sd m8 lecture 01.ppt - spin dynamicsspindynamics.org/documents/sd_m4_lecture_10.pdfclassical...
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NMR (CHEM8028)
Solid-state NMR: Anisotropic interactions and how we use them
Dr Philip WilliamsonJanuary 2015
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NMR: From Molecular to Cellular Level
!
SolutionMembraneMitochondrionCell
Increasing complexity
Key proteinsLipid/proteinassemblies
Tissues Organelles
Solid State NMR Liquid NMR
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Solid-state NMR spectra
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Solid-state NMR
• Anisotropic Interactions
• What are they, what do they do (to our spectra)
• How can we manipulate them
• Oriented samples
• Magic angle spinning
• How can we exploit them
• Cross polarization
• Dipolar recoupling
• How can we use them to probe structure/dynamics (2nd
series of lectures)4
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Outline (1)
• What is anisotropy
• How does it effect NMR spectra
• What interactions give rise to anisotropic properties?
• Describing interactions: tensors
• Chemical Shielding Anisotropy
– Orientational dependence of resonance frequency
– Powder spectra
• Dipolar interactions
• Quadrupolar interactions5
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What is anisotropy
• Something whose properties depend on its orientation
e.g. stress
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How does it effect the NMR spectrum
• Each molecular orientation gives rise to a difference resonance frequency
• In powder we have the sum of all distributions
• In the liquid state these anisotropic properties are averaged on the NMR timescale 7
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Which interactions in NMR
8QDipolarCSAJCS HHHHHH
Isotropic Anisotropic
JCS HHH
DipolarCSAJCS HHHHH
CSAJCS HHHH
CSHH
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Describing interactions: tensors (1)
We are concerned with 3 flavours
• Zero rank tensors
– Physical property independent of coordinate system in which it is described (scalar, distance)
• First rank tensors
– Coordinate, depends on frame of reference (vector, has size and direction)
• Second rank tensors
– Multiple first rank tensors e.g. stress (matrix)
• Higher rank exist – but we will not be considering9
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Describing interactions: tensors (2)
Rank zero tensor Rank one tensor
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r
B0
(0,0,Bz)Isotropic chemical shift,
J-coupling
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Describing interactions: tensors (3)
• Second rank tensors
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zz
yy
xx
PAS
000000
zzzyzx
yzyyyx
xzxyxx
i j k
i
j
k
x
y
z
zz
yy
xx
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Parameterizing 2nd rank tensors
• In cartesian notation tensors defined by principle components, Axx, Ayy andAzz
• Frequently parameterized with
• This assumes
• Thus the asymmetry 0.0<η<1.0 and anisotropy can be both positive and negative 12
xxyy
zz
zzyyxx
AA
aA
AAAATra
3
333aAaAaA yyxxzz
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Chemical Shielding Anisotropy (1)
• Perturbation of the magnetic field due to interaction with surrounding electrons
• Inherently asymmetric (e.g. electron distribution surrounding carbonyl group)
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Chemical Shielding Anisotropy (2)
• We can describe the perturbation of the main field (B0), by the second rank tensor,
• The Hamiltonian which describes the interaction with the modified field is:
Which can be written in a simplified form as:
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0
00
ˆ,ˆ,ˆ
BIIIH
zzzyzx
yzyyyx
xzxyxx
kkzkykxkCSA
0ˆ BIH k
kkkCSA
0
00
BB
zzzyzx
yzyyyx
xzxyxx
S
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Chemical Shielding Anisotropy (3)
Thus the chemical shielding Hamiltonian simplifies to:
and the resonance frequency of the line is:
Thus the resonance frequency is proportional to zz in the laboratory frame.
However, is usually defined in the principle axis system (PAS) not in the lab frame (LF). Therefore, we need to transform from the PAS to LF.
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0)(ˆ BIH k
zzk
kzkCSA
0)(
12 kzz
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Transformations
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z
x
y
zz
yyxx
z
x
y
Principle Axis System
Lab Frame
• Rotation characterized by the three Euler angles (α,β,γ)
• Multiple by rotation matrix R
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Transformation matrix
Can derive a rotation matrix which bring about the rotation described above:
To determine in the laboratory frame, need to apply to the chemical shielding tensor in the principle axis system:
This can be simplified to give general Hamiltonian for CSA in lab frame of:
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cossinsinsincos
sinsincoscossincossinsincoscoscossincossinsincoscoscossinsinsincoscoscos
,,R
),,(),,( 1 RR PASLAB
kzisokCS IBH ˆ2cossin1cos32
220
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Effect on resonance position
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z
x
y
zz =3000Hz
yy=-1500Hzxx =-1500Hz
σiso = 1/3(σxx+σyy+σzz) = 0Hz
δ = σzz-σiso = 3000 Hz
= (σyy-σxx)/
kzisokCS IBH ˆ2cossin1cos32
220
/2
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Powder Patterns
• In powders we have a random distribution of molecular orientations.
• Thus the lineshape is the weighted superposition of all the different orientations:
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..sin),,,(8
1)(2
0 0
2
02 tsts
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Empirical relation between PAS and MF1) Methyl carbons axially symmetric, axis along threefold symmetry
axis
2) Ring carbons three distinct tensor elements, most shielded perpendicular to plane, least shielded bisecting C-C-C angle of ring
3) Most shielded direction:1) Perpendicular to ring in aromatic carbons2) Along C3 axis for methyl carbons3) Perpendicular to the sp2 plane for carbonyl/carboxylic acids
4) Least shielded direction:1) In the ring plane, bisecting C-C-C angle2) Perpendicular to C3 axis for methyl groups3) In the sp2 place for carbonyl/carboxylic acids
5) Intermediate shielding1) Tangential to ring for aromatic systems2) In the sp2 plane and perpendicular to the C-C bond for COOH
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Dipolar Interaction
Classical interpretation
Classical interaction energy between two magnetic (dipole) moments when both are aligned with the magnetic field:
Quantum mechanical
where:
• Symmetric second rank axially symmetric tensor.
• Again we need to rotate from the PAS to LF to obtain resonance frequency.
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B0
1
2
)cos31(14
2213
12
0
r
E
21
122121212
21312
210
ˆˆ
.ˆ.ˆ3ˆˆ4
IDI
rIrIr
IIr
HD
200010001
4 312
210
rD
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Orientation dependence of dipolar interactionHomo-nuclear Dipolar Hamiltonian: Hetero-nuclear Dipolar Hamiltonian:
22
2121
2
312
210,
ˆˆˆˆ32
)cos31(4
IIIIr
H zzIID
zzISD II
rH 21
2
312
210,
ˆˆ22
)cos31(4
dip=20 kHz
dipdip
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Quadrupolar Interaction (1)If spin>1/2, nucleus contains an electronic quadrupole moment (Q).
Electronic quadrupole moment interacts with surrounding electron cloud (electric field gradient(EFG), V).
where:
Again we can define the anisotropy and asymmetry:
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kkQ IQIHˆˆ
zz
yy
xx
VV
V
IIeQQ
000000
)12(2
zz
xxyyQ
ZZQ
VVV
IIqQeQ
)12(2
2
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Quadrupolar Interaction (2)To calculate the resonance frequency, we must transform from the PAS of the EFG to the laboratory frame.
Retaining only the “secular terms” gives the following Hamiltonian in the LF:
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)1(ˆ32cossin1cos32
222 IIIH ZQQ
Q
Orientation dependence of a single crystal of Ala-d3
Powder spectrum of Ala-d3
Q
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Exploitation of anisotropic interaction
• Oriented samples
– Single Crystal studies
– Oriented Biological Membranes
• Dynamics
– Averaging of anisotropic interaction
• Local electronic environment
– Perturbation in chemical shielding anisotropy
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Dynamics: averaging of anisotropy
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Gel Phase
Liquid Crystalline Phase
Axis of rotational averaging
Rotational diffusion: Scaling of interaction by where is the angle between axis of motional averaging and the PAS of the interaction
1cos321 2
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Oriented samples
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Cys192/193
Field (B0)
C3
C3’
Orientation
0°
90°
Necessary to introduce macroscopic alignment:1) Crystallization2) Oriented membranes3) Fibres (Silk/DNA)
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Oriented samples – ligand orientations
B0 B0
Orientation±5° Mosaic Spread±5° Orientation±5° Mosaic Spread±5°
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Protein Backbone Orientation
Opella et al. 1998
15N chemicalshielding anisotropy
15N-1H hetero-nucleardipolar coupling
Bo
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Local electronic environment
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HCl
As we shall see next week, typically these parameters are obtained under conditions of magic-angle spinning to enhance signal to noise.
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An aside: spherical tensors
• Make the calculations a lot easier to handle
• Frequently used in papers
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Sensitivity and resolution enhancement in solid-state NMR
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Resume
33QDipolarCSAJCS HHHHHH
Isotropic Anisotropic
JCS HHH
DipolarCSAJCS HHHHH
CSAJCS HHHH
CSHH
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Oriented samples
• Increase resolution by orienting interactions, therefore all spins resonate at the same frequency
• As all spins resonate with the same frequency the sensitivity of the measurements is higher
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Magic-angle spinning
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Magic Angle Spinning
Seeks to reintroduce averaging process through mechanical rotation
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Magic Angle Spinning Probehead (Doty)
Sample rotors (Varian)
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Averaging of anisotropic interactions
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Averaging of anisotropic interactions
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The Hamiltonian becomes time dependent:
We can deconvolute this into the iso- and an-isotropic contributions:
where
and
Where C1, C2, S1 and S2 relate the anisotropic interaction to magnetic field (Appendix 1).
ZCS IttH ˆ),,,()(ˆ
),,(),,,( CSAisot
0iso
)22sin()22cos()sin()cos(),,(
22
11
tStC
tStCCSA
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Analysis of MAS spectra
• All anisotropic interactions become time dependent
• To analyze spectra need to treat these time dependencies
• Several mathematical descriptions that allow us to do this
– Average Hamiltonian Treatment
– Floquet Theory
– Piece wise integration
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Slow speed spinning• Rotational echoes apparent in
fid which characterise the anisotropy of the interaction
• At lower spinning speed the intensity of the sidebands characterises the anisotropic interaction ( and )
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Herzfeld-Berger Analysis
Expression exist to calculate the intensity of sidebands for a given anisotropic interaction:
where
and
411) Herzfeld and Berger, J.Chem.Phys 73 (1980) 6021
2
0 0
2),,(sin41)( rr NFNI
)exp(),,( CSAr iNF
)2sin(2
)2sin(2
)cos()sin(),,,(
)(),,,(
22
11
tStC
tStCt
ttt
rr
rr
rr
rr
CSA
isoiso
CSAisoCSA
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CSA analysis in reality
Several programs now available that now facilitate this task:
1) Tables – Paper by Herzfeld and Berger
2) matNMR (routines for analysis of both CSA and quadrupolar interactions in bothe static and MAS spectra) http://matnmr.sourceforge.net/ (requires matlab)
3) MAS sideband analysis (Levitt group homepage) http://www.mhl.soton.ac.uk/public/Main/index.html(requires mathematica)
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Effect of off-angle MAS
• Anisotropic interaction scaled by ½(3cos2-1)
• Useful for characterizing anisotropy whilst gaining some sensitivity
• Indicates why magic angle should be carefully set!
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When does MAS not work?
• Homogeneous interactions
– e.g. Homonuclear dipolar interactions
• Heterogeneous line-broadening
– e.g. Samples with conformational heterogeneity (lyophilized solids)
• Nuclei with large quadrupolar interactions
• When samples are not ‘solid’
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Applications of MAS
• Resolution/Sensitivity Enhancement
• Low speed spinning – characterisation of anisotropy
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Isotropic chemical shifts in the protein backbone are sensitive to secondary structure
Analysis of the principle components of the chemical shielding tensor reveals that larger changes are seen in 22making it a sensitive probe of protein secondary structure.
Wei et al. 2001 JACS 123: 6118-26
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Applications of MAS
• Low speed spinning
– anisotropymobility
Amyloid precursor protein in differing lipid environments has different propensity to oligomerise. Sideband analysis reveals changes in peptide mobility
Marenchino et al. Biophysical Journal 2008 46
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Magic-angle spinning and metabolomics
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Tale of a hungry worm
4kHz MAS spectrum of C.elegans (400MHz)
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Carbohydrate metabolism
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Fatty acid metabolism
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MAS-NMR and metabolism
Spectroscopically:• Simple markers for metabolites• Observe changes in metabolite levels• Labelling possible to aid in assignment
Biologically:• Genetics of C.elegans well characterized• Large library of mutations• Development well understood• Genes linked to phenotype• Behavioral differences
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A molecular view of biological systems
Structure of high affinity ligands
Membrane proteincomplexes Regulation of
intra-cellular trafficking
Whole organisms