COURSE SYLLABUS for CHEM 36 Textbook: I.

Organic Chemistry by Solomons and Frayle

Spectroscopy and Structure of Organic Molecules (First Long Examination) II. Alkenes and Alkynes-Part II: Addition Reactions and Synthesis III. Reactions Involving Radicals IV. Ethers and Alcohols (Second Long Examination) V. Oxidation, Reduction and Organometallic Compounds: Reactions Involving Alcohols and Carbonyl Compounds VI. Aldehydes and Ketones : Nucleophilic Addition Reactions of the Carbonyl Group (Third Long Examination) VII. Reactions Involving Aromatic Compounds VIII. Carboxylic Acids and Related Functional Groups: Nucleophlic AdditionElimination the Acyl Carbon IX. Amines: Properties, Synthesis and Biochemical Relevance (Fourth Long Examination)

CHEM 36 ORGANIC CHEMISTRY II I. Spectroscopy and Structure of Organic Compounds

Reference: Organic Chemistry. Solomons and Fryhle. 8th Edition

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Introduction
Spectroscopy: the study of the interaction of quantized energy (electromagnetic energy) with matter
Energy applied to matter can be absorbed, emitted, cause a chemical change, or be transmitted. In organic chemistry, we typically deal with molecular spectroscopy particularly absorption spectroscopy.

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 Examples of Spectroscopy Ultraviolet Spectroscopy Absorption of ultraviolet energy results to electronic transitions in molecules. UV spectroscopy indicates the presence of chromophores in a molecule particularly unsaturation, conjugated systems, carbonyl and aromatic systems. Infrared (IR) Spectroscopy
Infrared energy causes bonds to stretch and bend. IR is useful for identifying functional groups in a molecule.

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 Nuclear Magnetic Resonance (NMR) Spectroscopy Energy applied in the presence of a strong magnetic field causes absorption by the nuclei of some elements (most importantly, hydrogen and carbon nuclei). NMR is used to identify connectivity of atoms in a molecule. Mass Spectrometry (MS)
Molecules are converted to ions by one of several methods (including bombardment by a beam of electrons). The ions formed may remain intact (as molecular ions, M+), or they may fragment. The resulting mixture of ions is sorted by mass/charge (m/z) ratio, and detected. Molecular weight and chemical formula may be derived from the M+ and M+1 ions. Molecular structure may be deduced from the distribution of fragment ions.
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 Schematic absorption spectrum:

wavelength frequency change in energy

An absorption band is characterized primarily by two parameters: (a) the wavelength at which maximum absorption occurs (b) the intensity of absorption at this wavelength compared to baseline or background absorption
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 Spectroscopic transition: takes a molecule from one state to a state of a higher energy and its change in energy is given by E:

where h = Plancks constant

The energy gap of a transition is a molecular property and is a characteristic of a molecular structure.

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The Electromagnetic Spectrum

Electromagnetic radiation has the characteristics of both waves and particles. The wave nature of electromagnetic radiation is described by wavelength () or frequency (). The relationship between wavelength (or frequency) and energy (E) is well defined.

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 Wavelength and frequency are inversely proportional (= c/). The higher the frequency, the greater the energy of the wave. The shorter the wavelength, the greater the energy of the wave.

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I. Ultraviolet Spectroscopy
generally refers to electronic transitions occurring in the ultraviolet ( range 200-380 nm) region of the electromagnetic spectrum Electronic transitions are also responsible in the visible region ( range 380-800 nm) which is easily accessible instrumentally but are of less importance in the solution of structural problems since most organic compounds are colorless. An extensive region at wavelengths shorter than ~200 nm (vacuum UV) also corresponds to electronic transitions but this region is not accessible with standard instruments.

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 types of electronic transitions: n to * to * to * n to * the transitions are brought about by the presence of chromophores in the molecule ( a part of the molecule which can be a functional group or a single atom or group of atoms in a molecule which may not be associated with chemical functionality)
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Basic Instrumentation

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 In practice, double-beam instruments are used where the absorption of a reference cell, containing only solvent, is subtracted from the absorption of the sample cell. The energy source, the materials from which the dispersing device and detector are constructed must be appropriate for the range of wavelength scanned as transparent as possible to the radiation. For UV measurements, the cells and optical components are typically made of quartz and ethanol, hexane, water or dioxan are usually chosen as solvents.

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Quantitative Aspects
The y-axis of a UV spectrum may be calibrated in terms of the intensity of transmitted light (% transmission or absorption) or on a logarithmic scale i.e., in terms of Absorbance A:

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 BeerLambert law: Absorbance is proportional to the concentration and path length; intensity is usually expressed as molar absorbance or molar extinction coefficient :
Where M = molecular weight C = concentration (g/L) l = path length (cm)

UV absorption bands are characterized by the wavelength of maximum absorption (max) and . The values of vary from 10 and 105 and are conveniently tabulated as log10(). The presence of small amounts of strongly absorbing impurities may lead to errors in the interpretation of UV data.

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Classification of UV Bands
UV absorption bands have fine structures due to the presence of vibrational sub-levels but are rarely observed in solution due to collisional broadening. As transitions are associated with changes of electron orbitals, they are often described in terms of the orbitals involved or by another classification method:

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 A molecule may give rise to more than one band because it contains more than one chromophore or because more than one transition of a single chromophore is observed.

UV spectra typically contain far fewer features than IR, NMR or MS spectra and thus have a lower information content.

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Special Terms in UV Spectroscopy

Auxochromes (auxillary chromophores): groups which have little UV absorption by themselves, but which often have significant effects on the absorption (both max and ) of a chromophore to which they are attached; are atoms with one or more lone pairs ( -OH, -OR, -NR2, -halogen) bathochromic shift: shift of absorption maximum to longer wavelength hypsochromic shift: shift of absorption maximum to shorter wavelength Hyperchromic effect: an increase in absorption intensity Hypochromic effect: a decrease in absorption intensity
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Important UV Chromophores
Most of the reliable and useful data is due to relatively strongly absorbing chromophores ( > 200) which are mainly indicative of conjugated or aromatic systems. (1) Dienes and Polyenes
Extension of conjugation in

C chain is always associated with a pronounced shift towards longer wavelength (bathochromic shift) and towards greater intensity (hyperchromic shift).

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Bicyclic diene

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Table 1. The Effect of Conjugation on UV Absorption

When there are more than 8 conjugated double bonds, the absorption maximum of polyenes is such that they absorb light strongly in the visible region. Empirical rules (Woodward Rules) of good predictive value are available to estimate the positions of max in conjugated polyenes and conjugated carbonyl compounds.
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Woodward-Fieser Rules for Calculating the max of Conjugated Dienes and Polyenes Core Chromophore Transoid Diene 215 nm Substituent and Influence R- (Alkyl Group) .... +5 nm RO- (Alkoxy Group) .. +6 X- (Cl- or Br-) ......... +10 RCO2- (Acyl Group) .... 0 RS- (Sulfide Group) .. +30 R2N- (Amino Group) .. +60 Further -Conjugation C=C (Double Bond) ... +30 C6H5 (Phenyl Group) ... +60
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Cyclohexadiene* 260 nm

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(i) Each exocyclic double bond adds 5 nm. In the example on the right, there are two exo-double bond components: one to ring A and the other to ring B. (ii) Solvent effects are minor.
* When a homoannular (same ring) cyclohexadiene chromophore is present, a base value of 260 nm should be chosen. This includes the ring substituents. Rings of other size have a lesser influence.

max (calculated) = Base (215 or 260) + Substituent Contributions

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(2) Carbonyl compounds

All carbonyl derivatives exhibit weak ( < 100) absorption between 250 and 350 nm, and this is only of marginal use in determining structure. Conjugated carbonyl derivatives always exhibit strong absorption.

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Table 2. UV Absorption Bands in Common Carbonyl Compounds

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Woodward-Fieser Rules for Calculating the __> * max of Conjugated Carbonyl Compounds Core Chromophore R = Alkyl 215 nm R = H 210 nm R = OR' 195 nm Cyclopentenone 202 nm Substituent and Influence - Substituent R- (Alkyl Group) +10 nm Cl- (Chloro Group) +15 Br- (Chloro Group) +25 HO- (Hydroxyl Group) +35 RO- (Alkoxyl Group) +35 RCO2- (Acyl Group) +6

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- Substituent R- (Alkyl Group) +12 nm Cl- (Chloro Group) +12 Br- (Chloro Group) +30 HO- (Hydroxyl Group) +30 RO- (Alkoxyl Group) +30 RCO2- (Acyl Group) +6 RS- (Sulfide Group) +85 R2N- (Amino Group) +95 & - Substituents R- (Alkyl Group) +18 nm (both & ) HO- (Hydroxyl Group) +50 nm () RO- (Alkoxyl Group) +30 nm () Further -Conjugation C=C (Double Bond) ... +30 C6H5 (Phenyl Group) ... +60
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(i) Each exocyclic double bond adds 5 nm. In the example on the right, there are two exo-double bond components: one to ring A and the other to ring B.

(ii) Homoannular cyclohexadiene component adds +35 nm (ring atoms must be counted separately as substituents) (iii) Solvent Correction: water = 8; methanol/ethanol = 0; ether = +7; hexane/cyclohexane = +11 max (calculated) = Base + Substituent Contributions and Corrections
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(3) Benzene derivatives

exhibit medium to strong absorption with bands having characteristic fine structure and the intensity of the absorption being strongly influenced by substituents: Weak auxochromes: -CH3, -Cl, -OCH3 Groups which increase conjugation: -CH=CH2, -C(=O)-R, -NO2 Auxochromes whose absorption is pH dependent: -NH2 and -OH

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Table 3. UV Absorption Bands in Common Benzene Derivatives

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Table 3. cont.

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The added conjugation in naphthalene, anthracene and tetracene causes bathochromic shifts of these absorption bands.

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II. Infrared Spectroscopy: An Instrumental Method For Detecting Functional Groups

Electromagnetic radiation in the infrared (IR) frequency range is absorbed by a molecule at certain characteristic frequencies.
Energy is absorbed by the bonds in the molecule and they vibrate faster. The bonds behave like tiny springs connecting the atoms. The bonds can absorb energy and vibrate faster only when the added energy is of a particular resonant frequency. The frequencies of absorption are very characteristic of the type of bonds contained in the sample molecule.
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 The type of bonds present are directly related to the functional groups present. A plot of these absorbed frequencies is called an IR spectrum.

Infrared Spectrometer

An infrared spectrometer detects the frequencies absorbed by the sample molecule. Light of all the various IR frequencies is transmitted to the molecule and the frequencies absorbed are recorded. The absorption frequencies are specified as wavenumbers in units of reciprocal centimeters (cm-1).

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 Alternatively the wavelength () in units of microns (m) can be specified.

The spectrum is a plot of frequency on the horizontal axis versus strength of absorption on the vertical axis.

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 There are different types of stretching and bending vibrations induced by the absorption of infrared energy:

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 The actual relative frequency of vibration can be predicted:

Bonds with lighter atoms vibrate faster than those with heavier atoms.

Triple bonds (which are stiffer and stronger) vibrate at higher frequencies than double bonds:

Double bonds in turn vibrate at higher frequencies than single bonds.

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 The IR spectrum of a molecule usually contains many peaks. These peaks are due to the various types of vibrations available to each of the different bonds. Additional peaks result from overtone (harmonic) peaks which are weaker and of lower frequency. The IR is a fingerprint of the molecule because of the unique and large number of peaks seen for a particular molecule.

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Interpreting IR Spectra
Generally only certain peaks are interpreted in the IR.
Those peaks that are large and above 1400 cm-1 are most valuable.

Hydrocarbons
The C-H stretching regions from 2800-3300 cm-1 is characteristic of the type of carbon the hydrogen is attached to. C-H bonds where the carbon has more s character are shorter, stronger and stiffer and thus vibrate at higher frequency.

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 C-H bonds at sp centers appear at 3000-3100 cm-1 C-H bonds at sp2 centers appear at about 3080 cm-1 C-H bonds at sp3 centers appear at about 2800-3000 cm-1 C-C bond stretching frequencies are only useful for multiple bonds: C-C double bonds give peaks at 1620-1680 cm-1 C-C triple bonds give peaks at 2100-2260 cm-1 These peaks are absent in symmetrical double and triple bonds.

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 Example: octane

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 Example: 1- hexyne

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 Alkenes
The C-H bending vibration peaks located at 600-1000 cm-1 can be used to determine the substitution pattern of the double bond:

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 Example: 1-hexene

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 Aromatic Compounds
The C-C bond stretching gives a set of characteristic sharp peaks between 1450-1600 cm -1 Example: Methyl benzene

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 Other Functional Groups

Carbonyl Functional Groups
Generally the carbonyl group gives a strong peak which occurs at 1630-1780 cm-1.
The exact location depends on the actual functional group present:

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 Alcohols and Phenols

The O-H stretching absorption is very characteristic:
In very dilute solutions, hydrogen bonding is absent and there is a very sharp peak at 3590-3650 cm-1. In more concentrated solutions, the hydroxyl groups hydrogen bond to each other and a very broad and large peak occurs at 3200-3550 cm-1. A phenol has a hydroxyl group directly bonded to an aromatic ring.
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 Carboxylic Acids
The carbonyl peak at 1710-1780 cm-1 is very characteristic The presence of both carbonyl and O-H stretching peaks is a good proof of the presence of a carboxylic acid

Example: propanoic acid

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 Amines
Very dilute solution of 1o and 2o amines give sharp peaks at 3300-3500 cm-1 for the N-H stretching.
1o amines give two peaks and 2o amines give one peak. 3o have no N-H bonds and do not absorb in this region.

More concentrated solutions of amines have broader peaks. Amides have amine N-H stretching peaks and a carbonyl peak.

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Nuclear Magnetic Resonance Spectroscopy

NMR involves absorption of energy in the radiofrequency range of the electromagnetic spectrum. The nuclei of protons (1H) and carbon-13 (13C), and certain other elements and isotopes, behave as if they were tiny bar magnets. When placed in a magnetic field and irradiated with radio frequency energy, these nuclei absorb energy at frequencies based on their chemical environments.

NMR spectrometers are used to measure these absorptions.

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 Continuous-Wave (CW) NMR Spectrometers

the oldest type of NMR spectrometer The magnetic field is varied as the electromagnetic radiation is kept at a constant frequency. Different nuclei absorb the electromagnetic energy based on their chemical environment and produce peaks in different regions of the spectrum.

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 Fourier Transform (FT) NMR Spectrometers

The sample is placed in a constant (and usually very strong) magnetic field. The sample is irradiated with a short pulse of radio frequency energy that excites nuclei in different environments all at once. The resulting signal contains information about all of the absorbing nuclei at once. This signal is converted to a spectrum by a Fourier transformation. FT-NMR allows signal-averaging, which leads to enhancement of real spectral signals versus noise. The strong, superconducting magnets used in FT-NMR spectrometers lead to greater sensitivity and much higher resolution than continuous wave instruments.
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Diagram of a FT NMR Spectrometer

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 Chemical Shift: Peak Position in an NMR Spectrum

Nuclei in different chemical environments in a molecule will absorb at slightly different frequencies. The position of the signals in the spectrum is called the chemical shift. There are two reasons for differences in the magnetic environment for a proton:
1) The magnetic field generated by electrons circulating around the nucleus giving the signal 2) Local magnetic fields generated by electrons elsewhere in the molecule

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 Example: 1,4-dimethylbenzene

The spectrum is measured on a delta () scale in units of parts per million (ppm). Lower frequency is to the left in the spectrum; these absorptions are said to be downfield.
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 Example: 1,4-dimethylbenzene

Higher frequency is to the right in the spectrum: these absorptions are said to be upfield. The small signal at 0 corresponds to an internal standard called tetramethylsilane (TMS) used to calibrate the chemical shift scale.
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 Example: 1,4-dimethylbenzene

The number of signals in the spectrum corresponds to the number of unique sets of protons. 1,4-dimethylbenzene has protons in two unique environments and so shows two signals.
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 Integration of Peak Areas. The Integral Curve

The area under each signal corresponds to the relative number of hydrogen atoms in each unique environment within a molecule. The height of each step in the integral curve is proportional to the area of the signal underneath the step.
1,1,2-trichloroethane

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 Signal Splitting
The signal from a given proton will be split by the effect of magnetic fields associated with protons on adjacent carbons. Characteristic peak patterns result from signal splitting that are related to the number of protons on adjacent carbons.
1,1,2-trichloroethane

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Nuclear Spin: The Origin of the Signal

The nuclei of certain elements and isotopes have spin states that are quantized.
1H

has a spin quantum number I = 1/2 and has allowed spin states of +1/2 or -1/2.

Other nuclei with I = 1/2 are 13C, 19F and 31P and these also respond to an external magnetic field. Nuclei with I = 0 do not have spin (12C and 16O) and do not respond to an external magnetic field.

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Nuclear Spin: The Origin of the Signal

The nuclei of NMR-active nuclei behave like tiny bar magnets. In the absence of an external magnetic field these bar magnets are randomly orientated (a). In an external magnetic field they orient either with ( spin state) or against ( spin state) the magnetic field (b).

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 Nuclei aligned with the magnetic field are lower in energy than those aligned against the field. The nuclei aligned with the magnetic field can be flipped to align against it if the right amount of energy is added (E). The amount of energy required depends on the strength of the external magnetic field: The stronger the external magnetic field, the higher the radio frequency energy required to flip the nuclear spin.
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 At (a) there is no external magnetic field and therefore no energy difference between the two states. At (b) the external magnetic field is 1.41 Tesla and energy corresponding to a frequency of about 60MHz is needed to flip between the spin states. At (c) the external magnetic field is 7.04 Tesla energy corresponding to a frequency of about 300MHz is needed to flip between the spin states.
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Shielding and Deshielding of Protons

Protons in an external magnetic field absorb at different frequencies depending on the electron density around that proton.

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 High electron density around a nucleus shields the nucleus from the external magnetic field.
Shielding causes absorption of energy at higher frequencies (more energy is required for this nucleus to flip between spin states) - the signals are upfield in the NMR spectrum.

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 Lower electron density around a nucleus deshields the nucleus from the external magnetic field.
Deshielding causes absorption of energy at lower frequencies (less energy is required for this nucleus to flip between spin states) - the signals are downfield in the NMR spectrum.

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 Electronegative atoms draw electron density away from nearby protons and therefore deshield them. Circulation of electrons leads to a local induced magnetic field:
The induced field can reinforce or diminish the external field sensed by a proton (depending on the location of the proton), causing deshielding or shielding, respectively. Alkene and aromatic ring hydrogens are deshielded by the circulation of electrons. A terminal alkyne hydrogen is shielded by the circulation of electrons.

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Chemical Shift
Chemical shifts are measured in relation to the internal reference tetramethylsilane (TMS).
The protons of TMS are highly shielded because of the strong electron donating capability of silicon. The signal for TMS is well away from most other proton absorptions.

The scale for chemical shifts is independent of the magnetic field strength of the instrument (whereas the absolute frequency depends on field strength).

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 Thus, the chemical shift in units for protons on benzene is the same whether a 60 MHz or 300 MHz instrument is used.

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Chemical Shift Equivalent and Nonequivalent Protons

To predict the number of signals to expect in an NMR spectrum it is necessary to determine how many sets of protons are in unique environments. Chemically equivalent protons are in the same environment and will produce only one signal.

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 Homotopic Hydrogens
Hydrogens are chemically equivalent or homotopic if replacing each one in turn by the same group would lead to an identical compound.

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 Enantiotopic and Diastereotopic Hydrogen Atoms

If replacement of each of two hydrogens by some group leads to enantiomers, those hydrogens are enantiotopic.
In the absence of a chiral influence, enantiotopic hydrogens have the same chemical shift and appear in the same signal.

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 If replacement of each of two hydrogens by some group leads to diastereomers, the hydrogens are diastereotopic.
Diastereotopic hydrogens have different chemical shifts and will give different signals.

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Signal Splitting: Spin-spin Coupling

The signal from a given proton will be split by the effect of magnetic fields associated with protons on adjacent carbons. Characteristic peak patterns result from signal splitting that are related to the number of protons on adjacent carbons.
The effect of signal splitting is greatest between atoms separated by 3 or fewer bonds.

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 Signal splitting is not observed between homotopic or enantiotopic protons.

Signal splitting occurs only when two sets of protons have different chemical shifts (i.e., are not chemical shift equivalent).

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 The magnetic field sensed by a proton (Ha) being observed is affected by the magnetic moment of an adjacent proton (Hb):
A proton (Hb) can be aligned with the magnetic field or against the magnetic field, resulting in two energy states for Hb. The observed proton (Ha) senses the two different magnetic moments of Hb as a slight change in the magnetic field; one magnetic moment reinforces the external field and one substracts from it.

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 The signal for Ha is split into a doublet with a 1:1 ratio of peak areas. The magnitude of the splitting is called the coupling constant Jab and is measured in Hertz (Hz).

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 When two adjacent protons Hb are coupled to Ha, there are four possible combinations of the magnetic moments for the two Hbs:
Two of these combinations involve pairings of magnetic moments that cancel each other, causing no net displacement of signal. One combination of magnetic moments reinforces and another subtracts from the applied magnetic field. Ha is split into a triplet having a 1:2:1 ratio of signal areas.

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 When three adjacent protons are coupled to Ha, there are 10 possible combinations of the magnetic moments for the Hbs:
Four unique orientations exist and so Ha is split into a quartet with intensities 1:4:4:1.

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 The general rule for splitting is that if there are n equivalent protons on adjacent atoms, these will split a signal into n + 1 peaks. Coupled peaks have the same coupling constants J.
Comparison of coupling constants can help with the analysis of complex spectra.

Several factors complicate analysis of NMR spectra:

Peaks may overlap. Spin-spin coupling can be long-range (i.e., more than 3 bonds).

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 Splitting patterns in aromatic groups can be confusing:

A monosubstituted aromatic ring can appear as an apparent singlet or a complex pattern of peaks.

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 Much more complex splitting can occur when two sets of adjacent protons split a particular set of protons. In the system below, Hb is split by two different sets of hydrogens : Ha and Hc

Theortically Hb could be split into a triplet of quartets (12 peaks) but this complexity is rarely seen. The spectrum of 1-nitropropane shows splitting of Hb into only 6 peaks.

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Proton NMR and Rate Processes

An NMR spectrometer is like a camera with a slow shutter speed. The NMR spectrometer will observe rapid processes as if they were a blur, i.e., only an average of the changes will be seen. When a 1H NMR spectrum of very pure ethanol is taken, the hydroxyl proton is split into a triplet by the two adjacent hydrogens. When an 1H NMR of regular ethanol is taken the hydroxyl proton is a singlet.
Impure ethanol contains acid and base impurities which catalyze the exchange of hydroxyl protons. This rapid exchange is so fast that coupling to the adjacent CH2 is not observed. This process is called spin decoupling.
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 Spin decoupling is typical in the 1H NMR spectra of alcohols, amines and carboxylic acids.
The proton attached to the oxygen or nitrogen normally appears as a singlet because of rapid exchange processes.
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Carbon-13 NMR Spectroscopy

13C

accounts for only 1.1% of naturally occurring carbon:

has no magnetic spin and produces no NMR signal.

12C

One Peak for Each Unique Carbon Atom:

Since the 13C isotope of carbon is present in only 1.1% natural abundance, there is only a 1 in 10,000 chance that two 13C atoms will occur next to each other in a molecule. The low probability of adjacent 13C atoms leads to no detectable carbon-carbon splitting.

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1H

and 13C do split each other, but this splitting is usually eliminated by adjusting the NMR spectrophotometer accordingly.

The process of removing the coupling of 1H to an attached carbon is called broadband (BB) proton decoupling.

Most 13C NMR, therefore, consist of a single peak for each unique carbon.

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13C

Chemical Shifts

Just as in 1H NMR spectroscopy, chemical shifts in 13C NMR depend on the electron density around the carbon nucleus: Decreased electron density causes the signal to move downfield (desheilding). Increased electron density causes the signal to move upfield (sheilding).

Because of the wide range of chemical shifts, it is rare to have two 13C peaks coincidentally overlap.
A group of 3 peaks at 77 comes from the common NMR solvent deuteriochloroform and can be ignored.

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 Off-Resonance Decoupled Spectra

Broad-band decoupling removes all information about the number of hydrogens attached to each carbon. Off-resonance decoupling removes some of the coupling of carbons to hydrogens so that the coupled peaks will not overlap. Use of off-resonance decoupled spectra has been replaced by use of DEPT 13C NMR.

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 DEPT 13C NMR

DEPT (Distortionless Enhanced Polarization Transfer) spectra are created by mathematically combining several individual spectra taken under special conditions. The final DEPT spectra explicitly show C, CH, CH2 , and CH3 carbons. To simplify the presentation of DEPT data, the broadband decoupled spectrum is annotated with the results of the DEPT experiments using the labels C, CH, CH2 and CH3 above the appropriate peaks .

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 Example: 1-chloro-2-propanol
(a) The broadband decoupled spectrum and (b) a set of DEPT spectra showing the separate CH, CH2, and CH3 signals

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Introduction to Mass Spectrometry (MS)

A mass spectrometer produces a spectrum of masses based on the structure of a molecule. A mass spectrum is a plot of the distribution of ion masses corresponding to the formula weight of a molecule and/or fragments derived from it. The x-axis of a mass spectrum represents the masses of ions produced. The y-axis represents the relative abundance of each ion produced. The pattern of ions obtained and their abundance is characteristic of the structure of a particular molecule.
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The Mass Spectrometer

One common type is the Electron Impact Mass Spectrometer (EI MS).

Ionization (the formation of ions)

A molecule is bombarded with a beam of high energy electrons. An electron may be dislodged from the molecule by the impact, leaving a positively charged ion with an unpaired electron (a radical cation).
This initial ion is called the molecular ion (M+.) because it has the same molecular weight as the analyte.

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 Fragmentation
Excess vibrational energy is imparted to the molecular ion by collision with the electron beam - this causes fragmentation.
The fragmentation pattern is highly characteristic of the structure of the molecule.

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 Ion Sorting
The fragments are sorted according to their mass to charge ratio, (m/z). Most of the fragments detected have charge +1; the net effect is sorting of the ions by mass (m/z, where z = +1). The charged molecular ion (M+) and fragments pass through an analyzer that sorts the ions according to m/z.

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 One method of sorting involves directing the ions through a curved tube that passes through a magnetic field; as the magnetic field is varied, ions of different m/z values successfully traverse the tube and reach the detector.

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The Mass Spectrum

After ion sorting the results are plotted as a spectrum with m/z on the horizontal axis and relative abundance of each ion on the vertical axis. Data from a mass spectrometer can be represented as a graph or table. The most abundant (intense) peak in the spectrum is called the base peak and is assigned a normalized intensity of 100%. The masses are based on rounding of atom masses to the nearest whole number (in low resolution mass spectroscopy).

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 The data and fragmentation patterns for ammonia are as follows:

The base peak for ammonia is the molecular ion, but this is often not the case.
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 The small peak at m/z 18 comes from the small amount of 15N1H3 because of the small natural abundance of 15N compared to 14N. This peak is called an M+1 peak.
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Determination of Molecular Formulas and Molecular Weights

The Molecular Ion and Isotopic Peaks
The presence of heavier isotopes one or two mass units above the common isotope yields small peaks at M+.+1 and M+.+2.

The intensity of the M+.+1 and M+.+2 peaks relative to the M peak can be used to confirm a molecular formula.
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Predicted ratios of molecular ions for compounds containing various ratios of chlorine and bromine, based on natural isotopic abundance.

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 Example: In the spectrum of methane one expects an M+.+1 peak of 1.17% based on a 1.11% natural abundance of 13C and a 0.016% natural abundance of 2H:

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High-Resolution Mass Spectrometry

Low-resolution mass spectrometers measure m/z values to the nearest whole number. High-resolution mass spectrometers measure m/z values to three or four decimal places. The high accuracy of the molecular weight calculation allows accurate determination of the molecular formula of a fragment.
Example: One can accurately pick the molecular formula of a fragment with a nominal molecular weight of 32 using highresolution MS:

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 The exact mass of certain nuclides is shown below:

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Fragmentation
In EI mass spectrometry the molecular ion is highly energetic and can break apart (fragment). Fragmentation pathways are predictable and can be used to determine the structure of a molecule. The processes that cause fragmentation are unimolecular. The relative ion abundance is extremely important in predicting structures of fragments.

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 Fragmentation by Cleavage at a Single Bond

Cleavage of a radical cation occurs to give a radical and a cation but only the cation is observable by MS. In general the fragmentation proceeds to give mainly the most stable carbocation.
In the spectrum of propane the peak at 29 is the base peak (most abundant) 100% and the peak at 15 is 5.6%:

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 Fragmentation Equations
The M+. Ion is formed by loss of one of its most loosely held electrons .
If nonbonding electron pairs or pi electrons are present, an electron from one of these locations is usually lost by electron impact to form M+. Loosely held nonbonding electrons on nitrogen and oxygen, and electrons in double bonds are common locations for an electron to be lost (i.e., where the remaining unshared electron in M+. resides).

In molecules with only C-C and C-H bonds, the location of the lone electron cannot be predicted and the formula is written to reflect this using brackets.

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 Example: The spectrum of hexane

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 Example: spectrum of neopentane

Fragmentation of neopentane shows the propensity of cleavage to occur at a branch point leading to a relatively stable carbocation. The formation of the 3o carbocation is so favored that almost no molecular ion is detected.
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 Carbocations stabilized by resonance are also formed preferentially.

Alkenes fragment to give resonance-stabilized allylic carbocations.

Carbon-carbon bonds next to an atom with an unshared electron pair break readily to yield a resonance stabilized carbocation.

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 Carbon-carbon bonds next to carbonyl groups fragment readily to yield resonance stabilized acylium ions.

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 Alkyl substituted benzenes often lose a hydrogen or alkyl group to yield the relatively stable tropylium ion.

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 Other substituted benzenes usually lose their substitutents to yield a phenyl cation.

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 Fragmentation by Cleavage of 2 Bonds

The products are a new radical cation and a neutral molecule. Alcohols usually show an M+.-18 peak from loss of water.

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 Cycloalkenes can undergo a retro-Diels Alder reaction to yield an alkadienyl radical cation.

Carbonyl compounds can undergo a McLafferty Rearrangement:

where Y may be R, H, OH, OR etc.

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