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 11-21-2013, 01:14 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,775
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 Computation of DNP coupling factors of a nitroxide radical in toluene: seamless combination of MD simulations and analytical calculations

From The DNP-NMR Blog:

Computation of DNP coupling factors of a nitroxide radical in toluene: seamless combination of MD simulations and analytical calculations


Sezer, D., Computation of DNP coupling factors of a nitroxide radical in toluene: seamless combination of MD simulations and analytical calculations. Phys. Chem. Chem. Phys., 2013. 15(2): p. 526-540.


http://dx.doi.org/10.1039/C2CP42430D


Dynamic nuclear polarization (DNP) employs paramagnetic species to increase the NMR signal of nuclear spins. In liquids, the efficiency of the effect depends on the strength of the interaction between the electron and nuclear spins and the time scales on which this interaction is modulated by the physical motion of the spin-bearing molecules. An approach to quantitatively predict the contribution of molecular motions to the DNP enhancement using molecular dynamics (MD) simulations is developed and illustrated for the nitroxide radical TEMPOL in liquid toluene. A multi-resolution strategy that combines explicit treatment of the solvent at short distances from the free radical with implicit description at large intermolecular distances is adopted. Novel analytical expressions are obtained to correct for the finite spatial extent of the MD simulations. The atomistic and analytical descriptions are sewn seamlessly together by ensuring that for molecular trajectories that start in the near (explicit) region and end in the distant (implicit) region the analytical dipolar spectral densities reproduce the MD estimates. The spectral densities obtained from the developed approach are used to calculate DNP coupling factors separately for the ring and methyl protons of toluene. The agreement with previously reported experimental DNP data at a magnetic field of 3.4 T is noteworthy and encouraging. Maximum obtainable DNP enhancements at other magnetic fields are predicted.


Go to The DNP-NMR Blog for more info.
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
DNP enhanced NMR using a high-power 94 GHz microwave source: a study of the TEMPOL radical in toluene
From The DNP-NMR Blog: DNP enhanced NMR using a high-power 94 GHz microwave source: a study of the TEMPOL radical in toluene This paper was already published in 2010 but I just came across it recently. Please let me know if there are any papers you would like to see posted here, or that I missed.
nmrlearner News from NMR blogs 0 07-26-2013 09:32 PM
Nature and Structure of Aluminum Surface Sites Grafted on Silica from a Combination of High-Field Aluminum-27 Solid-State NMR Spectroscopy and First-Principles Calculations
Nature and Structure of Aluminum Surface Sites Grafted on Silica from a Combination of High-Field Aluminum-27 Solid-State NMR Spectroscopy and First-Principles Calculations Rachel Nathaniel Kerber, Anthony Kermagoret, Emmanuel Callens, Pierre Florian, Dominique Massiot, Anne Lesage, Christophe Cope?ret, Franc?oise Delbecq, Xavier Rozanska and Philippe Sautet http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja3008566/aop/images/medium/ja-2012-008566_0006.gif Journal of the American Chemical Society DOI: 10.1021/ja3008566 ...
nmrlearner Journal club 0 04-10-2012 02:44 AM
More accurate 1JCH coupling measurement in the presence of 3JHH strong coupling in natural abundance
More accurate 1JCH coupling measurement in the presence of 3JHH strong coupling in natural abundance Publication year: 2012 Source:Journal of Magnetic Resonance, Volume 215</br> Bingwu Yu, Hugo van Ingen, Subramanian Vivekanandan, Christoph Rademacher, Scott E. Norris, Darón I. Freedberg</br> J couplings are essential for measuring RDCs (residual dipolar couplings), now routinely used to deduce molecular structure and dynamics of glycans and proteins. Accurate measurement of 1 J CH is critical for RDCs to reflect the true structure and dynamics in the molecule of...
nmrlearner Journal club 0 03-09-2012 09:16 AM
[Stan NMR blog] Books about Quantum Computation
Books about Quantum Computation Books list: A huge collection of books on Quantum Computing with links to Amazon. Source: Stan blog library
nmrlearner News from NMR blogs 0 03-05-2012 04:29 PM
Understanding the radical mechanism of lipoxygenases using 31P NMR spin trapping.
Understanding the radical mechanism of lipoxygenases using 31P NMR spin trapping. Understanding the radical mechanism of lipoxygenases using 31P NMR spin trapping. Bioorg Med Chem. 2011 May 1;19(9):3022-8 Authors: Zoia L, Perazzini R, Crestini C, Argyropoulos DS Abstract In this paper, we use our quantitative (31)P NMR spin trapping methods, already developed for simple oxygen- and carbon-centered radicals, to understand the radical intermediates generated by enzymatic systems and more specifically lipoxygenases. Our methodology...
nmrlearner Journal club 0 08-25-2011 04:10 PM
Industrial Postdoctoral Chemist( analytical, organic or polymer) | Avomeen Analytical Services
Industrial Postdoctoral Chemist( analytical, organic or polymer) | Avomeen Analytical Services US - Ann Arbor Michigan, Ph.D. in Analytical, organic or polymer chemistry. Hands-on knowledge of following techniques Analytical instrumentation is preferred: FT-IR, NMR, GC, GC-MS, LC-MS, TGA, DSC, ICP, and SEM-EDS. Must be More...
nmrlearner Job marketplace 0 12-19-2010 01:50 AM
[NMR paper] Assignment of 1H, 13C and 15N NMR signals in the toluene 4-monooxygenase effector pro
Assignment of 1H, 13C and 15N NMR signals in the toluene 4-monooxygenase effector protein. Related Articles Assignment of 1H, 13C and 15N NMR signals in the toluene 4-monooxygenase effector protein. J Biomol NMR. 2000 Apr;16(4):359-60 Authors: Hemmi H, Studts JM, Chae YK, Markley JL, Fox BG
nmrlearner Journal club 0 11-18-2010 09:15 PM
[Stan NMR blog] Books about Quantum Computation
Books about Quantum Computation BOOKS LIST: A nearly complete collection with links to Amazon. More...
nmrlearner News from NMR blogs 0 08-21-2010 06:14 PM



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 12:28 PM.


Map