U. of Ottawa NMR Facility Blog Exact Simulaion of Quadrupolar Lineshapes in Solids

		BioNMR > NMR community > News from NMR blogs
[U. of Ottawa NMR Facility Blog] Exact Simulaion of Quadrupolar Lineshapes in Solids

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

06-26-2012, 06:18 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,184

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Exact Simulaion of Quadrupolar Lineshapes in Solids

Exact Simulaion of Quadrupolar Lineshapes in Solids

The NMR spectra for quadrupolar nuclei in solids contain a great deal of structural information. The evaluation of quadrupolar coupling constants, asymmetry parameters, isotropic chemical shifts, chemical shift spans, chemical shift skews and the angles relating the electric field gradient tensor to the chemical shift tensor is typically done by simulating the NMR spectrum with suitable software and fitting the simulated spectrum to the experimental data. Almost always, the spectra of quadrupolar nuclei in solids have been simulated using perturbation theory where the quadrupolar interaction is treated as a perturbation on the much larger Zeeman interaction. With the recent developments in the collection of ultra-wide line NMR spectra, quadrupolar nuclei with larger and larger quadrupolar coupling constants are being studied by NMR and the perturbation approach may not be valid. Errors between simulated and experimental spectra appear when the Larmor frequency is not significantly larger than the quadrupolar coupling constant.

Recently, a new program called QUEST (QUadrupolar Exact SofTware) has been written by Frédéric Parras from the research group of David Bryce at the University of Ottawa. As the name implies, this program is capable of simulating exactly the spectra of quadrupolar nuclei in solids without resorting to the assumptions of perturbation theory. QUEST is able to quickly calculate accurate lineshapes regardless of the ratio between the Larmor frequency and the quadrupolar coupling constant. It even works in cases where the Larmor frequency is much less than the quadrupolar coupling constant (i.e. NQR). The figure below shows a series of spectra calculated for a spin I=3/2 nucleus as a function of the ratio of the Larmor frequency, ?L , to the quadrupolar coupling constant, CQ. The spectra near the top are NMR-like and those near the bottom are NQR-like. QUEST is a fast, graphical, easy-to-use program able to handle multiple sites, export data in Bruker format, import experimental spectra for comparison to the simulations and simulate spectra as a function of the angle of the detection coil with respect to the magnetic field. The package also includes a very helpful well written pdf manual. The program is reported and described fully here. To take a look at the program in action, watch these tutorial videos prepared by the author. The complete program is available for free download here. I highly recommend it!

Source: University of Ottawa NMR Facility Blog

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR900 blog] QUEST – QUadrupolar Exact SofTware QUEST – QUadrupolar Exact SofTware QUEST is a new program for the exact simulation of solid-state NMR spectra of quadrupolar nuclei in stationary powdered samples which employs diagonalization of the combined Zeeman-quadrupolar Hamiltonian. The program may be used to simulate NMR spectra over the full regime of Larmor and quadrupolar frequencies, which encompasses scenarios ranging from high-field NMR to nuclear quadrupole resonance (NQR, where the Larmor frequency is zero) and does not make use of approximations when treating the quadrupolar interaction. The program, which uses a...	nmrlearner	News from NMR blogs	0	05-31-2012 03:59 AM
Unequal quadrupolar splitting intensities Hi everyone I'm running an experiment looking at a mesoporous organosilica soaked in benzene-d6. The pores are tubular and aligned more or less in the same direction, so the anisotropic environment causes quadrupolar splitting when looking at deuterium. However, the splitting intensities are not equal: the left peak tends to be noticeably larger (~10-20%) than the right. Have tried this with the sample at different orientations in the field. At some angles, such at 180 degrees, the peaks are nearly equal in intensity, but at the rest of them the left is higher. So my question is: what...	sir_manning	NMR Questions and Answers	0	02-06-2012 06:33 PM
Conformational Disorder of Membrane Peptides Investigated from Solid-State NMR Linewidths and Lineshapes. Conformational Disorder of Membrane Peptides Investigated from Solid-State NMR Linewidths and Lineshapes. Conformational Disorder of Membrane Peptides Investigated from Solid-State NMR Linewidths and Lineshapes. J Phys Chem B. 2011 Aug 1; Authors: Su Y, Hong M A challenge in the application of solid-state NMR spectroscopy to membrane proteins and peptides is the relatively broad linewidths compared to solution NMR spectra. To understand the linewidth contributions to membrane protein spectra, we have measured the inhomogeneous and homogeneous...	nmrlearner	Journal club	0	08-03-2011 12:00 PM
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations Abstract We present a novel structure determination approach that exploits the global orientational restraints from RDCs to resolve ambiguous NOE assignments. Unlike traditional approaches that bootstrap the initial fold from ambiguous NOE assignments, we start by using RDCs to compute accurate secondary structure element (SSE) backbones at the beginning of structure calculation. Our structure determination package, called rdc-Panda (RDC-based SSE PAcking with...	nmrlearner	Journal club	0	01-09-2011 12:46 PM
[NMR paper] Low temperature solid-state NMR experiments of half-integer quadrupolar nuclides: cav Low temperature solid-state NMR experiments of half-integer quadrupolar nuclides: caveats and data analysis. Related Articles Low temperature solid-state NMR experiments of half-integer quadrupolar nuclides: caveats and data analysis. J Magn Reson. 2004 May;168(1):66-74 Authors: Lipton AS, Heck RW, Sears JA, Ellis PD Solid-state NMR spectroscopy of half-integer quadrupolar nuclides has received a lot of interest recently with the advent of new methodologies and higher magnetic fields. We present here the extension of our previous low...	nmrlearner	Journal club	0	11-24-2010 09:51 PM
[NMR paper] Soft-pulsed aluminum-27 quadrupolar central transition NMR studies of ovotransferrin Soft-pulsed aluminum-27 quadrupolar central transition NMR studies of ovotransferrin http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Soft-pulsed aluminum-27 quadrupolar central transition NMR studies of ovotransferrin J Magn Reson. 1997 Dec;129(2):111-4 Authors: Aramini JM, Germann MW, Vogel HJ We have employed soft (Gaussian) pulses to examine 27Al NMR signals arising from Al3+ bound to ovotransferrin. In addition to enhancing the general detectability of 27Al...	nmrlearner	Journal club	0	08-22-2010 05:08 PM
[NMR paper] 2H NMR lineshapes of immobilized uniaxially oriented membrane proteins. 2H NMR lineshapes of immobilized uniaxially oriented membrane proteins. Related Articles 2H NMR lineshapes of immobilized uniaxially oriented membrane proteins. Solid State Nucl Magn Reson. 1993 Apr;2(1-2):21-36 Authors: Ulrich AS, Watts A As a method for the structure determination of integral membrane proteins or other large macromolecular complexes, a solid state 2H NMR approach is presented, capable of measuring the orientations of individual chemical bond vectors. In an immobilized uniaxially oriented sample, the bond angle of a...	nmrlearner	Journal club	0	08-21-2010 11:53 PM
[U. of Ottawa NMR Facility Blog] Solid State NMR of Half Integer Quadrupolar Nuclei Solid State NMR of Half Integer Quadrupolar Nuclei Many students who do liquid state NMR or solid state NMR of spin I=1/2 nuclei have very little appreciation for the information content and complexity of the solid state NMR spectra of spin I = n/2 quadrupolar nuclei (n= 3, 5, 7....). In part, I think this may be due to the mathematics involved with explaining the important effects. With this post, I attempt to describe the NMR spectrum of an I = 5/2 nucleus in the soild state without resorting to mathematics. I hope that this post helps to boost the understanding and appreciation for the...	nmrlearner	News from NMR blogs	0	08-21-2010 08:15 PM

« Previous Thread | Next Thread »

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