Experimental probes of molecular structure via EM-radiation interaction: Beer-Lambert law, NMR, IR, UV-Vis, mass spectrometry, and the selection rules derived from quantum mechanics. The empirical-grounding bridge between L2 molecular…
spectroscopy
Beer-Lambert law
Absorbance of monochromatic light through a uniform sample is proportional to path length and concentration: A = ε c ℓ. Deviates at high…
NMR spectroscopy
Nuclear magnetic resonance: nuclei with non-zero spin (¹H, ¹³C, ¹⁵N, ³¹P) in a strong magnetic field absorb RF radiation at characteristic…
Infrared spectroscopy
Vibrational spectroscopy exploiting resonant absorption of IR photons by bond-vibration modes. Functional-group fingerprints (C=O at…
UV-Vis spectroscopy
Electronic absorption spectroscopy in the ~200-800 nm range: promotes valence electrons between ground and excited states (π→π*, n→π*, d-d,…
Mass spectrometry
Analytical method that ionises molecules (EI, ESI, MALDI) and separates the ions by mass-to-charge ratio (m/z) in a mass analyser…
Spectroscopic selection rules
Quantum-mechanical constraints on which transitions between stationary states are allowed by a given radiation-matter coupling.…
Raman spectroscopy
Vibrational spectroscopy based on inelastic light scattering (Stokes / anti-Stokes shifts). Complementary to IR: Raman-active modes require…
Fluorescence
Radiative relaxation from an electronic excited state back to the ground state of the same spin multiplicity, typically on nanosecond…
J-coupling (scalar through-bond coupling)
Indirect spin–spin interaction between NMR-active nuclei mediated by the electronic structure of chemical bonds, producing multiplet…
IR vs Raman selection rules
IR active: ∂µ/∂Q ≠ 0. Raman active: ∂α/∂Q ≠ 0. Centrosymmetric mutual exclusion: IR-active ≠ Raman-active. Complementary vibrational…
EPR/ESR (electron paramagnetic resonance)
Microwave transition of unpaired-electron spin states in magnetic field. g-tensor + hyperfine → electronic structure of radicals, metal…
Circular dichroism (CD)
Differential absorbance of L/R circularly polarized light; reveals chirality + secondary structure. Far-UV protein CD (180-260 nm)…
Single-molecule spectroscopy
Fluorescence detection of individual molecules at ambient conditions (Moerner/Orrit 1989-90). smFRET, super-resolution. Betzig/Hell/Moerner…
Fourier-transform spectroscopy
Interferogram → FT gives spectrum; throughput (Jacquinot) & multiplex (Fellgett) advantages; standard for IR, NMR, MS.
2D NMR (COSY, NOESY, HSQC, HMBC)
Correlate spins via J-coupling (COSY, HSQC, HMBC) or NOE (NOESY); structure elucidation of large biomolecules.
Magic-angle spinning NMR
θ = 54.74° spinning averages out anisotropic broadening; high-res solid-state NMR; dynamic nuclear polarization boost.
Dynamic nuclear polarization (DNP)
Transfer large e⁻ Boltzmann polarization to nuclei at cryogenic T; 100× NMR signal boost; biradical polarizing agents.
EPR / ESR spectroscopy
Zeeman splitting of unpaired electrons; hyperfine coupling A; CW-EPR at X-band; pulsed DEER measures nm distances.
UV/Vis & TD-DFT electronic spectra
Beer-Lambert ε in cm⁻¹M⁻¹; TD-DFT or CASPT2 predicts excitation spectra; used for chromophore design.
Raman spectroscopy & SERS
Inelastic photon-phonon/vibrational scattering; Stokes/anti-Stokes; SERS factor 10⁶-10¹⁰ via plasmonic metals; single-molecule detection.
IR spectroscopy & functional-group identification
4000-400 cm⁻¹; group frequencies (OH 3200-3600, C=O 1700, C≡N 2250); FTIR, ATR modes; interpretation tables.
MS ionization (EI, ESI, MALDI, APCI)
EI for small molecules; soft ESI/MALDI for biomolecules; charge/m distribution reveals structure; Fenn/Tanaka 2002 Nobel.
Mass analyzers (ToF, quadrupole, Orbitrap, FT-ICR)
Resolution m/Δm 10⁴-10⁶; accurate mass ppm; TDMA ion mobility; proteomics, metabolomics workflows.
X-ray crystallography & phase problem
F_hkl = |F|e^(iφ); phase not directly measurable; MR, SAD/MAD, direct methods; protein structure determination.
Cryo-EM single-particle reconstruction
Vitrification + single-particle analysis; 2017 Nobel; resolution to 1.5 Å; challenges crystallography for large complexes.
Circular dichroism (CD)
Differential absorption of L/R circularly polarized light; probes secondary structure (α-helix, β-sheet); chirality.
Fluorescence lifetime & FRET
τ~ns; FRET E = 1/(1+(r/R₀)⁶) distance-dependent; nm-scale ruler for biomolecular interactions.