THz spectroscopy in biology

Transcription

1 Preparation of the concerned sectors for educational and R&D activities related to the Hungarian ELI project THz spectroscopy in biology Andrea Buzády 6. lecture Spectroscopy TÁMOP C-12/1/KONV projekt 1

2 Classical / quantum chemical modelling Vibrational and rotational spectra of (simple) molecules can be derived from different theoretical and empirical modelling. Quantum chemical modelling: Density Function Theory (DFT) Classic chemical modelling: Chemistry at HARvard Macromolecular Mechanics (CHARMM) glicin glicin 2

3 Classical / quantum chemical modelling Absorption peaks and related molecular motions of simple amino acid: glicin. 3

4 Amino acids peptides, proteins 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 L-valin D-valin 1.70 THz DL-valin T= 78K T=300K Terahertz spectroscopy of enantiopure and racemic polycrystalline valine Michael R. C. Williams, Alan B. True, Artur F. Izmaylov, Timothy A. French, Konstanze Schroecka and Charles A. Schmuttenmaer Phys. Chem. Chem. Phys., 2011,13,

5 Amino acids peptides, proteins Temperature dependence of L- (and D-) valine THz spectra. Varied temperature shifts the absorption peaks related to different vibration modes 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. Terahertz spectroscopy of enantiopure and racemic polycrystalline valine Michael R. C. Williams, Alan B. True, Artur F. Izmaylov, Timothy A. French, Konstanze Schroecka and Charles A. Schmuttenmaer Phys. Chem. Chem. Phys., 2011,13,

6 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 peaks feature at 2.25 THz corresponds to a single peak The 1.7 THz absorption peak does not change, the others blue-shift with increasing temperature Terahertz spectroscopy of enantiopure and racemic polycrystalline valine Michael R. C. Williams, Alan B. True, Artur F. Izmaylov, Timothy A. French, Konstanze Schroecka and Charles A. Schmuttenmaer Phys. Chem. Chem. Phys., 2011,13,

7 Amino acids peptides, proteins THz absorption spectra for the pure D- and L-tryptophan (Trp) enantiomers, their 1:1 mixture (DL-tryptophan) and F6-fluorine-substituted DL-tryptophan amino 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. R. Balu, S. K. Gregurick, E. J. Heilweil, Determination of enantiomeric composition by terahertz spectroscopy: mixtures of D- and L-tryptophan. Spectra are shifted along Y axis for better representation! 7

8 Amino acids peptides, proteins THz absorption spectra of several di- and tripeptides variability and uniqueness for each structure Longer peptide (top spectrum of a random 10-mer) showns loss of distinguishable absorption peaks, Absorbance most likely from spectral overlap or hydrated water. alanin valin Frequency (THz) Spectra are shifted along Y axis for better representation! 8

9 Amino acids peptides, proteins trialanines 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. Absorbance 2 structure of trialanine was known (X-ray crystallography). Third form discovered in this study was the dehydrated form: ap-ala 3. Frequency (THz) Applications of Terahertz Spectroscopy in Biosystems David F. Plusquellic, Karen Siegrist, Edwin J. Heilweil, and Okan Esenturk ChemPhysChem, 2007, 8,

10 Amino acids peptides, proteins A single atom difference can result in different THz absorbance More definite absorption peaks at low temperature (77 K) An oxigen (O) sulfur (S) substitution of serine cysteine results in characteristic spectrum Most relevant difference in the range of THz n e 1 single atom difference! x t Chemical Physics Letters 418 (2006) Terahertz spectroscopy of solid serine and cysteine T.M. Korter, R. Balu, M.B. Campbell, M.C. Beard, S.K. Gregurick, E.J. Heilweil Spectra are shifted along Y axis for better representation! 10

11 Amino acids peptides, proteins Low frequency range (0-100 THz) part of the absorbance spectra of L-serine and L- cysteine Most relevant difference is at 66 THz (peak of serine) Chemical Physics Letters 418 (2006) Terahertz spectroscopy of solid serine and cysteine T.M. Korter, R. Balu, M.B. Campbell, M.C. Beard, S.K. Gregurick, E.J. Heilweil Spectra are shifted along Y axis for better representation! 11

12 Amino acids peptides, proteins High alfa helical (secondary structure) content of myoglobin does not result in helix specific absorbance spectra. Absorbance Frequency (THz) 3D structure of myoglobin Multitude of amino acids in the chain results in overlapping absorption peaks, that leads to non-characteristic spectra. No peaks can be found. Applications of Terahertz Spectroscopy in Biosystems David F. Plusquellic, Karen Siegrist, Edwin J. Heilweil, and Okan Esenturk ChemPhysChem, 2007, 8,

13 Amino acids peptides, proteins A. Markelz, S. Whitmire, J. Hillebrecht, R. Birge, Phys. Med. Biol. 2002, 47, 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) 13

14 Nucleic 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 formed Further binding of 3 phosphates results in nucleic acid, like ATP, GTP, Is there any simple way to devine the spectra of a nucleic acid from the spectra of pure sacharose (ribose) and nucleobase and phosphate? NO! 14

15 Nucleic acids DNA, RNA Double stranded DNA absorption depends on humidity of air. The coiled-coil structure of DNA varies with the humidity as hydrogen bonding involving water molecules are more or less frequent under different conditions. 15

16 (poly)saccharides Protonated (H) and deuterated (D) sucrose spectra at different temperature shows varied position of absorbance peaks. Blueshift at low temperatures, then redshift after a critical temperature. 1 2 n e x t

17 (poly)saccharides Temperature induced shift of peaks Relative shift: f (T) /f (10K) -1 protonated and deuterated polycrystalline sucrose (from 10 to 300 K) Blueshift at low temperatures, then redshift after a critical temperature. 17

18 (poly)saccharides THz absorption spectra of glucose and fructose. Two simple sugar in crystal form. Typical widening of spectral peaks at high temperature. Characteristic peaks related to the different sugar molecules. M. Walther, B. M. Fischer, P. Uhd Jepsen, Chem. Phys. 2003, 288,

19 (poly)saccharides Simple sugar of sucrose in crystal form and glucose (now in amorphous powder form). Unstructured spectra of noncrystal (amorph) form sugars. M. Walther, B. M. Fischer, P. Uhd Jepsen, Chem. Phys. 2003, 288,

20 (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. 20

21 (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. 21