BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > NMR community > News from NMR blogs
Advanced Search
Home Forums Wiki NMR feeds Downloads Register Today's Posts



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
 
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Old 12-17-2013, 12:56 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Echoes, T2 Measurements and Diffusion

Echoes, T2 Measurements and Diffusion

In a perfectly homogeneous magnetic field, the T2 relaxation time constant can be measured directly from the free induction decay in the time domain or the full width at half height of the resonance in the frequency domain. The magnetic field however, is never perfectly homogeneous. Each microscopic volume element of the sample resides in a slightly different magnetic field and therefore the offset frequencies of the resonance in each volume element are slightly different from one another. The net effect on the spectrum of the entire sample is that the NMR resonances are broader than what one would expect from the T2 relaxation process alone. The distribution of offset frequencies due to magnetic field inhomogeneity is referred to as inhomogeneous broadening. In an inhomogeneous magnetic field, the FID decays faster, with time constant T2* where 1/T2* has a contribution from the natural relaxation rate, 1/T2, of the resonance and that due to the field inhomogeneity. In other words, when a sample is in an inhomogeneous magnetic field, the resonances are homogeneously broadened by the natural T2 relaxation process and inhomogeneously broadened by the non-uniform magnetic field. The measurement of T2 relies on separating the homogeneous broadening from the inhomogeneous broadening.

One of the first pulse sequences typically introduced in NMR textbooks is the spin echo or Hahn echo. This sequence consists of a 90° pulse followed by a delay, ?, during which offsets frequencies evolve. A 180° pulse is then applied after which another period of time, ? is allowed where offsets continue to evolve, producing an echo at 2?. The spin echo sequence has the ability to refocus the distribution of offset frequencies due to magnetic field inhomogeneity (inhomogeneous broadening) however it cannot refocus the natural distribution of frequencies due to the T2 relaxation process (homogeneous broadening). It would seem as if the spin echo sequence has the ability to separate out the homogeneous broadening from the inhomogeneous broadening and therefore should be able to be used to measure the T2 relaxation time constant in a scheme like the one shown in the figure below.



where the intensity of the signals as a function of 2? is fitted to an exponential decay to give T2. Can this sequence really be used to measure T2? Let's look a bit deeper.

A sample of tetrakis-trimethylsilyl silane ( Si(Si(CH3)3)4 ) was dissolved in CDCl3. The magnet was shimmed such that the full line width at half height of the 1H resonance was 2 Hz. A standard one-pulse proton spectrum and a Hahn echo spectrum (with ? set to 1 second) were collected. The same measurements were made after adjusting the magnetic field shims such that the full width at half height was 5 Hz and 13 Hz. The results are shown in the figure below.




The top panel shows the NMR spectra resulting from the one-pulse measurement. The spectra all have the same integrated area as expected. The middle panel shows the FID's from the one-pulse measurements. The initial intensity of each FID is the same since the initial intensity of the FID is proportional to the integrated area of the resonance in the frequency domain. The bottom panel shows the Hahn echoes collected with a value of ? =1 second (a value substantially shorter than T2). The receiver was turned on immediately after the 180° pulse to collect the entire echo. Unlike the one-pulse FID's which remained constant as a function of magnetic field inhomogeneity, the height of the Hahn echoes decreased as the magnetic field inhomogeneity increased, all other parameters being constant. This should convince you that the simple Hahn echo is not always suitable for T2 measurements as the intensity of the echo depends on the degree of inhomogeneous broadening. This is so because of molecular diffusion. During the one second ? delays, molecules move from one volume element to another in the sample and therefore change their offset frequencies over the course of the measurement. The net result for the entire sample leads a loss in echo intensity due to destructive interference in the time domain signal from the sum of all volume elements. The loss in echo intensity is worse the more inhomogeneous the field. The simple Hahn echo would be expected to work as a means to measure T2 only in cases where the diffusion is insignificant with respect to ? (solids or dissolved macromolecules).

How then are T2's measured for small molecules in solution where diffusion is fast? One uses a train of Hahn echoes where the ? delays for each echo are chosen sufficiently short such that diffusion is not a problem (typically on the order of msec or tens of msec). The T2 is calculated from a series of spectra collected as a function of the number of echoes in the train based on the overall time between the initial 90° pulse and the collection of the signal. Such a scheme is called a Carr Purcell Meiboom Gill (CPMG) sequence and is shown in the figure below.




Source: University of Ottawa NMR Facility Blog
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] A new sequence for single-shot diffusion-weighted NMR spectroscopy by the trace of the diffusion tensor.
A new sequence for single-shot diffusion-weighted NMR spectroscopy by the trace of the diffusion tensor. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary-Button_120x27px_FullText.gif Related Articles A new sequence for single-shot diffusion-weighted NMR spectroscopy by the trace of the diffusion tensor. Magn Reson Med. 2012 Dec;68(6):1705-12 Authors: Valette J, Giraudeau C, Marchadour C, Djemai B, Geffroy F, Ghaly MA, Le Bihan D, Hantraye P, Lebon V, Lethimonnier F ...
nmrlearner Journal club 0 05-31-2013 11:16 AM
NMR Excitation, Dephasing and Spin Echoes
NMR Excitation, Dephasing and Spin Echoes http://i.ytimg.com/vi/KtWnmFg-u5g/default.jpg NMR Excitation, Dephasing and Spin Echoes This short animation shows the process of NMR excitation in the laboratory and the rotating frame, as well as the dephasing that occurs from field inhomogeneity and the formation of the Hahn spin echo. Please credit (c)2010 Mark Cohen (mscohen@ucla.edu) during re-use. From:markcat3t Views:8653 http://gdata.youtube.com/static/images/icn_star_full_11x11.gif http://gdata.youtube.com/static/images/icn_star_full_11x11.gif...
nmrlearner NMR educational videos 0 01-29-2012 07:45 PM
Li Ion Diffusion in the Anode Material Li12Si7: Ultrafast Quasi-1D Diffusion and Two Distinct Fast 3D Jump Processes Separately Revealed by 7Li NMR Relaxometry
Li Ion Diffusion in the Anode Material Li12Si7: Ultrafast Quasi-1D Diffusion and Two Distinct Fast 3D Jump Processes Separately Revealed by 7Li NMR Relaxometry Alexander Kuhn, Puravankara Sreeraj, Rainer Po?ttgen, Hans-Dieter Wiemho?fer, Martin Wilkening and Paul Heitjans http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja2020108/aop/images/medium/ja-2011-020108_0005.gif Journal of the American Chemical Society DOI: 10.1021/ja2020108 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
nmrlearner Journal club 0 06-28-2011 04:32 AM
[NMR paper] Analysis of protein/ligand interactions with NMR diffusion measurements: the importan
Analysis of protein/ligand interactions with NMR diffusion measurements: the importance of eliminating the protein background. Related Articles Analysis of protein/ligand interactions with NMR diffusion measurements: the importance of eliminating the protein background. J Magn Reson. 2002 Apr;155(2):217-25 Authors: Derrick TS, McCord EF, Larive CK Pulsed-field gradient nuclear magnetic resonance (PFG-NMR) is a well-established method for the determination of translational diffusion coefficients. Recently, this method has found applicability in...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Improved spin-echo-edited NMR diffusion measurements.
Improved spin-echo-edited NMR diffusion measurements. Related Articles Improved spin-echo-edited NMR diffusion measurements. J Magn Reson. 2001 Dec;153(2):273-6 Authors: Otto WH, Larive CK The need for simple and robust schemes for the analysis of ligand-protein binding has resulted in the development of diffusion-based NMR techniques that can be used to assay binding in protein solutions containing a mixture of several ligands. As a means of gaining spectral selectivity in NMR diffusion measurements, a simple experiment, the gradient modified...
nmrlearner Journal club 0 11-19-2010 08:44 PM
[U. of Ottawa NMR Facility Blog] Gradient Spin Echoes for Selective Excitation
Gradient Spin Echoes for Selective Excitation Shaped excitation pulses can replace the non-selective hard pulses typically used in a one-pulse measurement to achieve selective excitation. Another method of achieving selective excitation is the gradient spin echo using a selective 180° pulse. This technique is demonstrated in the figure below. http://4.bp.blogspot.com/_5wBTR2kKTqA/S_UxeG5oXdI/AAAAAAAAAzc/BHWef-Tse7s/s400/grad_spin_echo.jpgA non-selective hard 90°x pulse is first given followed by a pair of identical pulsed field gradients sandwiching a soft selective 180° pulse about the y...
nmrlearner News from NMR blogs 0 08-21-2010 08:15 PM
[Stan NMR blog] Field noise effects on NMR signals: Hahn echoes and CPMG
Field noise effects on NMR signals: Hahn echoes and CPMG An article about the effects of field noise on spin echoes and CPMG decays. More...
nmrlearner News from NMR blogs 0 08-21-2010 06:14 PM
Introductory NMR & MRI: Video 06: Spin echoes, CPMG and T2 relaxation
Introductory NMR & MRI: Video 06: Spin echoes, CPMG and T2 relaxation http://i.ytimg.com/vi/B2HMAJQJ7ok/default.jpg Introductory NMR & MRI: Video 06: Spin echoes, CPMG and T2 relaxation Paul Callaghan gives an introduction to NMR and MRI. This is the 6th video of a 10 episode series produced by Magritek Ltd. From: magritek Views: 7207 http://gdata.youtube.com/static/images/icn_star_full_11x11.gif http://gdata.youtube.com/static/images/icn_star_full_11x11.gif http://gdata.youtube.com/static/images/icn_star_full_11x11.gif...
nmrlearner NMR educational videos 0 08-18-2010 01:38 AM



Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 02:28 PM.


Map