A brief interlude into
spectroscopy &
microscopy
Interaction of rays with matter
Absorb (certain
wave lengths?)
After we hit matter with rays, we
Scatter
Matter (electrons, could - collect the remaining
Visible light,
atoms, molecules,
Xrays, UV rays
molecular Move electrons radiation, photograph the
etc.
arrangements) to other levels material, use lenses to magnify,
Eject electrons pick up the scattered bits,
(ionize) measure the intensity of
Make molecule emission/absorption spectra etc.
rotate/vibrate
The interaction of light, x-rays, IR rays etc. with matter form the
basis of several diagnostic and design tools we use today
Remember Rutherford’s experiment!
Alpha particles bombardment of a very thin gold foil helped us eliminate the “plum
pudding” model of the atom! (& propose the dense nucleus version)
Spectroscopy & Microscopy
• Spectroscopy and microscopy are powerful analytical techniques that can reveal
structures and properties of matter at the atomic and molecular scale.
• These complementary methods (spatial imaging vs energy transfer) enable
scientists to gain unprecedented insights into the nature of the physical world.
• The basis of the experimental techniques is that materials absorb/emit/scatter rays
in different ways due to the differences in their structure
• These techniques have helped us understand the structure of matter at the simplest
level on the one hand, and design very complex materials with well-tuned properties
on the other.
NaCl under a microscope XRD spectrum of NaCl
Absorption Spectroscopy
• Measures the amount of light absorbed by a sample at specific wavelengths.
• By analyzing the absorption spectrum, scientists can identify the chemical composition and structure of the
sample.
An element’s absorption spectrum is its fingerprint (or barcode!). For e.g., in the visible range,
hydrogen atoms absorb light with wavelengths of 410 nm (violet), 434 nm (blue), 486 nm (blue-
green), and 656 nm (red). Each of the absorption lines corresponds to a specific electron jump.
Helium on the other hand 388.8, 447.1, 471.3, 492.1, 501.5, 504.7, 587.5, 667.8, 686.7, 706.5,
728.1 and 781.3 nanometres (nm).
Why do only certain wavelengths
of light get absorbed? How can
we use these chemical signatures
to understand the world?
Absorption and emission spectra in
astronomy
Such analyses have been key in understanding and identifying elemental compositions (of stars, for e.g.)
https://webbtelescope.org/contents/media/images/01F8GF9E8WXYS168WRPPK9YHEY
Absorption
Spectra: Images or
Plots?
• Both of these are from the sun!
• (K and H = Calcium, D = Sodium, E = Iron, C
and F =Hydrogen, and A and B = Molecular
Oxygen)
?? How do we obtain the sun’s absorption spectrum?
The
electromagnetic
spectrum
The different wavelengths of the
various rays in the spectrum help us
probe at different (small) length
scales!
On to X-rays!
From wikipedia
The
electromagnetic
spectrum
The different wavelengths of the
various rays in the spectrum help us
probe at different (small) length
scales because of underlying
different mechanisms!
On to X-rays!
From wikipedia
X-ray spectroscopy
Probing the Atomic Diffraction and Wide-Ranging
Structure Scattering Applications
X-ray spectroscopy utilizes high- When X-rays interact with the X-ray spectroscopic techniques
energy X-rays to investigate the atoms in a sample, they can be have diverse applications in
atomic composition and diffracted and scattered, materials science, chemistry,
electronic structure of materials creating unique diffraction physics, and biology, enabling
at the nanoscale level, revealing patterns that provide detailed researchers to study everything
vital insights about their information about the atomic from the composition of
physical & chemical properties. arrangement and crystal geological samples to the
structure. structure of proteins.
• Structure factor is a more formal way to know conditions of diffraction
• There are some allowed/forbidden planes of diffraction
• Relative peak intensities can help identify phase fractions
• Several factors:
• Atom identity
• Planes indices, multiplicity factor (equivalent {hkl} planes
• Temperature
• Crystallite size, defects (peak broadening)
A famous XRD image
The double helix
structure
Dimensions (3-
6nm) within helix
Location of
various groups
Photo 51 (an XRD image), taken in Rosalind Franklin’s lab in King’s College London, was
key in providing a validation for the double helix model proposed for DNA.
Watson & Crick’s Nature article is a great read:
https://www.nature.com/scitable/content/Molecular-Structure-of-Nucleic-Acids-16331/
FTIR
• IR rays cause bonds to stretch and vibrate. These
interactions produce spectra, which are characteristic of the
nature of bonds. We can use this knowledge to identify
bonds present in a molecule, based on its IR absorption
spectrum.
C-H stretch 3000-2850 cm-1
C-H bend 1470-1450 cm-1
C-H rock 1370-1350 cm-1
C-C stretch 1300-800 cm-1
O–H stretch, hydrogen bonded 3500-3200 cm-1
C–O stretch 1260-1050 cm-1 (s)
??
Spectra from nist.gov
Principles of Microscopy
Light and Contrast Optical Lenses Illumination
Resolution Enhancement and Imaging
Microscopes use Microscopy employ Key components of a Properly illuminating
light or other forms various methods to microscope are the sample is essential
of radiation to enhance contrast objective lens, which for microscopy,
magnify & visualize between different magnifies the whether it's
small objects that are structures or sample, and the transmitted light,
otherwise invisible to components within a eyepiece lens, which reflected light, or
the naked eye. The sample, making them further enlarges the specialized
resolution, or ability more easily image for viewing. techniques. Choice
to distinguish fine distinguishable. This Careful lens design is of illumination source
details, depends on includes staining, crucial for achieving and imaging method
the wavelength of phase contrast, & high-quality, depends on the
the radiation. differential aberration-free sample & desired
interference images. information.
contrast.
Microscopes give us stunning images!
Hibiscus pollen on a needle Fetal cat cross-section Nervous system of young sea star
Skilled microscopy work has been key in unravelling structures, three-dimensional
arrangements, etc. with increasing resolution
From: https://www.olympus-lifescience.com/
Optical (light) microscope vs SEM
• Optical microscopes are
• easy to use
• Require less work on sample prep
• Provide images in natural colour
• 1500x magnification & few 100 nm
resolution (Rayleigh limit)
• Scanning electron microscopes are
• Large, need to operate in vacuum
• Provide only greyscale images
• 100000x magnification & 1nm
resolution!
While SEM can focus over depth, the electrons can also
thermofisher.com
destroy some samples!
SEM image
New vistas
Improved analysis of experimental
AI/ML Tools spectra using ML algorithms
(increase efficiency, reduce errors,
get finer details, structure-property
relationships, prediction of spectra)
Enhance quality of microscopy
images using DS techniques
(increase clarity, reduce errors,
Theoretical
Experiments enhance inferences extracted from
Modeling data, include data analysis within
experiment)
Some references
Unruh et al., “Theory+AI/ML for microscopy and spectroscopy: Challenges and opportunities,”
MRS Bulletin, Vol. 47, 2022
Larsen et al., “Reconstructing the exit wave of 2D materials in high-resolution transmission electron
microscopy using machine learning,” Ultramicroscopy, Vol. 243, 2023
Qi et al., “Recent Progresses in Machine Learning Assisted Raman Spectroscopy,” Advanced
Optical Materials, Vol. 11, 2023
Haan et al., “Resolution enhancement in scanning electron microscopy using deep learning,”
Nature (Scientific Reports), Vol. 9, 2019
Yan et al., “FRDA: Fingerprint Region based Data Augmentation using explainable AI for FTIR
based microplastics classification,” Science of the total environment, Vol. 896, 2023
Several sources on web (as mentioned in the slides)
Remarks
We discussed absorption spectra (visible and IR) and also X-ray diffraction spectra
In microscopy we examined optical and electron microscopies
From elemental composition of stars to the presence of C-O bonds in a sample, these
diagnostic techniques allow us to understand matter
All the techniques require very sophisticated instruments and expertimental
expertise.
However, the role of Data Science, ML & AI in improving the way we use each of these
tools is now very important
