operation (best done by using the one-button approach as described in NMR News 98-05). A 650 MB CD-Writer is also available. The CD system, although much smaller in capacity, has the huge advantage of random access to the data plus the insensitivity to magnetic fields.

B

C

C18 Sep-Pak A cartridge allowing the separation of non-reducing carbohydrates with hydrophobic aglycons from undesired by-products.
CDE Common Desktop Environment. The graphical interface used by VNMR starting with version 5.3B and up. For current version click here.
current user name The user currently logged in into the system. All files created will have permissions that only allow this user to access them. Furthermore, the system places files automatically in the appropriate location for a given user.

D

data archiving see archiving data
data station A UNIX work station not connected to a spectrometer console. Used to process and analyze data and/or plotting. Currently there is one such station called d600 and located in the sub-basement room 3G
depth gauge Every sample needs to be positioned properly in the magnet. Since a user cannot see inside the probe in the magnet, this is achieved by using a depth gauge which adjusts the spinner and the sample relative to each other (for picture click here).
deuterium The 2H isotope of hydrogen. An NMR-active, spin=1 nucleus with a natural abundance of only 0.015% and a Larmor frequency of 46.05 MHz at 7.0 T (300 MHz for 1H).
digital resolution The FID from an NMR sample is recorded as a large number of points (4K to 64K or even more). The number of digitization points determines the attainable digital resolution which is the number of Hz between individual points. For an example see Appendix (FID or 1D spectra).
direct detection Refers to the direct observation of an FID obtained from heteronuclei such as 13C, 31P etc. Techniques such as APT, DEPT belong into this category. See also indirect detection.
DirectDrive The u500 is of this new architecture type introduced in about 2006. DirectDrive followed the INOVA design. For an overview see spectrometers. The letter u was retained as it was before a Unity-type console.

E

ethernet Host computers and data stations are linked together by an extensive cable network which allows the transfer of data in a fast and reliable way. In fact, the information you are reading right now has been transferred via ethernet from the server to your computer and is then displayed by the WWW browser.

F

FID Free Induction Decay. The superposition of all the frequencies in a spectrum as a function of time. The signal decays due to relaxation processes. FID example.
field strength The magnetic field in Tesla (T) of a magnet determines the basic frequency (Larmor frequency) of the spectrometer. For 1H/13C:
  7.0T -> 300/75.4 MHz
11.7T -> 500/125.7 MHz
14.1T -> 600/150.9 MHz
filename.fid VNMR saves spectra in a directory with the extension .fid. filename can be chosen by the user with some limitations regarding special characters.
F-keys SUN keyboards have a row of keys numbered from F1 to F12 at the top of the keyboard. Limitations in VNMR allow only the use of F1 to F9 though.
FTP File Transfer Protocol which allows the transfer of any form of data from one computer to another via the network. Due to its open (not encrypted) transfer of username and password it is no longer available on the NMR systems.
Use SCP instead.

G

gradients Gradients allow the elimination of undesired artifacts on a per scan basis rather than by phase cycling. They also allow coherence pathway selection and in some experiments very effective suppression of solvent peaks.

H

HETCOR Heteronuclear correlation: the traditional way of recording correlation spectra between 1H and heteronuclei before the arrival of indirect detection probes and techniques.
host computer The SUN computer (also called work station) connected to the Varian NMR console. This is the computer a user interacts with when acquiring spectra: the mouse, the keyboard and the monitor.

I

INOVA Most of our spectrometers are of the Varian INOVA type. INOVA identifies a spectrometer design that followed UNITY and UNITY+. For more details regarding our spectrometers and their capabilities click here.
inverse (or indirect) detection probe Probes optimized to record protons at the highest possible sensitivity. They can record heteronuclei such as 13C only in an indirect way, e.g. via HMQC or similar 2D experiments. What happens in these cases is that the signals from 99% of the molecules (12C!) are suppressed and the 13C satellites are recorded (1.1%). This is known as indirect detection.

J

K

L

Larmor frequency The basic resonance frequency of NMR-active nuclei in MHz. The values depend on the nucleus' magnetic properties and the magnetic field in which it is measured.
lock gain/power The strength of the lock signal depends on the power and the gain used. In many cases it is not overly critical but saturation should be carefully avoided.
locking To eliminate the effect of field drift, a sample is "locked" to the frequency of the deuterium signal of its solvent (or one of the deuterium signals if the solvent has several D such as in CD3OD). For more details click here.
lock signal Values between 80 and 100 are ideal for almost all applications. Gradients affect the lock signal strongly. In CD3OD in particular, it is therefore recommended to adjust lock gain/power when the spinner is turned off otherwise the lock might be temporarily lost which is undesirable.

M

macros A collection of commands and/or nested macros. A macro can be very simple (example: sc is a macro that executes the command dscale) or highly complex with logical statements and many pages long.
magnetic field strength see field strength
Mercury+ The name Mercury+ is used for Varian spectrometers that are of a more routine nature than the INOVA series. Our only Mercury+ is called m400 and was installed in August 2004.
multi user A computer which is used by many people by means of different user names. While only one person can sit at the keyboard and use the system, there might be others using the system remotely and a variety of system tasks are executed automatically in the background.

N

nested macro A macro that is called into action inside another macro.
NMR tubes All three Varian spectrometers use 5 mm tubes. 0.7 mL is the ideal volume which is equivalent to a sample height of about 55 mm. Lower sample volume makes shimming very difficult.

O

optical mouse Uses an invisible light beam which is moved over a tablet with a very fine perpendicular grid. By counting the number of lines, the mouse can sense in which way it is moving and moves the cursor on screen accordingly. There are no mechanical parts such as a rolling ball in this type of mouse, which makes them much less vulnerable to malfunctioning due to dirt buildup. More about mice.

P

paramagnetic substances The commonly measured nuclei such as 1H, 13C etc. are diamagnetic in nature. Paramagnetic nuclei behave  differently in a magnetic field, most notably they cause substantial line broadening effects. Examples are Mn, Ni and many other transition metals.
parameter set A collection of parameters relevant to the correct acquisition and processing of an NMR experiment. 
PFG Stands for pulsed field gradients indicating that a probe is capable of doing gradient-enhanced spectroscopy.
phase cycling Essentially all NMR experiments produce undesired artifacts that need to be eliminated. The traditional way to do this is through phase cycling, i.e. taking pulses and receiver phases through x, y, -x, -y or in degrees: 0, 90, 180, 270. A more modern approach for this is via gradients.
procpar Every experiment recorded with VNMR results in a folder called name_you_chose.fid. Inside this folder are the actual data, a text file and procpar which contains all parameters to make a spectrum look exactly the same when it is reprocessed.
ProTune ProTune allows tuning of the probe from the keyboard. The tuning and matching rods are turned by motors connected to the probe via flexible cables.

A movie of ProTune in operation can be seen by clicking on this icon: . Please note that it is of substantial size (93 Mbyte) for very limited entertainment value (no Oscar nominations expected).

Q

R

S

saturation A condition whereby more lock power is sent to the sample than it can dissipate, resulting in sample heating and unstable lock conditions. Simple check: reduce lock level by 6 dB and lock level should drop to approximately half. If it drops by significantly less then the lock is saturated and the lock power should be reduced.
SCP Secure Copy protocol which uses encrypted usernames and passwords; replaces FTP which is no longer available for security reaons.
sensitivity Strongly depending on the field of the magnet and the age of the hardware (probe, electronics). It is measured as the signal-to-noise ratio of a peak in a standard sample, measured in an exactly predetermined way to allow comparisons between spectrometers.
shimming Optimize the homogeneity of the magnet for a given sample. Electric currents in the shim coils create small magnetic fields which compensate inhomogenieties by the large static field.
spectral dispersion Chemical shift separation (i.e. the "dispersion") of NMR lines increases with the field. In ppm the values are by definition independent of field but in Hz the separation is proportional to the field strength also called Larmor frequency.
Solaris Solaris is the name of the UNIX operating system used by all SUN host computers and data stations. For currently used version click here.
solvents The list of commercially available deuterated solvents is very long and not all can be implemented. A supported solvent is one for which parameter sets have been stored, buttons created for easy use, references defined etc. for the all supported NMR techniques in the AO-VNMR system.
supported solvents see solvents.
supported techniques see techniques.
switchable probe A probe that allows recording of protons and indirect detection of 13C (both with somewhat reduced sensitivity) and also the direct detection of 13C (e.g. APT) and 31P without any cable switching (keyboard-controlled). The lower 1H sensitivity is often of limited concern given that 1H is the most sensitive nucleus.

T

tape drive A DDS-2 archive tape drive is attached to the d600 data station. Tapes have a 4 Gbyte capacity (without compression) and can be obtained in E3-51A. Archiving can be done as a one button operation.
techniques The list of NMR techniques in the AO-VNMR system is spectrometer-dependent and expanding ever so slowly over time. For a summary of the currently availble 1D and 2D techniques click here.
Tesla see field strength
tuning Tuning is used to optimize the performance of a probe for a given NMR sample; in particular, the reflection of the radio frequency pulses is minimized. For more details click here.
two-dimensional Techniques such as COSY, NOESY are examples of homonuclear 2D experiments, HMQC, HMBC are heteronuclear 2D experiments.

U

UNITY Since the upgrade of u500 in November 2006, we have no longer any Unity-type consoles. For more details click on u500.
unsupported solvents see solvents
user name A name recognized by the host computer or data station as a legitimate user of the system. Together with a password allows access to and use of the system.

V

VNMR Varian's NMR software package. For information about current versions click here.
VNMRJ Varian's NMR software package based on the Java programming language. For information about current versions click here.

W

X

Y

Z

0

1

2

2D see two-dimensional

3

4

5

6

7

8

9

top of page