andrea buzády - pte-ttk fizikai inté · pdf file · 2014-04-14andrea...
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„Preparation of the concerned sectors for educational and R&D activities related to the Hungarian ELI project ”
THz spectroscopy in biology
Andrea Buzády
6. lectureSpectroscopy
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 1
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 2
6. lecture
Spectroscopy – Biological applicationClassical / quantum chemical modelling
• Quantum chemicalmodelling: DensityFunction Theory (DFT)
• Classic chemicalmodelling: Chemistry atHARvardMacromolecularMechanics (CHARMM)
Vibrational and rotationalspectra of (simple) molecules can be derivedfrom different theoreticaland empirical modelling.
glicin
glicin
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6. lecture
Spectroscopy – Biological applicationClassical / quantum chemical modelling
Absorption peaks and related molecularmotions of simpleamino acid: glicin.
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 4
6. lecture
Spectroscopy – Biological application
Terahertz spectroscopy of enantiopure and racemic polycrystalline valineMichael R. C. Williams, Alan B. True, Artur F. Izmaylov, Timothy A. French, Konstanze Schroecka and Charles A. SchmuttenmaerPhys. Chem. Chem. Phys., 2011,13, 11719-11730
Amino acids → peptides, proteins
D-valin
L-valin
DL-valin
T= 78KT=300K• Widening of peaks at room temperature
compared to low temperature (78 K)• L and D stereisomers have similar
spectra• DL racemat mixture has different
spectrum from D and L-valin• DL-valine does not split into multiple
peaks at low temperature, although it does sharpen
1.70 THz
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 5
6. lecture
Spectroscopy – Biological application
Terahertz spectroscopy of enantiopure and racemic polycrystalline valineMichael R. C. Williams, Alan B. True, Artur F. Izmaylov, Timothy A. French, Konstanze Schroecka and Charles A. SchmuttenmaerPhys. Chem. Chem. Phys., 2011,13, 11719-11730
Amino acids → peptides, proteins
Temperature dependence of L- (and D-) valine THz spectra.Varied temperature shifts the absorptionpeaks related to different vibrationmodes in different manner.
The absorption coefficients (in cm-1) have been corrected and offset by the temperature at which the spectrum was collected (from 78 K to 298 K in steps of 20 K) for better presentation.
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 6
6. lecture
Spectroscopy – Biological application
Terahertz spectroscopy of enantiopure and racemic polycrystalline valineMichael R. C. Williams, Alan B. True, Artur F. Izmaylov, Timothy A. French, Konstanze Schroecka and Charles A. SchmuttenmaerPhys. Chem. Chem. Phys., 2011,13, 11719-11730
Amino acids → peptides, proteins
Peak points (obtained by fitting Voigt functions to each spectrum on previous slide)Overlapping features between 1.5 and 1.9 THz consisted of three peaksfeature at 2.25 THz corresponds to a single peak
The 1.7 THz absorption peak does notchange, the others blue-shift withincreasing temperature
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 7
6. lecture
Spectroscopy – Biological application
R. Balu, S. K. Gregurick, E. J. Heilweil, Determination of enantiomeric compositionby terahertz spectroscopy: mixtures of D-and L-tryptophan.
Amino acids → peptides, proteins
Spectra are shifted along Y axis for better representation!
THz absorption spectra for the pure D-and L-tryptophan (Trp) enantiomers, their 1:1 mixture (DL-tryptophan) and F6-fluorine-substituted DL-tryptophanamino acid in the solid state.• L-Trp and D-Trp stereoisomers
show identical spectra, whereas the DL-Trp mixture has a distinctly unique spectrum.
• The F6-DL-Trp also shows characteristic spectral features, different from the DL-Trp mixture.
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 8
6. lecture
Spectroscopy – Biological applicationAmino acids → peptides, proteins
Spectra are shifted along Y axis for better representation!
THz absorption spectra ofseveral di- and tripeptides
variability and uniqueness for each structureLonger peptide (top spectrum of a random 10-mer) showns loss of distinguishable absorption peaks,
most likely from spectral overlap or hydrated water.
alanin valinFrequency (THz)
Abs
orba
nce
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 9
6. lecture
Spectroscopy – Biological application
Applications of Terahertz Spectroscopy in BiosystemsDavid F. Plusquellic, Karen Siegrist, Edwin J. Heilweil, and Okan EsenturkChemPhysChem, 2007, 8, 2412 – 2431
Amino acids → peptides, proteins
Three different crystalline forms of trialanine.Although the conformational forms of the monomers are similar, the parallel and hydrated antiparallel β-sheets have different space groups (P12 and C2, respectively, the dehydrated form is unknown but likely (C2). These spectra indicate the sensitivity to the different space groups as well as the impact of the hydrogen bonded (structural) water.
2 structure of trialanine was known (X-ray crystallography). Third form discoveredin this study was the dehydrated form: ap-Ala3. Frequency (THz)
Abs
orba
nce
trialanines
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 10
6. lecture
Spectroscopy – Biological application
Chemical Physics Letters 418 (2006) 65–70Terahertz spectroscopy of solid serine and cysteineT.M. Korter, R. Balu, M.B. Campbell, M.C. Beard, S.K. Gregurick, E.J. Heilweil
Amino acids → peptides, proteinsA single atom difference can resultin different THz absorbance• More definite absorption peaks at
low temperature (77 K)• An oxigen (O) → sulfur (S)
substitution of serine → cysteineresults in characteristic spectrum
• Most relevant difference in therange of 0-100 THz
1 single atom difference!
Spectra are shifted along Y axisfor better representation!
next
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 11
6. lecture
Spectroscopy – Biological applicationAmino acids → peptides, proteins
Chemical Physics Letters 418 (2006) 65–70Terahertz spectroscopy of solid serine and cysteineT.M. Korter, R. Balu, M.B. Campbell, M.C. Beard, S.K. Gregurick, E.J. Heilweil
Spectra are shifted along Y axisfor better representation!
Low frequency range (0-100 THz) part of the absorbancespectra of L-serine and L-cysteineMost relevant difference is at 66 THz (peak of serine)
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 12
6. lecture
Spectroscopy – Biological application
Applications of Terahertz Spectroscopy in BiosystemsDavid F. Plusquellic, Karen Siegrist, Edwin J. Heilweil, and Okan EsenturkChemPhysChem, 2007, 8, 2412 – 2431
Amino acids → peptides, proteins
3D structure of myoglobinFrequency (THz)
Abs
orba
nce
High alfa helical(secondary struc-ture) content of myoglobin doesnot result in helixspecific absorban-ce spectra.
Multitude of amino acids in the chain results in overlapping absorption peaks, that leads to non-characteristic spectra. No peaks can be found.
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6. lecture
Spectroscopy – Biological applicationAmino acids → peptides, proteins
A. Markelz, S. Whitmire, J. Hillebrecht, R. Birge, Phys. Med. Biol. 2002, 47, 3797.
• Longer amino acid chain → more vibration• More collective vibration → more crowding and
overlapping in the spectrum• Result: non-characteristic, featureless spectra
linearly increasing absorbance at low THz range(0-2 THz)
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 14
6. lecture
Spectroscopy – Biological applicationNucleic acids → DNA, RNA
Nucleic acids consist of one nucleobase from 5 possible (A,G,T,C,U)Nucleobase binds either to ribose or deoxyribose, in case of RNA or DNA, respectively → (deoxy)ribonucleoside is formedFurther binding of 3 phosphates results in nucleic acid, like ATP, GTP, …
Is there any simpleway to devine thespectra of a nucleicacid from thespectra of puresacharose (ribose) and nucleobaseand phosphate? NO!
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6. lecture
Spectroscopy – Biological applicationNucleic acids → DNA, RNA
Double stranded DNA absorption depends onhumidity of air.The coiled-coil structureof DNA varies with thehumidity as hydrogenbonding involving watermolecules are more orless frequent underdifferent conditions.
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6. lecture
Spectroscopy – Biological application(poly)saccharides
1
1
2
2
Protonated (H) and deuterated (D) sucrose spectra at differenttemperature shows varied positionof absorbance peaks.
Blueshift at low temperatures, then redshift after a critical temperature.
next
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6. lecture
Spectroscopy – Biological application(poly)saccharides
Temperature induced shift of peaksRelative shift:
protonated and deuteratedpolycrystalline sucrose(from 10 to 300 K)
f(T)/f(10K)-1
Blueshift at low temperatures, then redshift after a critical temperature.
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 18
6. lecture
Spectroscopy – Biological application(poly)saccharides
M. Walther, B. M. Fischer, P. Uhd Jepsen, Chem. Phys. 2003, 288, 261.
THz absorption spectra of glucose and fructose.
Two simple sugar incrystal form.
Typical widening of spectral peaks athigh temperature.
Characteristicpeaks related to thedifferent sugarmolecules.
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6. lecture
Spectroscopy – Biological application(poly)saccharides
M. Walther, B. M. Fischer, P. Uhd Jepsen, Chem. Phys. 2003, 288, 261.
Simple sugar of sucrose in crystalform and glucose(now in amorphouspowder form).
Unstructuredspectra of non-crystal (amorph) form sugars.
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6. lecture
Spectroscopy – Biological application(poly)saccharides
P.C. Upadhya, Y. C. Shen, A. G. Davies, E. H. Linfield, Vib. Spectrosc. 2004, 35, 139.
The THz spectra of (a) D-glucose, (b) D-mannose, (c) D-galactose and (d) D-fructose• Widening of peaks at high temperature
compared to peaks at low temperature (4 K)• At high temperature some specific peaks
present at low temperature disappear.
Measured at 4 and 295 K. The spectra at 4 K are vertically offset for clarity.
TÁMOP-4.1.1.C-12/1/KONV-2012-0005 projekt 21
6. lecture
Spectroscopy – Biological application(poly)saccharides
P.C. Upadhya, Y. C. Shen, A. G. Davies, E. H. Linfield, Vib. Spectrosc. 2004, 35, 139.
THz absorption spectra of (a) maltose and (b) lactose.
The spectra at 4 K are vertically offset for clarity.