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LEZIONE 2
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LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Mar 26, 2015

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Jocelyn Coyle

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Page 1: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

LEZIONE 2

Page 2: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Different Isotopes Absorb at Different Frequencies

low frequency high frequency

15N 2H 13C 19F 1H

50 MHz 77 MHz 125 MHz 200 MHz 470 MHz 500 MHz

31P

Page 3: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Resonance Frequencies Depends on Magnetic Field

low field high field

1H

200 MHz 400 MHz 600 MHz 700 MHz 800 MHz 950 MHz

1H 1H 1H 1H 1H

Page 4: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Rapporto giromagneticoE= ħ m B E= ħ B

La separazione in energia dipende dal valore del rapporto giromagnetico

Page 5: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

La frequenza di precessione di un determinato nucleo ad un determinato campo magnetico è detta FREQUENZA DI PRECESSIONE DI LARMOR

Frequenza di precessione

0 = - B0 /2π

Se cosi fosse, ogni nucleo attivo entrerebbe in risonanza con il campo esterno alla sua frequenza e tutti gli isotopi uguali si comporterebbero allo stesso modo (un unico segnale).

Es: al campo magnetico di 11.7 T, La FREQUENZA DI PRECESSIONE DI LARMOR del nuclide 1H è 500 MHz.

Page 6: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

La costante di schermo

Dipende dall’intorno elettronico

Page 7: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Campi magnetici elevati determinano un aumento della risoluzione e della sensibilità

Page 8: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Chemical shift

refrefppm

Es: 1= 500.131 MHz 0=500.13 MHz1-0=1000 Hz

= 1000/500.13x106

(ppm)= 2.0

Page 9: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

TMS (Tetramethylsilane)

chemical shift

Page 10: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Spettro 1H NMR di Vanillina

Page 11: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

750 MHz 1H NMR Spettro di Tyrosine Kinase

Page 12: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

1H NMR Spettro di vari solventi

Page 13: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

13C NMR del Fullerene (C60)

Page 14: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

1H Chemical Shift Table

tot= local + magn+ rc + el + solv

Pople, 1960

Page 15: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Fattori che influenzano il chemical shift

Caratteristiche funzionaliEffetti induttiviEffetti mesomeri

Effetti attraverso lo spazioEffetti paramagnetici

Page 16: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Effetti induttivi

Page 17: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Effetto della Sostituzione sul Chemical Shift

CHCl3 CH2Cl2 CH3Cl 7.26 5.32 3.05 ppm

-CH2-Br -CH2-CH2Br -CH2-CH2CH2Br 3.30 1.69 1.25 ppm

Page 18: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Shoolery Equation

Il chemical shift dipende dalla sommatoria degli effetti di tutti I sostituenti

Page 19: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Effetti Mesomeri

Page 20: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Competizione traeffetto mesomero ed effetto induttivo

3.74

3.93

Page 21: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Fattori che influenzano il chemical shift

Caratteristiche funzionaliEffetti attraverso lo spazioCorrenti d’anello Anisotropia magneticaEffetti sterici

Effetti paramagnetici= el +anis+st

Page 22: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Correnti d’anello

Page 23: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Correnti d’anello

Modelling 1H NMR Spectra of Organic Compounds: Theory, Applications and NMR prediction Software  Di Raymond Abraham,Mehdi Mobli

Pople -Dipole model

Page 24: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

0.42

Page 25: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Anisotropia di schermo indotta dai legami chimici

Page 26: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Anisotropia

Page 27: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Equazione di Mc Connell

C-H 90

C-C 140

C≡C -340

x 1036 m-3mol-1

=

= cosR

(Heq-Hax)= ca. 0.50 ppm

Page 28: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

NMR in macromolecole NMR in macromolecole biologichebiologiche

Page 29: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Legami a idrogeno

CH3OH

5.34 ppm

CH3OHDiluito in CDCl3

1.1 ppm

C6H5OH C6H5OHDiluito in CDCl3

7.45 ppm 4.60 ppm

12.1 ppm

Page 30: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Water

Benzene(d6) 0.5

CCl4 1.1

CDCl3 1.5

THF 2.5

Ac(d6) 2.8

DMSO 3.3

H2O 4.7

EtOD 5.3

Pyr(d5) 5.0

Solvent Shift (ppm)

Page 31: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

pH dipendenza

Page 32: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Catena polipeptidica

Page 33: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

CH3

HH

H(helices)H(sheets)

H2O

aromatic

NH sidechains

NH backbone

Page 34: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

The amount of shielding the nucleus experiences will vary with the density of the surrounding electron cloud If a 1H nucleus is bound to a more electronegative atome.g. N or O as opposed to C, the density of the electron cloud will be lower and it will be less shielded or “deshielded”. These considerations extend beyond what is directly bonded to the H atom as well.

Simple shielding effects--electronegativity

N

H

C

H

more electronwithdrawing--less shielded

less electronwithdrawing--more shielded

Page 35: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

less shielded higher resonance frequency

more shielded lower resonance frequency

amides (HN) aliphatic/alpha/beta etc.(HC)

most HN nuclei come between 6-11 ppm while mostHC nuclei come between -1 and 6 ppm.

Simple shielding effects-electronegativity

Page 36: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

One consequence of these effects is that aromatic protons, which are attached to aromatic rings, are deshielded relative to other HC protons. In fact, aromatic ring protons overlap with the amide (HN) region.

aromatic region (6-8 ppm)

amide region (7-10 ppm)

More complex shielding effects:Aromatic protons

Questo lo hai già visto nella descrizione delle molecole organiche

Page 37: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Example: shielding by aromatic side chains in folded proteins

Picture shows the side chain packing in the hydrophobic core of a protein--the side chains are packed in a very specific manner, somewhat like a jigsaw puzzle

a consequence of this packing is that some protons may be positioned within the shielding cone of an aromatic ring such as Phe 51. Such protons will exhibit unusually low resonance frequencies (see picture at left). Note that such effects depend upon precise positioning of side chains within folded proteins

++

shielded methylgroup

methyl regionof protein spectrum

Page 38: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.
Page 39: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Amino acid structures and chemical shifts

note: the shifts are somewhat different from theprevious page because they are measured on the free aminoacids, not on amino acids within peptides

Page 40: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

It should now be apparent to you that different types of proton ina protein will resonate at different frequencies based on simple chemical considerations. For instance, H protons will resonate in a region centered around the relatively high shift of 4.4 ppm, based on the fact that they are adjacent to a carbonyl and an amine group, both of which withdraw electron density. But not all H protons resonate at 4.4 ppm: They are dispersed as low as ~3 and as high as ~5.5. Why?

“H region”

“Average” or “random coil” chemical shifts in proteins

Page 41: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

“Average” or “random coil” chemical shifts in proteins

One reason for this dispersion is that the side chains of the 20 aminoacids are different, and these differences will have some effect on the H shift.

The table at right shows “typical” values observed for different protons in the 20 amino acids. These were measured in unstructured peptides to mimic the environment experienced by the proton averaged over essentially all possible conformations. These are sometimes called “random coil” shift values.

Note that the Hshifts range from ~4-4.8, but Hshifts in proteins range from ~3 to 5.5. So this cannot entirely explain the observed dispersion.

Page 42: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Regions of the 1H NMR Spectrumare Further Dispersed by the 3D Fold

What would the unfolded protein look like?

Regions of the 1H NMR Spectrum are Further Dispersed by the 3D Fold

Page 43: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

A simple reason for the increased shift dispersion is that the environment experienced by 1H nuclei in a folded protein (B) is not the same as in a unfolded, extended protein or “random coil” (A).

shift of particular proton in folded protein influenced by groups nearby in space, conformation of the backbone, etc. Not averaged among many structures because there is only one folded structure.

So, some protons in folded proteins will experience very particular environments and will stray far from the average.

shift of particular proton in unfolded protein is averaged over many fluctuating structures

will be nearrandom coilvalue

“Average” or “random coil” chemical shifts in proteins

Page 44: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

poorlydispersed amides

poorlydispersed aromatics

poorlydispersed alphas

poorlydispersed methyls

very shielded methyl

unfoldedubiquitin

foldedubiquitin

You can tell if your protein is folded or not by looking at the 1D spectrum...

Page 45: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.
Page 46: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.
Page 47: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

What specifically to look for in a nicely folded protein

noticearomatic/amideprotons withshifts above 9and below 7

notice alpha protonswith shifts above 5

notice all these methyl peaks withchemical shifts around zero or evennegative

Page 48: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Linewidths in 1D spectra: aggregation andconformational flexibility

Linewidths get broader with larger particle size, due to faster transverse relaxation rates. We’ll learn the physical basis for the faster relaxation later. Broader than expected linewidths can indicate that the protein is aggregated. It can also indicate that the protein has conformational flexibility, i.e. that its structure is fluctuating between several slightly different forms. We’ll learn why this is when we cover the effect of protein dynamics on NMR spectra. Conformational flexibility also tends to reduce dispersion by averaging the environment experienced by a nucleus.

Page 49: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

An example of analyzing linewidths and dispersion:

Hill & DeGrado used measurements of chemical shift dispersion and line broadening in the methyl region of 1D spectra to gauge the effect of mutations at position 7 on the conformational flexibility of 2D protein

leucine and valine mutants have poordispersion and broad lines, despite being very stably foldedand not aggregated (circular dichroism and analytical ultra- centrifugation measurements). These mutants are folded but flexible.

Hill & DeGrado (2000) Structure 8: 471-9.

Page 50: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

13C NMR

The rules discussed for 1H spins, (shielding and deshielding effects) hold also for 13C spins. Some general features of 13C should be pointed out:

Unlike 1H atoms, 13C atoms may form a different number and type of chemical bonds. Therefore, the so called paramagnetic contributions (see later) are much more effective for deshielding. The chemical shift range of 13C spins spans more than 200 ppm

Page 51: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Range of observed shifts for 13C

Page 52: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

A protein 13C NMR spectrum (low resolution)

Backbone CO and side chain COO- signals

Aromatic signals

Aliphatic

Page 53: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

13C NMR

The rules discussed for 1H spins, (shielding and deshielding effects) hold also for 13C spins. Some general features of 13C should be pointed out:

The amino acid dependence of chemical shift values is stronger for 13C atoms than in 1H atoms. Therefore, each amino acid has an almost unique

pattern of 13C chemical shifts

Page 54: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

13C chemical shifts are residue-specific

Page 55: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

13C NMR and Secondary Structure

The chemical shift from secondary structure can be used to get the secondary structure arrangement directly from 13C shifts of Ca, Cb and C’ spins

Page 56: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Fig. 1. Simulated 13C   chemical-shift distribution of

(a) Ala and (b) Met. (•) Strand; (   ) coil; (

 

) helix.

http://www.proteinscience.org/content/vol11/issue4/images/large/45016-14f1_F1TT.jpeg
Page 57: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

13C

Page 58: LEZIONE 2. Different Isotopes Absorb at Different Frequencies low frequencyhigh frequency 15 N 2H2H 13 C 19 F 1H1H 50 MHz 77 MHz 125 MHz 200 MHz 470 MHz.

Use of chemical shifts as source of structural information

•CSI

•Molecular fragement replacement (3 to 9 aa)

BMRB – Biological Magnetic Resonance Bank

A Repository for Data from NMR Spectroscopy on Proteins, Peptides,

Nucleic Acids, and other Biomolecules

http://www.bmrb.wisc.edu/

BMRB – Biological Magnetic Resonance Bank

A Repository for Data from NMR Spectroscopy on Proteins, Peptides,

Nucleic Acids, and other Biomolecules

http://www.bmrb.wisc.edu/


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