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

Go Back   BioNMR > Educational resources > NMR Questions and Answers
Advanced Search



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 12-24-2005, 12:14 PM
Junior Member
 
Join Date: Dec 2005
Posts: 1
Points: 12, Level: 1
Points: 12, Level: 1 Points: 12, Level: 1 Points: 12, Level: 1
Level up: 23%, 38 Points needed
Level up: 23% Level up: 23% Level up: 23%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 12
Downloads: 0
Uploads: 0
Default Answered: How do you use NMR to tell the conformation of a molecule?

I'm looking at an NMR and its chemical shifts and J-coupling values and I need some help on using J-coupling to tell conformation. Anyone have some tips, pointers, anything?nemeczek, thankyou for your answer. I am aware of the karplus equation and finding the dihedral angle. I'm not entirely sure what to do with that information though. Can you give me a few pointers?Ensur, thankyou for trying to help. I know what my compound is supposed to be and I know the basics of reading NMR. I'm working on 1H NMR by the way. I need to know how the dihedral angle tells you the specific conformation though.
Reply With Quote


1 out of 1 members found this post helpful. Did you find this post helpful? Yes | No
Best Answer - Posted by nemeczek
Find the Karplus curve which describes the dependence of J on the value of the H-C-C-H dihedral angle.First of all, you need to be sure that the rate of interconvertion between the conformations is slow at the NMR time scale. If it is too fast, you will observe the average conformation by NMR. It can still provide you some information as to the population distribution between the conformations, though.If your molecule contains a six- or five-membered ring, the dihedral angle between H(axial)-C-C-H(axial) is obviously different than for its equatorial-equatorial counterpart. It would manifest itself in a different value of J.

  #2  
Unread 12-24-2005, 12:14 PM
Junior Member
 
Join Date: Dec 2005
Posts: 1
Points: 2, Level: 1
Points: 2, Level: 1 Points: 2, Level: 1 Points: 2, Level: 1
Level up: 3%, 48 Points needed
Level up: 3% Level up: 3% Level up: 3%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 2
Downloads: 0
Uploads: 0
Provided Answers: 1
Default How do you use NMR to tell the conformation of a molecule?

Find the Karplus curve which describes the dependence of J on the value of the H-C-C-H dihedral angle.First of all, you need to be sure that the rate of interconvertion between the conformations is slow at the NMR time scale. If it is too fast, you will observe the average conformation by NMR. It can still provide you some information as to the population distribution between the conformations, though.If your molecule contains a six- or five-membered ring, the dihedral angle between H(axial)-C-C-H(axial) is obviously different than for its equatorial-equatorial counterpart. It would manifest itself in a different value of J.
Reply With Quote


Did you find this post helpful? Yes | No
  #3  
Unread 12-24-2005, 09:26 PM
Junior Member
 
Join Date: Dec 2005
Posts: 1
Points: 2, Level: 1
Points: 2, Level: 1 Points: 2, Level: 1 Points: 2, Level: 1
Level up: 3%, 48 Points needed
Level up: 3% Level up: 3% Level up: 3%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 2
Downloads: 0
Uploads: 0
Default How do you use NMR to tell the conformation of a molecule?

Which NMR are you looking at? C13 or H1?I'm most familiar with H1. What I do is just read each signal at a time. First, if I'm given the compund, I'll calculate the index of hydrogen deficiency to tell me if I have any crazy double or triple bonds or aromatic compounds.Then I'll count how many unique signals I have. And then I'll take it one at a time. If one of the signals is a 3H doublet, I can draw a C with 3 H's on it, and a second C connected to that C, with 1 H on it since the reading is a doublet (remember coupling).I wish I could help you out with 13C but, don't quite remember it as well.As for chemical shifts, http://wwwchem.csustan.edu/Tutorials/NMRTABLE.HTM will tell you what kind of substrates produce which chemical shifts. Best thing to do is just memorize them.

Content provided by Yahoo Answers.
Reply With Quote


Did you find this post helpful? Yes | No
Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[CNS Yahoo group] How to add bond between protein residue and a small molecule in CNS
How to add bond between protein residue and a small molecule in CNS Dear All, I'm stuck in a step where in i need to connect a bond an amino acid residue and a small molecule in CNS Thank you. Joseph More...
nmrlearner News from other NMR forums 0 08-07-2011 01:35 AM
[Question from NMRWiki Q&A forum] How can I calculate a carbon-proton coupling constant for a molecule?
How can I calculate a carbon-proton coupling constant for a molecule? I'm trying to explain a missing HMBC peak, and having a coupling constant less than 10 Hz would do that nicely. It's a formamidine derivative with a 3 bond correlation N=CHNC The C is a quaternary carbon in a benzene ring. Any help would be appreciated. Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 02-04-2011 07:12 PM
[NMR paper] Identification of a novel glycosaminoglycan core-like molecule. I. 500 MHz 1H NMR ana
Identification of a novel glycosaminoglycan core-like molecule. I. 500 MHz 1H NMR analysis using a nano-NMR probe indicates the presence of a terminal alpha-GalNAc residue capping 4-methylumbelliferyl-beta-D-xylosides. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles Identification of a novel glycosaminoglycan core-like molecule. I. 500 MHz 1H NMR analysis using a nano-NMR probe indicates the presence of a terminal alpha-GalNAc residue capping...
nmrlearner Journal club 0 08-22-2010 03:41 AM
Small Molecule NMR Scientist (B.S./ M.S.) at Novartis Ag (Cambridge, MA)
Small Molecule NMR Scientist (B.S./ M.S.) at Novartis Ag (Cambridge, MA) using the state-of-the-art NMR methodologies. As an NMR scientist within the team, you will be responsible for ... in small molecular NMR with demonstrated success in modern NMR methodologies. Demonstrated skills in data collection... More...
nmrlearner Job marketplace 0 08-19-2010 02:32 AM
How can one determine quantity of an organic molecule by its NMR spectra?
quantity , as in how much? with the its NMR spectra information
9106 NMR Questions and Answers 3 08-18-2004 08:21 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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 On
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 11:44 AM.


Map