Organic Chemical Analysis (of organic compounds)

How to Find Identity! Melting point (or boiling point) Chromatography IR spectrum Polarimetry Refractometry MS spectrum NMR spectrum Then, Identity is certain!

Melting Point Determination (or boiling point) WhyVerify product identity, characterize new products, measure purity, possibly identify material from a list of compounds. HowVariety of apparatuses – all measure exactly the same thing – phase transition, Mixed melting point useful in identification Can’tTell structure or identity, except by comparison

Liquid Chromatography WhyTo analyze and/or separate mixtures of compounds, identify by comparison to known compounds HowColumn (gravity, flash), thin-layer (TLC), Chromatotron  (radial chromatography), High Pressure (Performance) Liquid Chromatography (HPLC) Can’tTell structure or identity, except by comparison – more certain than MP or BP

Automated HPLC Shimadzu-2010HT

Infrared Spectroscopy (FT-IR) WhyIdentify major functional groups in an organic molecule, check purity, gauge minor electronic effects (conjugation or lack thereof), provide a fingerprint of a compound (reproducible) HowThin Film, NaCl plates, KBr pellet, Attenuated Total Reflectance (ATR) FT-IR Can’tTell exact structure (except with rigorous decade-long training), though fingerprint comparison can confirm known structure

FT-IR (x 2) PE Spectrum RX

Polarimetery WhyMeasure optical activity ([  ]) and/or optical purity (and %ee) for chiral compounds HowPolarimeter (also indirect methods based on diastereomeric mixture using NMR or GC) Can’tTell structure or absolute configuration (R or S)

Refractometery WhyMeasure refractive index (n D ) – another physical property for a chemical, indicates purity, useful for binary liquid mixtures (gives accurate ratios), also used in wine and beer making industries (fermentable sugar content) HowRefractometer Can’tOnly useful for liquids

Mass Spectrometry (MS) WhyTo identify compound, Find molecular mass, identify material by comparison with known samples, high resolution MS verifies molecular formula (C n H m N a O b X c ) VERY IMPORTANT: universally used to unequivocally identify drugs, pesticides, explosive (especially in airport security checkpoints), and many other substances, but must have pure substance to compare with, first. HowNominal resolution (most common, especially in GC/MS), high resolution (HRMS) – currently up to 6 decimal places Multiple methods of running analysis (EI, CI, FAB, MALDI- TOF, to name a few) Can’tTell structure directly, except by comparison by “library search”

Automated GC/MS HP 5890-II

X-ray Crystallography WhyTo determine 3-D structure of chemical compounds. Ultimate proof of exact structure. HowUsing an X-ray diffractometer. Must have high quality crystals. Requires extensive experience in interpretation of data. Can’tFind structure of liquids. Absolute configuration is possible, but not guaranteed (mirror image problem)

Nuclear Magnetic Resonance (NMR) WhyTo determine different types of hydrogens or carbons (or other atoms) within a molecule and possibly the structure (connectedness) and geometry. How 1 H NMR, 13 C NMR (other nuclei are possible – 19 F, 31 P) 1D and 2D NMR techniques CanCan do almost anything! Really!!!

NMR Spectrometer

1D and 2D NMR Experiments DEPTDistortionless Enhancement of Polarization Transfer Tells the number of hydrogens on carbon – methyl, methylene, methine, and quaternary COSYCorrelation Spectroscopy (COSY), Tells which hydrogens are neighbors – three bonds away HETCORHeteronuclear Correlation Spectroscopy Tells which carbon is directly connected to which hydrogen NOENuclear Overhauser Enhancement (NOE) Can give structural information – can tell how close two hydrogen are that are many bonds away

Palytoxin