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 04-29-2015, 03:14 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,732
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 Dead Time and Phase

Dead Time and Phase

The phase of an NMR peak depends on the sine/cosine character of the free induction decay (FID) when the receiver is turned on. Positive and negative cosine FIDs will yield positive and negative in-phase peaks, respectively whereas positive or negative sine FIDs will yield peaks 90° out of phase. FIDs that are neither a pure sine nor pure cosine with yield peaks which are out of phase to an extent dependent on the cosine/sine character of the FID. In a perfect world, the receiver is gated on immediately after a perfect 90° pulse and all FID’s are cosines producing positive in-phase NMR peaks. In the real world however, there are problems with acoustic ringing, pulse breakthrough imperfect pulses of finite duration and finite electronic switching times. These problems produce a dead time between the end of the pulse and time at which the receiver is gated on during which data cannot be collected. As a result the FID may not be a perfect cosine function and a phase correction will need to be applied after Fourier transform. The first two figures below illustrate this point for a single off-resonance NMR signal as the dead time is increased. The first figure shows the FID’s as a function of increasing dead time from bottom to top while the second figure shows the Fourier transformed spectra without phase correction as a function of dead time from left to right.
When there is more than one signal, the FID is an interferogram representing the sum of all time domain signals, each with a different frequency. Since each component has a different frequency, its phase is affected to a different extent as a result of the dead time. Higher frequency time domain components (i.e. those representing peaks further off-resonance) are affected more than lower frequency components (i.e. those representing peaks closer to being on-resonance). This is illustrated in the figure below for the 1H NMR data for p-xylene. The left-hand portion of top panel of the figure shows the FID containing both methyl and aromatic components while the right-hand portion of the top panel shows an expansion of the initial portion of the same FID. The bottom panel of the figure shows a stacked plot of the NMR spectra collected as a function of dead time. One can see that the phase of the aromatic peak furthest off-resonance is affected to a greater extent by an increased dead time than the methyl peak closer to resonance.
The last figure also shows a stacked plot of the 1H NMR spectra of p-xylene as a function of dead time.
In this case, the methyl signal was set on-resonance. One notices immediately that the phase of the on-resonance methyl peak is unaffected by an increase in the dead time whereas that of the off-resonance aromatic peak is severely affected. The on-resonance methyl peak is not affected by an increase in dead time as its time domain signal is a simple exponential with no sine/cosine oscillations. A loss of the beginning of a simple exponential FID due to the dead time still leaves a simple exponential and thus the phase is not affected.


Thank you to Dr. Micheal Lumsden of the NMR Facility of Dalhousie University for suggesting the subject of this post.


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 images] Solution Phase NMR Spectroscopy
http://spectroscopy.st-and.ac.uk/files/blocks_image_3_1.jpg 25/05/2014 5:12:38 AM GMT Solution Phase NMR Spectroscopy More...
nmrlearner NMR pictures 0 05-25-2014 05:12 AM
A system for accurate and automated injection of hyperpolarized substrate with minimal dead time and scalable volumes over a large range
From The DNP-NMR Blog: A system for accurate and automated injection of hyperpolarized substrate with minimal dead time and scalable volumes over a large range Reynolds, S., et al., A system for accurate and automated injection of hyperpolarized substrate with minimal dead time and scalable volumes over a large range. J Magn Reson, 2014. 239(0): p. 1-8. http://www.ncbi.nlm.nih.gov/pubmed/24355621
nmrlearner News from NMR blogs 0 03-10-2014 10:57 PM
A system for accurate and automated injection of hyperpolarized substrate with minimal dead time and scalable volumes over a large range
From The DNP-NMR Blog: A system for accurate and automated injection of hyperpolarized substrate with minimal dead time and scalable volumes over a large range Reynolds, S., et al., A system for accurate and automated injection of hyperpolarized substrate with minimal dead time and scalable volumes over a large range. J Magn Reson, 2013. 239C(0): p. 1-8. http://www.ncbi.nlm.nih.gov/pubmed/24355621
nmrlearner News from NMR blogs 0 01-20-2014 06:34 PM
Addendum to the paper “Dead-time free measurement of dipole–dipole interactions between electron spins” by M. Pannier, S. Veit, A. Godt, G. Jeschke, and H.W. Spiess [J. Magn. Reson. 142 (2000) 331–340]
Addendum to the paper “Dead-time free measurement of dipole–dipole interactions between electron spins” by M. Pannier, S. Veit, A. Godt, G. Jeschke, and H.W. Spiess Publication year: 2011 Source: Journal of Magnetic Resonance, In Press, Corrected Proof, Available online 3 September 2011</br> Hans Wolfgang, Spiess</br> The development of four-pulse DEER as described, which has been published in the Journal of Magnetic Resonance more than 10 years ago. The corresponding paper is an example where a slight advance, such as adding a refocusing pulse, which in retrospect looks so simple,...
nmrlearner Journal club 0 09-03-2011 07:32 PM
Solid-state and unilateral NMR study of deterioration of a Dead Sea Scroll fragment.
Solid-state and unilateral NMR study of deterioration of a Dead Sea Scroll fragment. Solid-state and unilateral NMR study of deterioration of a Dead Sea Scroll fragment. Anal Bioanal Chem. 2011 Jul 30; Authors: Masic A, Chierotti MR, Gobetto R, Martra G, Rabin I, Coluccia S Unilateral and solid-state nuclear magnetic resonance (NMR) analyses were performed on a parchment fragment of the Dead Sea Scroll (DSS). The analyzed sample belongs to the collection of non-inscribed and nontreated fragments of known archaeological provenance from the John...
nmrlearner Journal club 0 08-02-2011 11:40 AM
[U. of Ottawa NMR Facility Blog] First-Order Phase Errors
First-Order Phase Errors The phase of a signal in an NMR spectrum is described here and is determined by the axis on which the magnetization vector resides after the observe pulse relative to the receiver. The phase of the spectrum is typically corrected such that the peak in the real spectrum is entirely in absorption mode while that in the imaginary spectrum is entirely in dispersion mode. The correction in phase is referred to as the zero-order phase correction. A zero-order phase correction applies to all peaks in the spectrum regardless of their offset, ?, from resonance. There are...
nmrlearner News from NMR blogs 0 01-18-2011 02:44 AM
[U. of Ottawa NMR Facility Blog] The Phase of an NMR Spectrum
The Phase of an NMR Spectrum Most students know that the phase of an NMR spectrum has to do with the degree to which the NMR resonances are above or below the baseline of the spectrum (i.e. the amount of absorption and dispersion character). Most students have also learned that the phase of a periodic time domain function depends only on the value of the function at time zero. Thus, the only difference between a cosine and a sine function is where the function starts at time zero. A sine is said to be 90° out of phase with respect to a cosine. Many students do not understand the connection...
nmrlearner News from NMR blogs 0 11-19-2010 06:22 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 08:28 AM.


Map