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  
Unread 01-16-2016, 04:41 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,185
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 Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone

From The DNP-NMR Blog:

Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone


Kucuk, S.E., T. Biktagirov, and D. Sezer, Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone. Phys Chem Chem Phys, 2015. 17(38): p. 24874-84.


http://www.ncbi.nlm.nih.gov/pubmed/26343351


A computational analysis of the Overhauser effect is reported for the proton, methyl carbon, and carbonyl carbon nuclei of liquid acetone doped with the nitroxide radical TEMPOL. A practical methodology for calculating the dynamic nuclear polarization (DNP) coupling factors by accounting for both dipole-dipole and Fermi-contact interactions is presented. The contribution to the dipolar spectral density function of nuclear spins that are not too far from TEMPOL is computed through classical molecular dynamics (MD) simulations, whereas the contribution of distant spins is included analytically. Fermi contacts are obtained by subjecting a few molecules from every MD snapshot to ab initio quantum mechanical calculations. Scalar interaction is found to be an essential part of the (13)C Overhauser DNP. While mostly detrimental to the carbonyl carbon of acetone it is predicted to result in large enhancements of the methyl carbon signal at magnetic fields of 9 T and beyond. In contrast, scalar coupling is shown to be negligible for the protons of acetone. The additional influence of proton polarization on the carbon DNP (three-spin effect) is also analyzed computationally. Its effect, however, is concluded to be practically insignificant for liquid acetone.


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
Molecular simulations for dynamic nuclear polarization in liquids: a case study of TEMPOL in acetone and DMSO
From The DNP-NMR Blog: Molecular simulations for dynamic nuclear polarization in liquids: a case study of TEMPOL in acetone and DMSO Kucuk, S.E., et al., Molecular simulations for dynamic nuclear polarization in liquids: a case study of TEMPOL in acetone and DMSO. Phys Chem Chem Phys, 2015. 17(9): p. 6618-28. http://www.ncbi.nlm.nih.gov/pubmed/25665728
nmrlearner News from NMR blogs 0 05-11-2015 09:06 PM
[NMR paper] Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations. Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations. Phys Chem Chem Phys. 2014 Jul 23; Authors: Zhu T, Zhang JZ, He X Abstract In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated...
nmrlearner Journal club 0 07-24-2014 11:56 AM
[NMR images] Proton and carbon NMR spectroscopy
http://www.southampton.ac.uk/nmr/images/capabilities_images/strych_hmbc_215.jpg 3/06/2014 10:43:59 AM GMT Proton and carbon NMR spectroscopy More...
nmrlearner NMR pictures 0 06-03-2014 10:43 AM
[NMR images] Proton and carbon NMR spectroscopy
http://www.southampton.ac.uk/nmr/images/capabilities_images/strych_hmbc_215.jpg www.southampton.ac.uk 14/02/2014 5:48:03 PM GMT Proton and carbon NMR spectroscopy More...
nmrlearner NMR pictures 0 02-14-2014 05:47 PM
Rationalizing Overhauser DNP of nitroxide radicals in water through MD simulations
From The DNP-NMR Blog: Rationalizing Overhauser DNP of nitroxide radicals in water through MD simulations Sezer, D., Rationalizing Overhauser DNP of nitroxide radicals in water through MD simulations. Phys Chem Chem Phys, 2014. 16(3): p. 1022-32. http://www.ncbi.nlm.nih.gov/pubmed/24284869
nmrlearner News from NMR blogs 0 01-31-2014 06:44 PM
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
nmrlearner News from NMR blogs 0 11-21-2013 01:14 AM
[NMR paper] Enzyme Active Site Interactions by Raman/FTIR, NMR, and Ab Initio Calculations.
Enzyme Active Site Interactions by Raman/FTIR, NMR, and Ab Initio Calculations. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Enzyme Active Site Interactions by Raman/FTIR, NMR, and Ab Initio Calculations. Adv Protein Chem Struct Biol. 2013;93:153-82 Authors: Deng H Abstract Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and...
nmrlearner Journal club 0 09-11-2013 09:15 PM
[NMR paper] Ab initio NMR chemical-shift calculations based on the combined fragmentation method.
Ab initio NMR chemical-shift calculations based on the combined fragmentation method. Related Articles Ab initio NMR chemical-shift calculations based on the combined fragmentation method. Phys Chem Chem Phys. 2013 Apr 12; Authors: Tan HJ, Bettens RP Abstract NMR chemical shift is a molecular property that can be computed from first principles. In this work we show that by utilizing our combined fragmentation method (CFM), one is able to accurately compute this property for small proteins. Without nonbonded interactions, the root mean...
nmrlearner Journal club 0 04-16-2013 07:46 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 08:27 AM.


Map