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Raman Spectroscopy and its Application in
Biology
Chandrabhas Narayana Chemistry and Physics of Materials
Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India
[email protected] http://www.jncasr.ac.in/cbhas
Lecture for TSU Seminar, February 19, 2013
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Light Scattering Laboratory
Study of
Physical
Properties of
Material
Raman
Spectroscopy
Brillouin
Spectroscopy
X-rays from
Synchrotron
Source
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Light Scattering Laboratory
• Elastic/acoustic properties of Nano systems (Nanotubes, Graphene) and bulk systems (pyrochlore, topological insulators, Li-Plastics Battery)
• Vibrational properties of Graphenes, Fast Ionic conductors, multiferroics, Metal Organic Framework solids, Molecular Solids etc.
• Ultra high pressure studies (both vibrational and structural) of ionic conductors, semiconductors, molecular solids such as Hydrogen, Silane, binary nitrides, Aluminium, multiferroics.
• Drug-Protein interactions, diagnostics using surface enhanced Raman spectroscopy
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What happens when light falls on a material?
Transmission
Reflection
Absorption
Luminescence
Elastic Scattering
Inelastic Scattering
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Why are Sky and Sea Blue? CASR
Why is this water not Blue? CASR
Why is some parts of the water in swimming pool Blue/not Blue?
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Vibrations in Molecules
HCl HF
H2O
NH3
SF6
Sym. Stretching
Asym. Stretching Sym. Bending
Asym. Bending
n1 = 3835 cm-1 n2 = 1648 cm-1 n3 = 3939 cm-1
n = 2991 cm-1 n = 4139 cm-1
n1 = 3505.7 cm-1 n2 = 1022 cm-1 n3 = 3573.1 cm-1
n1 = 774.55 cm-1 n4 = 523.56 cm-1 n3 = 947.98 cm-1
n5 = 643.35 cm-1 n6 = 348.08 cm-1 n2 = 615.02 cm-1
n4 = 1689.7 cm-1
8086 cm-1 = 1 eV
Room Temp = 25 meV
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Classical Picture of Raman
Stokes Raman Anti-Stokes Raman
Induced Polarization Polarizability
Taylor Series Expansion
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Energy diagram and
Quantum picture
Vibrational states Electronic states
Virtual states
g
ex
photon
<eg,p2|Her|p2,eb> <eb,p2|Hep|p1,ea> <ea,p1|Her|p1,eg>
|Es-Eb|x|Ei-Ea| S a,b
Raman cross section
If Ei = Ea or Es = Eb
We have Resonance Raman effect
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Raman spectra of CCl4
Sym. Stretching
asym. Stretching asym. Bending
Sym. Bending
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Raman spectra of CCl4
Isotope effect Cl has two isotopes 35Cl and 37Cl Relative abundance is 3:1
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RAMAN OF ISO-STRUCTURAL CRYSTALS
Diamond spectra is similar to the crystalline Silicon and Germanium but is shifted to higher Raman frequency because of lighter weight and bond strength.
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Raman, Fluorescence and IR
Scattering Absorption
and emission Absorption
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Problems with Raman:
a)Very Weak – for every 109 photons only 1
photon Raman
a)Resonant Raman not feasible with every sample.
b)Absorption a better process than scattering
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How do we see color? CASR
How do we see color? CASR
How do we see color?
Additive Substractive
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Plasmons in Nanoparticles CASR
Origin of
Surface Enhanced Raman Spectroscopy
• Initially – thought to be depended on Surface
Area of the rough surface
• It was shown that the scattering cross section far
exceeded the number of molecules on the rough
surface.
• It was proposed that the origin was due to
surface plasmons – hence a truly nano
phenomenon.
• Alkali and Ag the best, Au and Cu the next best,
Al, In, Pt followed by transition metals and then
bad conductors.
• Exciting wavelength, polarization, exact nature of
the nanostructure also effect the SERS
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Earlier SERS was thought to be due to creation of larger surface area
Now we understand it to orignate from the surface plasmon of the nano structures
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Surface Enhanced Raman Scattering
(SERS) Raman signal intensity gets enhanced when molecules are
adsorbed on metal nanoparticles, colloids, island films etc.
Pathways for enhancement :
Electromagnetic enhancement
Enhanced local optical fields of metallic nanostructure
Chemical enhancement
Molecule-nanostructure system provide new energy states
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Raman Spectrometers
Micro–Raman setup
US Patent No. US 8,179,525 B2 (2012), G.V. Pavan Kumar et al Current Science (2007) 93, 778.
Stage
Objective lens
Dichroic Mirror
Camera Edge filter
Focusing lens
Computer
Mono- chromator
CCD
Optical fiber
LASER
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New Nanoparticle Architecture for SERS application
Gayathri Kumari and Pavan Kumar G.V.
Gayatri Kumari and C. Narayana J. Phys. Chem. Letters 3, 1130 (2012)
G.V. Pavan Kumar et al. J. Phys. Chem. C 111, 4388 (2007)
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Gayathri Kumari
28
Ag Core – Au Shell
Nanoparticles with hot spots
100 nm 100 nm
100 nm
a) c)
b) d)
Au : Ag = 0.1 Au : Ag = 0.8
Au : Ag = 0.4
100 nm 100 nm
100 nm
a) c)
b) d)
100 nm 100 nm
100 nm
100 nm 100 nm100 nm100 nm 100 nm100 nm
100 nm
a) c)
b) d)
Au : Ag = 0.1 Au : Ag = 0.8
Au : Ag = 0.4
G.V. Pavan Kumar et al. J. Phys. Chem. C 111, 4388 (2007)
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29
SERS from Hot Spots
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1
0
5000
10000
15000
20000
25000
30000
a) Ad
Tp
Imd
ATP
Hb
Ram
an
In
ten
sit
y
Au : Ag
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1
0
100000
200000
300000
400000
500000
b)
Ra
ma
n I
nte
ns
ity
Au : Ag
Ad
ATP
TP
Imd
Hb
Ad – Adenine, TP – Thiophenol, Imd – Imidazole,
ATP – adenosine Triphosphate, Hb - Hemoglobin
G.V. Pavan Kumar et al. J. Phys. Chem. C 111, 4388 (2007)
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Gold Silica Silver Sandwich Structure
• The Silica layer between Gold and Silver can be the
buffer layer.
• The SERS enhancement was possible by controlling
the gold layer.
Triple layer nanostructure:
Shoute, L. C. T. et al Applied Spectroscopy, 2009, 63, 133
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Ag Ag
SiO2 Au
(a) (b) (c) (d)
Gold Silica Silver Sandwich Nanoparticles
Gayatri Kumari and C. Narayana J. Phys. Chem. Letters, 3, 1130 (2012)
TEM images at the different stages of formation of sandwich nanoparticles
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Gold Silica Silver Sandwich Nanoparticles
FESEM picture of Ag@SiO2@Au
Gayatri Kumari and C. Narayana J. Phys. Chem. Letters, 3, 1130 (2012)
SERS from Au-SiO2-Ag nanostructures
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SERS from Au-SiO2-Ag nanostructures
Gayatri Kumari and C. Narayana J. Phys. Chem. Letters, 3, 1130 (2012)
10-5 M of Thiophenol 10-7 M of Thiophenol
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Ag@SiO2@Au
SiO2@Au
Small Molecule Interaction with
Oncogenic Kinases, Aurora A and
Aurora B
Soumik Sidhanth, Partha P. Kundu, D. Karthikeyan, Tapas K. Kundu
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Soumik Sidhanth
Tapas Kumar Kundu
Soumik Siddhanta et al, RSC Advances (2013) in press
D. Karthigeyan et al, PNAS (USA) under Review
Dhanasekaran Karthigeyan
The relative localization of Aurora A and Aurora B in mitotic cells is shown above. The kinases play a role in cytokinesis too, where they are concentrated in the mid-body region.
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Overexpression of Aurora A by gene amplification or other means, leads to aneuploidy, which in turn leads to oncogenesis. Mitotic progression is disrupted and normal spindle orientation of chromosomes is not achieved. The cell fails to undergo cytokinesis, producing tetraploid progeny.
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Structure of Aurora A Kinase
N-Terminal
C-Terminal
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J. M. Elkins et al, Journal of Medicinal Chemistry 55, 7841-7848 (2012)
Structure of Aurora A Kinase
J. Nowakowski et al, Structure 10, 1659-1667 (2002)
Soumik Siddhanta et al, RSC Advances (2013) in press
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Structure of Aurora A Kinase
Aurora A and Aurora B are very much identical and have only 4 residues different in the catalytic part This makes it difficult to make specific Inhibitors for these molecules for these
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SERS spectra of Aurora A kinase and Aurora B kinase in presence of silver nanoparticles. λ= 632.8 nm; signal accumulation time = 30 s
Aurora A kinase Aurora B kinase
SERS of Aurora Kinase
Tyrosine Phenylanaline Amide I
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Soumik Siddhanta et al, RSC Advances (2013) in press
SERS spectra of Aurora A/Aurora B kinase (black) and denatured Aurora A/Aurora B kinase (red).
Effect of Denaturing of the Protein
Aurora A kinase Aurora B kinase
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Soumik Siddhanta et al, RSC Advances (2013) in press
Active sites of Aurora A kinase
This Aurora A-adenosine complex shows the hinge region (green), Glycine rich loop(red) and activation loop (purple).
The position of a conserved Threonine residue, Thr-288, which is phosphorylated during activation of Aurora A, is shown by a star.
Type I inhibitors bind to the ATP binding site through the formation of 1–3 hydrogen bonds to the kinase ‘‘hinge’’ residues and through hydrophobic interactions in and around the region occupied by the adenine ring of ATP.
Type II inhibitors use the ATP-binding site, and also exploit unique hydrogen bonding and hydrophobic interactions made possible by the DFG residues of the activation loop being folded away from the conformation required for phosphate group transfer
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Conclusions
• SERS can be used to validate the autodock and molecular dynamics simulations with the knowledge of the structure of the protein.
• SERS gives the interactions in the proteins in their active state, in physiological conditions.
• Thus helps in the derivatization of the small molecule for producing effective drug as well as fast screening of the potential molecules.
• With better control over molecular dynamics simulation, it opens up new avenues in the drug discoveries.
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Acknowledgements R. Dhanya Venkat Srinu Badram Soumik Sidhanth Gayathri K Partha Pratim Kundu Dr. Diptikanta Swain Dr. Gopal K Pradhan Dr. Pavan Kumar Dr. Kavitha G Dr. Md. Seikh Dr. Murugavel Dr. Navneeth Ms. Sonia Balan Dr. Nashiour Rohman Dr. Veena HG
POCE Students: Rangarajan Gayathri Nair Sruthi Vibha
Collaborators Tapas Kundu Ranga Uday V. Nagaraja Hans Agren
Funding sources: DST, DBT, JNCASR, Swedish Research Links