Synthesis and Mass Spec Notes

Synthesis: Adding Carbon Chains

The only method for adding carbon chains in synthesis involves S_N2 reactions with terminal alkynes and primary or methyl alkyl halides.
These reactions are essentially the same; the difference lies in which starting material is converted into which reactant.

Triple bonds always have two carbons; thus, alkynes can add two or more carbons.
The alkyne can have a hydrogen, methyl, ethyl, or extended chain.
To add one carbon, use an alkyl halide such as methyl chloride or bromide.
Adding two or more carbons requires using alkynes.

If a three-carbon chain needs to be added, either the starting material can be converted into a terminal alkyne, followed by S_N2 with an alkyl halide, or the starting material can be converted into an alkyl halide, followed by reaction with a terminal alkyne.
SN2 reactions cannot occur directly at sp^2 hybridized centers, such as on an alkene. Therefore, halogens cannot be directly attached to an alkene for SN2 reactions.

If a triple bond is added, but it's not in the desired location, consider the other synthetic route.
To obtain a trans-alkene from a triple bond, use sodium metal and ammonia (Na, Metal, NH3), not NaNH2.
If an alkane is formed, hydrogenation can be used to adjust the position of the double bond.
If the initial route places the triple bond far from the desired location, the alternative route is likely more efficient.
If the desired product is a trans-alkene, reduce the triple bond using sodium and ammonia (Na, Metal, NH_3).
Moving an alkene down the chain can be achieved through multiple steps involving HBr and peroxide additions, followed by tert-butoxide treatments.

The most successful route involves converting a starting material into an alkyl halide and then reacting it with a terminal alkyne.
To add a chain using this method, irradiate an internal alkyne to facilitate S_N2 reaction and chain extension.

Carbonyl groups can be synthesized from triple bonds using either hydroboration or hydration with H_3O^+. Mercury is not always necessary.

Attempt syntheses by converting the starting material into either a terminal alkyne or an alkyl halide.
When adding carbons, remember to go through a terminal alkyne intermediate.
If adding two carbons, both routes (alkyne or alkyl halide intermediate) are possible; if adding one carbon, only the alkyl halide route works.
Common reactions in synthesis include HBr with peroxide for anti-Markovnikov addition, and Br2 or Cl2 with light or heat for alkane halogenation.

Mass spec is used to determine the molecular formula of a compound.
It differs from IR and NMR spectroscopy, which involve state-to-state transitions with electromagnetic radiation.

The sample is first vaporized and then bombarded with a high-energy stream of electrons, dislodging a valence electron and forming a cation radical.
For example, methane (CH_4) loses an electron to become a cation radical.

The cation radical is unstable and fragments into a cation and a free radical.
Only the cation (positively charged species) is detected by the mass spectrometer.
For example, the methane cation radical can fragment into CH3^+ (cation) and H[ ildestyle{\cdot}] (free radical) or H^+ (cation) and [ ildestyle{\cdot}]CH3 (free radical).

Cations are accelerated through an electric field; smaller cations reach the detector first.
The detector measures the mass-to-charge ratio (m/z), which, for singly charged ions, is effectively the mass of the fragment.
Isotopes are considered in mass calculations.

The mass spectrum displays peaks corresponding to different fragment masses.
The base peak is the tallest peak, representing the most abundant fragment.
The parent peak (M+) represents the molecular weight of the original molecule before fragmentation.
The mass spectrum displays peaks corresponding to different fragment masses and intensities.

The detector reads the positive charge.
When cutting the molecules, ensure there is a positive charge on at least one fragment.
The base peak is the most abundant peak and corresponds to the most stable fragment.

Chlorine has two abundant isotopes: chlorine-35 and chlorine-37.
The atomic mass of chlorine is 35.45 g/mol, indicating that chlorine-35 is more abundant.
The ratio of chlorine-35 to chlorine-37 is roughly 3:1 (75% to 25%).
If the M+2 peak is present with a 3:1 ratio, it suggests the presence of one chlorine atom in the molecule.

Bromine has two isotopes: bromine-79 and bromine-81, with their average molecular weight at 79.9.
Bromine-79 and bromine-81 are present in roughly a 1:1 ratio (50% to 50%).
If the M+2 peak is almost the same height as the M+ peak, it indicates the presence of one bromine atom in the sample.

Molecular formulas will include carbons, hydrogens, oxygen, and at most one bromine or one fluorine.