Compendium

Spectroscopy Reference Tables — NMR Chemical Shifts, IR Bands, MS Fragments, UV-Vis

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Spectroscopy Reference Tables

Working reference for the four core structural-determination spectroscopies a synthetic / analytical chemist hits daily: NMR (1H, 13C, heteronuclear, 2D), IR, UV-Vis, and mass spectrometry. Tables are tuned to characterize unknowns, debug reaction outcomes, and predict where a structural feature will appear. All chemical shifts are δ in ppm relative to standard references; all IR frequencies are in cm⁻¹ (wavenumber); UV-Vis wavelengths in nm; mass spec masses in Da unless noted.

This note bundles two Tier-3 catalogs:

  1. NMR + IR reference tables — the spectroscopies dominating wet-lab structure proof.
  2. MS + UV-Vis reference tables — the spectroscopies dominating quantitation and chromophore analysis.

Part 1 — 1H NMR Chemical Shift Tables

Reference standard

  • TMS (tetramethylsilane) Si(CH₃)₄ — δ = 0.00 ppm. Internal standard for 1H and 13C in organic solvents. CAS 75-76-3, bp 26.6 °C.
  • For aqueous samples: DSS (sodium 2,2-dimethyl-2-silapentane-5-sulfonate, δ 0.0) or TSP (3-(trimethylsilyl)propionate, δ 0.0).
  • Field strength irrelevant to ppm but determines resolution and 2nd-order effects (AB → AX as ν₀ increases).

Common deuterated NMR solvents (residual 1H signal, 13C signal)

SolventResidual 1H (δ ppm)13C (δ ppm)bp °CNotes
CDCl₃7.26 (s)77.16 (t, J ≈ 32 Hz)61Workhorse; mildly acidic, decomp by light to HCl
DMSO-d₆2.50 (quintet, J=1.9)39.52 (septet)189Polar, hydroscopic; resolves OH/NH
CD₃OD3.31 (quintet) + 4.87 (HOD)49.00 (septet)65Exchange of OH/NH/COOH protons
D₂O4.79 (HOD)n/a (use ext ref)101Aqueous; pH-dependent shifts
C₆D₆7.16 (s)128.06 (t)80Aromatic anisotropy; resolves overlap
Acetone-d₆2.05 (quintet)29.84 + 206.2656Useful for ketone solubility
THF-d₈1.72 + 3.5825.31 + 67.2166Low temp work
CD₂Cl₂5.32 (t)53.84 (quintet)40Low temp (−95 °C)
Toluene-d₈2.08 + 6.97–7.0920.43 + 125.13–137.48110Aromatic anisotropy, vol. high
Pyridine-d₅7.21 + 7.58 + 8.74123.87 + 135.91 + 150.35116H-bond acceptor; rearranges OH
TFA-d11.50116.6 (q) + 164.2 (q)72Strong acid; for insoluble bases

1H NMR shift ranges by environment (δ ppm in CDCl₃)

Saturated alkyl (no heteroatom, no carbonyl α)

Typeδ (ppm)Notes
CH₃ (terminal methyl)0.8–1.0Triplet adjacent to CH₂
CH₂ (methylene)1.2–1.4Multiplet in alkyl chain
CH (methine)1.5–2.0Multiplet; depends on branching
Cyclopropane CH0.0–0.6Anomalously upfield ring-current effect
Cyclohexane CH₂ (ax/eq)1.1–1.6 / 1.5–1.9Anisotropic distinction

α to carbonyl (C=O)

α positionCH₃CH₂CH
α to ketone/aldehyde2.0–2.52.2–2.62.4–2.7
α to ester C(=O)OR2.0–2.32.1–2.52.3–2.6
α to acid C(=O)OH2.0–2.52.2–2.62.4–2.7
α to amide C(=O)NR₂2.0–2.32.1–2.42.3–2.6
α to nitrile CN2.1–2.52.3–2.72.6–3.0
α to nitro NO₂4.1–4.44.2–4.64.4–4.8

α to O

α positionCH₃CH₂CH
α to ester OR (alkyl-O-C(=O)R)3.6–3.84.0–4.34.5–5.0
α to ether OR3.3–3.53.4–3.63.6–4.0
α to alcohol OH3.4–3.63.5–3.93.7–4.1
α to OAc (acetate)3.74.0–4.24.8–5.3
α to OTs/OMs3.74.2–4.44.9

α to N

α positionCH₃CH₂CH
α to amine (1°/2°/3°)2.2–2.62.5–3.02.7–3.2
α to amide N-CO-R2.8–3.13.0–3.43.2–3.7
α to N⁺ ammonium3.0–3.53.3–3.8—

α to halogen

HalogenCH₃CH₂CH
F4.2–4.64.54.8
Cl3.0–3.53.4–3.63.9
Br2.7–3.03.3–3.53.9
I2.2–2.73.0–3.34.2

Sp / sp² hydrogens

Typeδ (ppm)Notes
Terminal alkyne RC≡CH1.8–3.1Cone anisotropy upfield of vinyl
Internal alkynen/aNo H
Vinyl =CH₂ (terminal)4.6–5.0Two singlets or doublets
Vinyl =CHR (1,1-disub or internal)5.0–6.0J(cis) 6–12, J(trans) 12–18
Allylic CH–CR=CR2.0–2.6
Aromatic mono-substituted7.2–7.4 (para)Tight cluster
Aromatic EWG (NO₂, CN, C=O)+0.2 to +0.8ortho most affected
Aromatic EDG (OMe, NR₂)−0.1 to −0.4ortho most affected
Pyridine7.3 (H3,5), 7.6 (H4), 8.6 (H2,6)H2,6 most downfield
Furan6.3 (H3,4), 7.4 (H2,5)
Thiophene7.0 (H3,4), 7.3 (H2,5)
Indole6.5 (H3), 7.0–7.6 (Ar), 8.0 (NH)
Pyrrole6.2 (H3,4), 6.7 (H2,5), 8 (NH)
Imidazole7.0 (H4,5), 7.7 (H2)

Aldehydes, acids, exchangeable

Typeδ (ppm)Notes
RCHO aldehyde9.6–10.0Highly diagnostic
ArCHO aryl aldehyde9.8–10.1
RCOOH carboxylic acid10–13Broad; exchange
ArCOOH11–13Broad
Alcohol OH0.5–5Highly variable; concentration / temp dependent
Phenolic OH4–12H-bonded internally → high δ
Primary amine NH₂1–5Broad
Secondary amine NH1–5Broad
Amide NH₂/NH5–9Broad; sometimes resolved
Imine N-H7–11Sharp if non-exchanging
Enol OH (β-diketone)13–17Strongly H-bonded
H₂O (HOD in CDCl₃)1.56Sharp; conc-dependent

Coupling constants J (Hz)

TypeJ rangeNotes
Vicinal 3J (H-C-C-H) sp³6–8Karplus angular dep
Vicinal cis 3J (Newman 0°)0–10 (10)Eclipsed max
Vicinal anti 3J (180°)9–14 (12–14)Anti-periplanar max
Vicinal gauche (60°)1–4Min
Geminal 2J (H-C-H sp³)10–15Negative sign convention
Geminal 2J sp² (=CH₂)0–3
Vinyl cis 3J (=CH-CH=)6–12Diagnostic E/Z
Vinyl trans 3J12–18
Vinyl gem 2J0–3
Aromatic ortho 3J7–9
Aromatic meta 4J1–3
Aromatic para 5J0–1
Allylic 4J (CH–C=C–H)1–3
Long-range W-coupling1–3
Pyridine 3J(H2-H3)4–6
Pyridine 3J(H3-H4)7–9
Furan 3J(H3-H4)3–4
1JCH (one-bond C-H)120–250Hybridization indicator: sp³ 125, sp² 160, sp 250
1JCC30–50
1JHFn/a (no direct H-F bond)2JHF 45–80, 3JHF 5–25, 4JHF 0–4
1JCF160–280
1JHD1(CDCl₃ residual triplet)

Multiplicity patterns (n+1 rule for equivalent neighbors)

n equiv neighborsMultipletPascal’s triangle intensities
0singlet (s)1
1doublet (d)1:1
2triplet (t)1:2:1
3quartet (q)1:3:3:1
4quintet (quint)1:4:6:4:1
5sextet1:5:10:10:5:1
6septet (sept)1:6:15:20:15:6:1
Complexmultiplet (m)irregular

Compound multiplets: dd (doublet of doublets), ddd, dt, td, dq, dquint — explicitly report J values for each.

Part 2 — 13C NMR Chemical Shift Tables

Reference standard

  • TMS δ = 0.00; CDCl₃ central peak δ = 77.16.
  • 1.1% natural abundance → need ~10× more sample or longer acquisition than 1H. Modern cryoprobes restore parity.

Sp³ carbon ranges (δ ppm, CDCl₃)

Typeδ rangeNotes
CH₃ (sp³)0–30Terminal primary
CH₂ (sp³)15–55Methylene
CH (sp³)25–60Methine
Quaternary C (sp³)30–50No 1H attached (DEPT silent)
C-O alcohol (sp³)60–90
C-O ether (sp³)50–85
C-O ester OR (sp³)60–80
C-N amine (sp³)40–60
C-N amide (sp³)40–55
C-S thioether (sp³)25–45
C-Cl (sp³)25–80
C-Br (sp³)20–40
C-I (sp³)−20 to 40Heavy atom effect upfield
C-F (sp³)70–95Large 1JCF 160-180 Hz
C-Si (sp³, TMS)0
C-N(CO) imide40–55

Sp² and sp carbon ranges

Typeδ rangeNotes
C=C alkene100–150E/Z dispersion small in 13C
Aromatic C (unsubst)125–130C6H6 = 128.5
Aromatic C (ipso-EDG, OMe, NR₂)145–160Donates electron density to ortho
Aromatic C (ipso-EWG, NO₂, CN)110–125Often anomalously upfield
Aromatic CH (ortho/meta/para variation)110–145
C=C terminal vinyl CH₂=110–120
C≡C terminal alkyne C-H65–75
C≡C internal alkyne80–95
C≡N nitrile115–125
C=O ketone (saturated)200–220
C=O ketone (conjugated, aryl)190–205
C=O aldehyde190–205
C=O ester/lactone165–175
C=O amide/lactam165–180
C=O carboxylic acid170–185
C=O carbamate150–160
C=O carbonate150–158
C=O acyl chloride165–175
C=O anhydride165–170
C=O urea155–160
C=O isocyanate N=C=O120–125
C=N imine150–165
C=N oxime145–160
C=N hydrazone145–160
C=S thione200–220
CO₂124.2(gas)
CS₂192.3

Other nuclei

19F NMR

  • CFCl₃ (Freon-11) δ = 0 reference; 100% natural abundance, 0.83× 1H sensitivity. Range −300 to +50 ppm.
  • CF₃ aliphatic ~ −60 to −80; CF₃ aromatic −55 to −65; aromatic F −110 to −130; vinyl F −90 to −130; allyl F −95; F-OC=O −70 to −95; SF₆ +57; XeF₂ −193.
  • TFA (trifluoroacetic acid) δ = −76.5; HFIP CF₃ δ ≈ −76.4.
  • Useful for following fluorinated pharmaceuticals (~25% of approved drugs contain F).

31P NMR

  • H₃PO₄ 85% δ = 0 reference. 100% natural abundance.
  • Phosphate esters −5 to +5; phosphonate +20 to +40; phosphine R₃P −60 to +60 (PPh₃ = −5, PMe₃ = −62, PCy₃ = +10); phosphine oxide R₃P=O +20 to +50; phosphonium R₄P⁺ +20 to +30; PCl₃ +220; PCl₅ −80 (5-coord); P(OMe)₃ +141; P(OEt)₃ +138.

11B NMR

  • BF₃·Et₂O δ = 0 reference. 80% abundance, quadrupolar (I=3/2, line broadening).
  • Boronic acid RB(OH)₂ +30; boronate ester +30; trialkylborane +85; BH₃·THF −1; BH₃·SMe₂ −20; BCl₃ +47; BF₃ 0; BF₄⁻ −1.

15N NMR

  • Liquid NH₃ (−400 ppm vs MeNO₂) or CH₃NO₂ (δ = 0) reference. 0.37% abundance → use HSQC indirect detection; or 15N-enriched substrate.
  • Amine −300 to −400; amide −200 to −280; aniline −325; nitro −10 to +20; nitrile −120 to −140; pyridine −60; imine −80 to −150; azide central N −175, terminal N −145 / −300.

2D NMR experiments

ExperimentCorrelatesUse caseAcquisition time
COSY (Correlation Spectroscopy)1H ↔ 1H, 2-3JSpin-system mapping10–30 min
TOCSY (Total CS) / HOHAHA1H ↔ 1H, all-J in spin systemWhole-chain ID, sugar rings30 min–2 h
NOESY (Nuclear Overhauser Effect)1H ↔ 1H, <5 Å through spaceStereochem, conformation, large molecules4–24 h
ROESYSame as NOESY but for ~1 kDa moleculesSmaller molecules where NOE crosses zero2–12 h
HSQC (Heteronuclear Single Quantum Coh.)1H ↔ 13C (or 15N), 1-bondDirect C–H mapping, faster than 13C alone30 min–4 h
HMQC1H ↔ 13C, 1-bond, older variant of HSQCSimilar; HSQC preferred30 min–4 h
HMBC (Heteronuclear Multiple Bond)1H ↔ 13C, 2-3 bondQuaternary C, connectivity through C=O4–16 h
HOESY1H ↔ 19F, 31P, etc through-spaceHeteronuclear spatialhours
INADEQUATE13C ↔ 13C, 1JCCCarbon skeleton, very low sensitivity24–72 h
DEPT-9013C with CH onlyEditing5–30 min
DEPT-13513C: CH+CH₃ up, CH₂ down, Q absentMultiplicity editing5–30 min
APT (Attached Proton Test)13C: CH₂/Q down, CH/CH₃ upDEPT predecessor5–30 min
HSQC-TOCSY1H-13C HSQC × TOCSY relayCarbohydrate/peptide assignment8–24 h

Part 3 — IR Spectroscopy Reference Table

Fundamental regions

Region (cm⁻¹)BondsStrength
4000–2500X-H stretches (O-H, N-H, C-H, S-H)Strong
2500–2000Triple bonds (C≡C, C≡N) and cumulated double bonds (C=C=C, N=C=O, C=C=O)Weak-medium
2000–1500Double bonds (C=O, C=N, C=C, aromatic)Strong (especially C=O)
1500–500Single bonds (C-O, C-N, C-X), bending, fingerprintVariable; diagnostic for ID

O-H, N-H, C-H stretches

Groupν (cm⁻¹)ShapeNotes
O-H alcohol (free, dilute)3580–3650SharpGas phase / dilute
O-H alcohol (H-bonded, neat/liquid)3200–3550BroadTypical condensed phase
O-H carboxylic acid2500–3300Very broadDiagnostic — extends below CH stretch
O-H phenol~3500Broad, sharperIntramolec H-bond shifts
N-H primary amine (RNH₂)3300–3500Two bandsSymmetric + asymmetric
N-H secondary amine (R₂NH)3300–3500One band
N-H primary amide3160 + 3340Two bands
N-H secondary amide~3270 + ~3070 (overtone of amide II)
N-H ammonium R₄N⁺H2500–3300Broad
C-H sp³2850–3000SharpMethyl 2872 sym, 2962 asym; methylene 2850 sym, 2926 asym
C-H sp² (vinyl, aromatic)3000–3100SharpAromatic 3030; vinyl 3010
C-H sp (alkyne)~3300SharpTerminal alkyne C-H
C-H aldehyde2700–2900Two bandsFermi doublet 2820 + 2720
S-H thiol2550–2600Weak, sharp
P-H phosphine2275–2440Weak
Si-H silane2100–2360Sharp
B-H boron hydride2300–2500Broad

Triple bonds and cumulated

Groupν (cm⁻¹)Notes
C≡N nitrile (aliphatic)2240–2260Strong, sharp
C≡N nitrile (aromatic)2220–2240Conjugation lowers
C≡N isocyanide R-NC2110–2165
C≡C terminal alkyne2100–2150Weak, sharp
C≡C internal alkyne2200–2260Often very weak (low dipole)
N=C=O isocyanate2240–2280Very strong
N=C=S isothiocyanate2050–2150
N=N=N azide2090–2170
C=C=O ketene2120–2150
N=C=N carbodiimide2120–2150
CO₂2349 + 667Atmospheric interference

Carbonyl region (C=O) 1670–1820

C=O typeν (cm⁻¹)Notes
Anhydride (acyclic)1750 + 1820Two bands, asym + sym; cyclic ~1750 + 1865
Acyl halide RCOCl1790–1815RCOF higher, RCOBr lower
Ester aliphatic1730–1750 (~1735)β-lactone 1820; γ-lactone 1770; δ-lactone 1735
Aryl ester (PhCOOR)1715–1730Conjugation lowers ~20
Vinyl ester (CH₂=CHOCOR)1760–1780
Aldehyde (saturated)1720–1740
Aryl aldehyde1700–1715Conjugation lowers
Ketone (saturated)1705–1720 (~1715)
α,β-unsaturated ketone1665–1685Conjugation lowers ~20–30
Cyclohexanone1715
Cyclopentanone1745Ring strain raises
Cyclobutanone1780More strain
Cyclopropanone1815Extreme strain
Carboxylic acid (dimer)1700–1720Plus 2500–3300 O-H broad
Carboxylate RCOO⁻1550–1610 + 1380–1420Symmetric / asymmetric
Amide primary RCONH₂1650–1690 (Amide I) + 1620 (NH₂ bend)
Amide secondary RCONHR1630–1680 (Amide I) + 1530 (Amide II, N-H bend + C-N)
Amide tertiary RCONR₂1630–1680No Amide II
Lactam (cyclic amide)varies by ring size; γ-lactam 1700; β-lactam 1750
Carbamate RNHCOOR1700–1740
Urea RNHCONHR1640–1690
Carbonate RO-CO-OR1740–1780
Quinone (1,4)1660–1680

Other double-bond region (1500–1680)

Groupν (cm⁻¹)Notes
C=C alkene (isolated)1620–1680Weak; symmetric alkenes nearly IR-silent
C=C conjugated diene1600 + 1650Two bands
C=C aromatic1450 + 1500 + 1600Ring breathing, 2–4 bands
C=N imine1640–1690
N=N azo1575–1630Weak; visible in Raman
C=S thione1100–1200Weak

Nitro, sulfonyl, phosphate (highly diagnostic)

Groupν (cm⁻¹)Notes
NO₂ aliphatic1350 + 1550Symmetric + asymmetric
NO₂ aromatic1340 + 1525Conjugation lowers
N-O nitroso1550–1600 (C-NO)
N=O hydroxylamine920–950
O-N=O nitrite1610–1680 + 750–820
S=O sulfoxide1030–1070
O=S=O sulfone1140 + 1310Two strong bands
O=S=O sulfonate / sulfonic acid1140 + 1325–1350
O=S=O sulfonamide1140 + 1340
P=O phosphate1100–1200
P=O phosphonate1230–1260
P-O-C950–1050
P-OH2350–2500 (broad)
Si-O-Si siloxane1000–1100Broad
C-F1000–1400Several bands
C-Cl600–800
C-Br500–700
C-I500–600

Aromatic substitution pattern (overtone region 1650–2000 cm⁻¹)

Weak overtones + combinations whose pattern identifies substitution:

  • Monosubstituted: 4 bands
  • 1,2-disub (ortho): 2 bands
  • 1,3-disub (meta): 3 bands (one weak)
  • 1,4-disub (para): 2 bands
  • 1,2,3-trisub: 2 bands
  • 1,2,4-trisub: 3 bands
  • 1,3,5-trisub: 1 band (strong, ~1900)
  • Pentasub: 1 band
  • Hexasub: 0 bands

C-O single bond region (1000–1300)

Typeν (cm⁻¹)
Ester C-O-C(=O)1200 (asym) + 1100 (sym) — two bands
Ether aliphatic1080–1150
Ether aromatic1200–1275 (Ar-O) + 1020–1075 (Ar-O-CH₃)
Alcohol primary C-O1050
Alcohol secondary1100
Alcohol tertiary1150
Phenol C-O1200
Anhydride C-O-C1040–1100 + 1175–1300

IR sample prep methods

  • ATR (attenuated total reflectance): diamond/Ge/ZnSe crystal, drop sample on, press, scan. Modern default. No prep. Penetration depth 1–2 μm. Quantitative IR can be done.
  • KBr pellet: 1–2 mg sample, 200 mg KBr, mortar/pestle, hydraulic press 8 t. Best peak shape but hygroscopic.
  • Nujol mull: solid + mineral oil paste on NaCl plates. CH bands of Nujol at 2900, 1460, 1377 cm⁻¹ obscure regions.
  • Thin film of neat liquid between NaCl/KBr plates.
  • Solution IR: CCl₄ (deprecated, ozone) / CHCl₃ / CS₂; matched cells, 0.1–1 mm path.

Part 4 — UV-Vis Spectroscopy

Beer-Lambert law

A = ε l c

Where A = absorbance (dimensionless), ε = molar absorptivity (L·mol⁻¹·cm⁻¹), l = path length (cm), c = concentration (mol/L).

Linear range: A = 0.1–1.0 typically. Above A=2, deviations from linearity and stray light.

Molar absorptivity ranges

Transition typeε (L·mol⁻¹·cm⁻¹)Notes
π → π* (allowed)10,000–100,000Strongest organic absorption
n → π* (forbidden)10–200Weak; e.g., C=O n→π* around 280 nm
d → d (transition metals, octahedral)1–100Forbidden, intensified by Jahn-Teller / vibronic coupling
d → d (tetrahedral, no inversion)100–1000Higher than octahedral
Charge transfer (LMCT, MLCT)10,000–50,000Strong; basis of many colors
f → f (lanthanides)0.1–10Very weak, sharp
f → d (actinides, some lanthanides)100–1000

Common chromophores λmax (nm)

Chromophoreλmax (nm)εSolventNotes
C=C (ethylene)17515,000hexaneBelow cutoff for most solvents
C=C-C=C (butadiene, transoid)21721,000hexaneWoodward-Fieser base
C=C-C=C-C=C (hexatriene)26843,000hexane
Cyclohexadiene 1,3 (cisoid)2568,000hexane
Acetone (n→π*)28015hexane
Cyclohexanone29017hexane
Acrolein (π→π*+ n→π*)210, 31511000, 13hexane
Benzene184 (E1), 204 (E2), 254 (B-band)60000, 7900, 200EtOH”Benzenoid” 254
Toluene261225EtOH
Naphthalene220, 275, 312116000, 5600, 250EtOH
Anthracene252, 376220000, 8000EtOH
Tetracene274, 474EtOHOrange
Pentacene580Blue-purple
β-Carotene451, 482140000hexaneVisible orange
Lycopene444, 470, 503185000hexaneRed
Chlorophyll a430 (Soret), 663 (Q)EtOHGreen (absorbs red+blue)
Methylene blue66495000waterBlue
Crystal violet59087000waterPurple
Indigo61022000DMSOBlue
KMnO₄5252400waterPurple (MnO₄⁻ MLCT)
Cu(H₂O)₆²⁺80012waterd-d, faint blue
[Co(NH₃)₆]³⁺47256waterd-d, orange
[Fe(phen)₃]²⁺ ferroin51011000waterMLCT, red
Eosin Y51495000EtOHPhotoredox dye
Ru(bpy)₃²⁺452 (MLCT)14600waterPhotoredox, orange
Fluorescein49087000pH>8

Woodward-Fieser rules for conjugated diene λmax

Base values

  • Acyclic transoid (s-trans) diene: 217 nm
  • Acyclic cisoid (s-cis) diene: 253 nm
  • Homoannular cisoid diene (ring): 253 nm
  • Heteroannular transoid diene (two rings): 215 nm

Increments (additive)

SubstituentΔλ (nm)
Each alkyl group or ring residue+5
Each exocyclic double bond+5
Each double-bond extension (added C=C)+30
–OR (alkoxy)+6
–SR (thioether)+30
–OAc (acyloxy)0
–Cl, –Br+5
–NR₂+60
Solvent correction (hexane vs MeOH for C=O)varies (see below)

For α,β-unsaturated carbonyls (Fieser-Kuhn)

  • Base: acyclic / six-ring enone 215 nm; 5-ring 202; aldehyde 207; acid/ester 195.
  • α-substituent (alkyl/ring res): +10
  • β-substituent: +12
  • γ and higher: +18 each
  • Each extending C=C: +30
  • Exocyclic C=C: +5
  • Homoannular diene: +39
  • –OH α/β/γ/δ: +35 / +30 / +50 / —
  • –OR α/β: +35 / +30
  • –OAc α/β/γ/δ: +6 / +6 / +6 / +6
  • Solvent correction from EtOH base: hexane −11, CHCl₃ +1, ether −7, water +8

UV cutoffs (solvent transparency low-λ limit)

SolventUV cutoff (nm)
Water190
MeCN190
n-Hexane195
Heptane195
Cyclohexane200
MeOH205
Et₂O215
EtOH210
1,4-Dioxane220
iPrOH210
DCM230
CHCl₃245
CCl₄265
EtOAc256
THF220
Benzene280
Toluene285
Pyridine305
Acetone330
DMF270
DMSO268

Instrumentation note

Modern double-beam UV-Vis: Agilent Cary 60 (single-beam Xenon flash), Cary 3500 (multi-cell parallel), Thermo Genesys 30/180, PerkinElmer Lambda 365, Shimadzu UV-1900i. Diode-array (Agilent 8453 legacy, now 8454 / Cary 8454) for sub-second full-spectrum. NanoDrop One/8000 (Thermo) for 1–2 μL DNA/protein quantitation.

Part 5 — Mass Spectrometry

Ionization methods

MethodIons formedSample typeTypical analytes”Hard/Soft”
EI (Electron Impact) 70 eVM⁺• radical cation + many fragmentsGC-volatile, < 1 kDaSmall organics, metabolitesHard (extensive fragmentation)
CI (Chemical Ionization)[M+H]⁺, [M-H]⁻ (NCI)GC-volatileHalogenated (NCI esp. for explosives, pesticides)Soft
ESI (Electrospray)[M+H]⁺, [M+Na]⁺, [M+nH]ⁿ⁺Polar; LC-coupledDrugs, peptides, proteins (multi-charge)Very soft
nano-ESIas ESI, lower flow nL/minBiomolecules limited sampleProteomicsVery soft
MALDI[M+H]⁺ singly-charged predominantlySolid matrix-spotProteins, polymers, lipids, intact massSoft
APCI (Atmospheric Pressure CI)[M+H]⁺, [M-H]⁻LC-coupled, moderate polarityLipids, steroidsSoft-medium
APPI (Atmospheric Pressure Photoionization)M⁺•, [M+H]⁺LC, nonpolarPAHs, lipidsSoft
DART (Direct Analysis in Real Time)[M+H]⁺Surface, ambientForensics, food safetySoft
DESI (Desorption Electrospray)[M+H]⁺Surface imagingMS imaging tissue sectionsSoft
FAB (Fast Atom Bombardment)[M+H]⁺Glycerol matrixReplaced by ESI/MALDISoft (historical)
ICP (Inductively Coupled Plasma)atomic ions M⁺ElementalTrace metal analysisAtomization

Mass analyzers

AnalyzerMass accuracyResolution (m/Δm at FWHM)Speed (Hz)Use
Quadrupole (Q)100–500 ppmunit (~1000)10Cheap, robust, MRM/SRM target quant
Triple-quad (QqQ)100–500 ppmunitup to 500 SRMTargeted quant (drug pharmacokinetics, residue) — gold standard
Ion trap (IT, 3D, linear)100–500 ppmunit (4000 zoom)10–30 MS/MSMSn, fast scanning
TOF (Time of Flight)1–10 ppm10,000–50,000up to 100Untargeted small mol, proteomics
QTOF (quad-TOF)1–5 ppm30,000–50,00050DDA proteomics, metabolomics
Orbitrap (Makarov 1999, com. 2005)<1 ppm100,000–500,000 (Astral 200k+)1–40 (resolution-dependent)Proteomics gold standard, metabolomics
FT-ICR (Fourier Transform Ion Cyclotron)<0.1 ppm1,000,000+0.1–1 (long acquire)Petroleomics, ultra-high-res
Sector (magnetic)1 ppm60,000slowHistorical, dioxin trace

Common fragmentation patterns

PatternMechanismm/z signatureSubstrate
α-cleavageBond next to carbonyl breaksLoss of R from RCOR’ → R’CO⁺ (acylium)Ketones, aldehydes, ethers, amines
McLafferty rearrangementγ-H transfer to C=O, β-C-C cleavage → enol cation + alkeneLoss of even-mass alkene (28 for ethylene, 42 propylene, 56 butene)Carbonyls with γ-H
Retro-Diels-Alder (rDA)Cyclohexene fragment revertsDiene + dienophile cationsCyclohexenes, terpenoids
Loss of small neutralsDirect bond cleavage−18 H₂O, −17 OH, −15 CH₃, −28 CO, −29 CHO, −31 OCH₃, −45 COOH, −46 NO₂, −17 NH₃, −27 HCN, −60 AcOH, −90 TMSOH, −36/38 HCl, −80/82 HBrAll
Onium reaction (i, charge-induced)Charge migration → cleavageVariousHeteroatom-containing
Tropylium formationAr-CH₂-X → C₇H₇⁺ (m/z 91)91 strongly diagnosticBenzylic substrates
Phenyl cationLoss of substituent from arylm/z 77 (C₆H₅⁺)Aromatic
AcyliumRCO⁺m/z 43 (acetyl), 105 (benzoyl), 57 (propanoyl), 71 (butanoyl)Carbonyls

Common low-mass diagnostic ions

m/zCompositionOrigin
15CH₃⁺Methyl
17OH⁻, NH₃ neutralLoss in pos mode
18H₂OLoss
28CO, N₂, C₂H₄Loss
29CHO⁺Aldehyde
30CH₂=NH₂⁺, NOAmine α-cleavage
31CH₃O⁺ (methoxy)Methyl ester
39C₃H₃⁺ (cyclopropenyl)Hydrocarbon
41C₃H₅⁺ (allyl)Hydrocarbon
43CH₃CO⁺ (acetyl), C₃H₇⁺Acetate ester / propyl
45CHO₂⁺ (formate), CHS⁺
55C₃H₃O⁺, C₄H₇⁺
57CH₃CH₂CO⁺, C₄H₉⁺ tBuEthyl ester / propyl ester / Boc
58(CH₃)₂CO⁺• (acetone McL), C₃H₈N⁺
59C₃H₇O⁺ (iPrO/PrO), CONH(CH₃)₂⁺
73TMS⁺ (Me₃Si⁺)TMS derivatives in GC-MS
77C₆H₅⁺ (phenyl)Aromatic
91C₇H₇⁺ (tropylium)Benzylic
105C₆H₅CO⁺ (benzoyl), C₈H₉⁺Benzoate / xylyl
128naphthalene M⁺•
152biphenylene, fluorene
154biphenyl
178anthracene/phenanthrene M⁺•
252benzo[a]pyrene
391DEHP m/z 391 [M-149]⁺Plasticizer contamination
149dialkyl phthalate base peakPlasticizer contamination

Isotope patterns

ElementIsotopes (abundance %)Pattern
H¹H 99.985, ²H 0.015Negligible
C¹²C 98.93, ¹³C 1.07+1 peak ≈ 1.1% × C
N¹⁴N 99.64, ¹⁵N 0.36+1 ≈ 0.4% × N
O¹⁶O 99.76, ¹⁷O 0.04, ¹⁸O 0.20+2 ≈ 0.2% × O
F¹⁹F 100None
P³¹P 100None
S³²S 95.02, ³³S 0.75, ³⁴S 4.21+2 ≈ 4.4% × S
Cl³⁵Cl 75.78, ³⁷Cl 24.22M:M+2 ≈ 3:1 for 1 Cl; 9:6:1 for 2 Cl; 27:27:9:1 for 3 Cl
Br⁷⁹Br 50.69, ⁸¹Br 49.31M:M+2 ≈ 1:1 for 1 Br; 1:2:1 for 2 Br
I¹²⁷I 100None (but heavy, mass 127)
Si²⁸Si 92.23, ²⁹Si 4.68, ³⁰Si 3.09+1 ~5%, +2 ~3% × Si
Sn¹¹⁶Sn 14.5, ¹¹⁷Sn 7.7, ¹¹⁸Sn 24.2, ¹¹⁹Sn 8.6, ¹²⁰Sn 32.6, ¹²²Sn 4.6, ¹²⁴Sn 5.8Distinctive multiplet
B¹⁰B 19.9, ¹¹B 80.1M−1 ≈ 25% × B
Pt¹⁹⁴ 32.9, ¹⁹⁵ 33.8, ¹⁹⁶ 25.2, ¹⁹⁸ 7.2Multiplet
Pd¹⁰²Pd, ¹⁰⁴, ¹⁰⁵, ¹⁰⁶, ¹⁰⁸, ¹¹⁰Six isotopes

Accurate mass (HRMS) — common monoisotopic exact masses

ElementMonoisotopic mass (Da)
¹H1.00783
¹²C12.00000 (defined)
¹⁴N14.00307
¹⁶O15.99491
¹⁹F18.99840
³¹P30.97376
³²S31.97207
³⁵Cl34.96885
⁷⁹Br78.91834
¹²⁷I126.90447
²⁸Si27.97693
²³Na22.98977
³⁹K38.96371

Tolerance for molecular formula assignment: <5 ppm typical from QTOF/Orbitrap; <1 ppm from Orbitrap Astral / FT-ICR. Rule of nitrogen (odd nominal mass → odd N count for CHN organic), DBE = C − H/2 + N/2 + 1 (degrees of unsaturation).

Common adducts (ESI positive mode)

AdductΔm/z
[M+H]⁺+1.00728
[M+Na]⁺+22.98922
[M+K]⁺+38.96316
[M+NH₄]⁺+18.03383
[M+H+MeCN]⁺+42.03383
[M+H+MeOH]⁺+33.03404
[2M+H]⁺dimer
[2M+Na]⁺dimer

ESI negative mode:

AdductΔm/z
[M−H]⁻−1.00728
[M+HCOO]⁻+44.99765
[M+Cl]⁻+34.96940
[M+OAc]⁻+59.01330

MS modes for quantitation

  • Full scan — record all m/z; lowest sensitivity, broadest coverage.
  • SIM (Selected Ion Monitoring) — single quad / IT; record specific m/z; 10–100× sensitivity boost; for known targets.
  • SRM / MRM (Selected/Multiple Reaction Monitoring) — triple quad; precursor → fragment transition; ~1000× sensitivity; targeted pharma quant gold standard.
  • PRM (Parallel Reaction Monitoring) — QTOF/Orbitrap; precursor + all fragments at high res; complements MRM with no transition pre-selection.
  • DIA (Data-Independent Acquisition) — fragment all precursors in m/z windows; proteomics, broad metabolomics.
  • DDA (Data-Dependent Acquisition) — fragment top-N most intense precursors per scan; discovery proteomics.

Adjacent

Graph View

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