Organic Chemistry Nitrogen Compounds, Spectroscopy, and Biomolecules Syllabus

Over what wavenumber range does a typical IR spectrum run, and where is the fingerprint region?

A typical IR spectrum spans roughly $4000$ to $400\,\text{cm}^{-1}$. The fingerprint region is below about $1500\,\text{cm}^{-1}$, containing complex bending/skeletal vibrations unique to each molecule.

How do bond strength and atomic mass affect the IR stretching frequency of a bond?

Frequency follows $\tilde{\nu} \propto \sqrt{\frac{k}{\mu}}$, where $k$ is the bond force constant (stronger/stiffer bond = higher $\tilde{\nu}$) and $\mu$ is the reduced mass ($\mu = \frac{m_1 m_2}{m_1 + m_2}$; lighter atoms = higher $\tilde{\nu}$). Thus $\ce{C-H}$ absorbs high, and triple bonds absorb higher than double bonds.

What characteristic IR absorption identifies a carbonyl ($\ce{C=O}$) group, and roughly where does a ketone appear?

A strong, sharp $\ce{C=O}$ stretch appears around $1650$–$1750\,\text{cm}^{-1}$; a typical ketone is near $1715\,\text{cm}^{-1}$. Its high intensity comes from the large dipole change.

How do the IR stretches of an O-H (alcohol) and N-H (amine) differ in shape and position?

The alcohol $\ce{O-H}$ stretch is broad and strong near $3200$–$3550\,\text{cm}^{-1}$ (hydrogen bonding). The amine $\ce{N-H}$ stretch is around $3300$–$3500\,\text{cm}^{-1}$, sharper, and shows one band for a secondary amine but two bands for a primary amine ($\ce{-NH2}$).

How does a carboxylic acid O-H stretch appear in the IR, and how does it distinguish an acid from an alcohol?

A carboxylic acid shows a very broad $\ce{O-H}$ stretch spanning roughly $2500$–$3300\,\text{cm}^{-1}$ (often obscuring $\ce{C-H}$ peaks), combined with a strong $\ce{C=O}$ near $1710\,\text{cm}^{-1}$. The extreme breadth (from strong H-bonded dimers) distinguishes it from an alcohol's narrower O-H.

Give the approximate IR stretching wavenumbers for $\ce{C#N}$ (nitrile) and $\ce{C#C}$ (alkyne).

Nitrile $\ce{C#N}$ absorbs near $2200$–$2260\,\text{cm}^{-1}$ (medium, sharp); alkyne $\ce{C#C}$ near $2100$–$2260\,\text{cm}^{-1}$ (often weak). Both fall in the distinctive triple-bond window around $2100$–$2300\,\text{cm}^{-1}$.

When interpreting an IR spectrum to identify functional groups, which region is most diagnostic and why?

The region above $\sim 1500\,\text{cm}^{-1}$ is most diagnostic because it holds characteristic functional-group stretches ($\ce{O-H}$, $\ce{N-H}$, $\ce{C-H}$, $\ce{C=O}$, $\ce{C#N}$). The fingerprint region below $1500\,\text{cm}^{-1}$ is used to confirm identity by matching against a reference.

In $^1\text{H}$ NMR, what does the chemical shift ($\delta$) of a proton signal tell you?

It reveals the electronic (chemical) environment of the proton. Deshielded protons (near electronegative atoms or in the field of aromatic/carbonyl groups) appear at higher $\delta$ (downfield); shielded protons appear at lower $\delta$ (upfield). $\delta$ is measured in ppm relative to TMS at $\delta = 0$.

Why is TMS (tetramethylsilane) used as the reference standard in NMR, and what is its assigned shift?

TMS, $\ce{Si(CH3)4}$, is assigned $\delta = 0$. Its 12 equivalent protons give a single strong upfield signal, it is chemically inert and volatile (easily removed), and silicon's low electronegativity makes its protons highly shielded, so almost all organic signals appear downfield of it.

Give the approximate $^1\text{H}$ NMR chemical shift ranges for aromatic H, aldehyde H, and alkane C-H.

Aromatic H: $\delta \approx 6.5$–$8.0$; aldehyde $\ce{CHO}$ H: $\delta \approx 9$–$10$; alkane $\ce{C-H}$: $\delta \approx 0.5$–$1.5$. Protons on carbons bearing electronegative atoms fall around $\delta \approx 3$–$4.5$.

What does the integration of a $^1\text{H}$ NMR signal represent?

The area under a peak (its integration) is proportional to the number of equivalent protons giving rise to that signal. Integrations give the relative ratio of protons in each environment, not the absolute number directly.

State the n+1 rule for splitting in $^1\text{H}$ NMR and give an example.

A proton with $n$ equivalent neighboring protons (on adjacent carbons) is split into $n+1$ peaks (a multiplet). For example, the $\ce{CH2}$ of an ethyl group has 3 neighbors and appears as a quartet, while the $\ce{CH3}$ has 2 neighbors and appears as a triplet.

What causes spin-spin splitting (coupling) in $^1\text{H}$ NMR?

Coupling arises because the magnetic field felt by a proton is slightly altered by the spin orientations of nonequivalent protons on adjacent atoms. This splits the signal into multiple lines whose spacing is the coupling constant $J$ (in Hz).

What splitting pattern (peak-intensity ratios) does a triplet and a quartet show, and where do these ratios come from?

A triplet shows intensities $1:2:1$ and a quartet $1:3:3:1$. These ratios follow Pascal's triangle, reflecting the number of equivalent spin combinations of the $n$ neighboring protons.

How does $^{13}\text{C}$ NMR differ from $^1\text{H}$ NMR in terms of what the number of signals tells you?

The number of signals in a (proton-decoupled) $^{13}\text{C}$ spectrum equals the number of chemically distinct carbon environments in the molecule. It directly counts carbon types and typically shows singlets (no C-C coupling), unlike proton NMR which shows splitting.

Over what chemical shift range do $^{13}\text{C}$ NMR signals typically appear, and where do carbonyl and aromatic carbons fall?

$^{13}\text{C}$ shifts span roughly $\delta \approx 0$–$220$ ppm. Carbonyl carbons appear very downfield ($\delta \approx 160$–$220$), aromatic/alkene carbons at $\delta \approx 100$–$150$, and saturated $\ce{C-H}$ carbons at $\delta \approx 0$–$50$.

Why is $^{13}\text{C}$ NMR less sensitive than $^1\text{H}$ NMR?

The NMR-active isotope $\ce{^13C}$ has a natural abundance of only about $1.1\%$ (most carbon is $\ce{^12C}$, which is NMR-silent), and its magnetic moment is smaller. Both factors make $^{13}\text{C}$ signals much weaker, requiring more scans.

When determining a structure from combined spectra, what unique information does each of IR, $^1\text{H}$ NMR, and mass spectrometry provide?

IR identifies functional groups (e.g. $\ce{C=O}$, $\ce{O-H}$); $^1\text{H}$ NMR reveals the number, environment, count (integration), and connectivity (splitting) of hydrogens; mass spectrometry gives molecular mass and fragmentation clues to the carbon skeleton. Together they pin down the full structure.

What is the degree of unsaturation (index of hydrogen deficiency) and how is it calculated for $\ce{C_nH_mN_pO_q}$?

It counts rings plus $\pi$ bonds. For a formula $\ce{C_nH_mN_pO_q}$: $\text{DoU} = \frac{2n + 2 + p - m}{2}$ (oxygen is ignored; halogens count like H). Each degree = one ring or one double bond; a benzene ring counts as 4.

In mass spectrometry, what is the molecular ion ($M^+$), and how is it produced?

The molecular ion is the radical cation formed when the intact molecule loses one electron, usually by electron impact: $\ce{M + e- -> M^{+\bullet} + 2e-}$. Its $m/z$ value equals the molecular mass of the compound, giving the relative molecular mass directly.

What information do fragment ion peaks in a mass spectrum provide?

When the molecular ion breaks apart, it forms smaller cations detected at lower $m/z$. The mass differences between peaks (and between a fragment and $M^+$) reveal which groups were lost (e.g. loss of 15 = $\ce{CH3}$, loss of 29 = $\ce{CHO}$ or $\ce{C2H5}$), helping deduce structure.

How does the base peak in a mass spectrum relate to the fragmentation, and what makes a fragment abundant?

The base peak is the tallest peak (assigned $100\%$ relative abundance) and corresponds to the most stable/abundant cation formed. Fragments that give stable carbocations (e.g. tertiary, allylic, benzylic, or acylium ions) tend to be most abundant.

What characteristic isotope pattern in a mass spectrum indicates the presence of chlorine versus bromine?

Chlorine ($\ce{^35Cl}$:$\ce{^37Cl} \approx 3:1$) gives $M$ and $M+2$ peaks in a $3:1$ ratio. Bromine ($\ce{^79Br}$:$\ce{^81Br} \approx 1:1$) gives $M$ and $M+2$ peaks of nearly equal height ($1:1$).

What is the M+1 peak in a mass spectrum, and what causes it?

The small M+1 peak arises mainly from the natural $1.1\%$ abundance of $\ce{^13C}$. Its height relative to $M^+$ roughly estimates the number of carbon atoms: $\%(M{+}1) \approx 1.1 \times (\text{number of carbons})$.

How can accurate (high-resolution) mass measurement determine a molecular formula?

High-resolution MS measures $m/z$ to several decimal places using exact isotopic masses (e.g. $\ce{^12C} = 12.0000$, $\ce{^1H} = 1.00783$, $\ce{^16O} = 15.9949$). Because different formulas of the same nominal mass have distinct exact masses, only one formula matches the measured value.

Classify carbohydrates as monosaccharides, disaccharides, and polysaccharides with an example of each.

Monosaccharides are single sugar units (e.g. glucose, fructose); disaccharides are two units joined by a glycosidic bond (e.g. sucrose, maltose, lactose); polysaccharides are many units (e.g. starch, glycogen, cellulose). The general formula of many monosaccharides is $\ce{C_nH_{2n}O_n}$.

What is a glycosidic bond, and how do the linkages in cellulose and starch differ?

A glycosidic bond is the C-O-C linkage joining two sugar units, formed by a condensation reaction (losing water). Starch/amylose uses $\alpha$-1,4 linkages (digestible, helical), whereas cellulose uses $\beta$-1,4 linkages (straight chains forming strong fibers humans cannot digest).

Draw the general structure of an $\alpha$-amino acid and describe its zwitterion form.

An $\alpha$-amino acid has the structure $\ce{H2N-CHR-COOH}$: an amino group and a carboxylic acid on the same ($\alpha$) carbon, plus a variable side chain R. At intermediate pH it exists as a zwitterion, $\ce{H3N+-CHR-COO-}$, with both a positive and negative charge but net neutral.

What is the isoelectric point (pI) of an amino acid?

The pI is the pH at which the amino acid exists predominantly as a zwitterion with zero net charge and does not migrate in an electric field. Below the pI it is net positive; above it, net negative. It occurs where the average charge is zero.

What bond links amino acids in a peptide, and how does protein secondary structure arise?

Amino acids are joined by peptide (amide) bonds, $\ce{-CO-NH-}$, formed by condensation between one amino acid's $\ce{-COOH}$ and another's $\ce{-NH2}$. Secondary structure ($\alpha$-helix, $\beta$-pleated sheet) arises from hydrogen bonding between backbone $\ce{C=O}$ and $\ce{N-H}$ groups.

Distinguish the four levels of protein structure.

Primary: the sequence of amino acids (peptide bonds). Secondary: local folding ($\alpha$-helices, $\beta$-sheets) held by backbone H-bonds. Tertiary: overall 3D shape of one chain from side-chain interactions (H-bonds, ionic, disulfide, hydrophobic). Quaternary: assembly of multiple polypeptide subunits.

What is the general structure of a triglyceride (fat), and how is it formed?

A triglyceride is an ester of glycerol (propane-1,2,3-triol) with three fatty acid chains, formed by condensation (esterification) releasing three water molecules. Its structure is a glycerol backbone bearing three $\ce{-O-CO-R}$ ester linkages.

How do saturated and unsaturated fatty acids differ in structure and physical properties?

Saturated fatty acids have no $\ce{C=C}$ double bonds; their straight chains pack tightly, giving higher melting points (solids, e.g. animal fats). Unsaturated fatty acids have one or more $\ce{C=C}$ (often cis), introducing kinks that prevent tight packing, lowering the melting point (oils, liquid).

What are the three components of a nucleotide, the building block of nucleic acids?

A nucleotide consists of (1) a phosphate group, (2) a pentose sugar (deoxyribose in DNA, ribose in RNA), and (3) a nitrogenous base (adenine, guanine, cytosine, and thymine in DNA or uracil in RNA). Nucleotides link via phosphodiester bonds to form the strand.

State the base-pairing rules in DNA and the bond type that holds the pairs together.

Adenine pairs with thymine (A–T, two hydrogen bonds) and guanine pairs with cytosine (G–C, three hydrogen bonds). These complementary hydrogen-bonded base pairs join the two antiparallel strands of the DNA double helix, with a sugar-phosphate backbone on the outside.