Chapter 5: Oxygenic compounds (C5318094)

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Water accounts for 57% of total body weight of the average human, and up to 75% in infants.

Water breaks down the major macromolecules (i.e. nutrients not yet broken down) into its constituents, known as hydrolysis. These include:






Amino acids

Nucleic acid



Fatty acids

“So is Baptism in the Holy Spirit subsequent to conversion, or not?” Emily asked.

“Paul’s amazement you can be baptized and not receive the Holy Spirit (Acts 19:3) shows that persons water baptized should have the Holy Spirit,” Mandy replied, “However, in Acts 19:3, despite the persons were baptized in water, it was only until the laying of hands that the Spirit came upon them. But then, you have Cornelius who had the infilling of the Spirit before baptism.”

“I can’t see a normative for precede, proceed, or at,” Victoria commented, “But let the Pentecostal bad girl believe whatever she wants .”

Solubility is determined by the maxim “like dissolves like”, because solubility requires the ability to break intermolecular forces and mingle, and therefore requires the two molecules to have intermolecular forces of the same [order of] strength. As non-polar bonds do not have the strength to break into polar bonds, non-polar and polar molecules do not mingle. Water is polar, because there is a great difference in electronegativity between oxygen and hydrogen.

Hydrophobic molecule

Amphipathic molecule

Hydrophilic molecule

Dislike water


Like water

Because unlike water, these molecules are nonpolar

Different portions of the same molecule can be hydrophilic and hydrophobic. This is so especially in larger molecules

Because like water, these molecules are polar

1 Alcohols

Alcohols ([mathjax]R-OH[/mathjax]) are compounds containing a hydroxyl group [mathjax]-OH[/mathjax]. Although its appearance is analogous to water; rather than the lower angle of [mathjax]104.5^{\circ}[/mathjax] [found in water], the bond angle is closer to the standard [mathjax]109.5^{\circ}[/mathjax] found in the [mathjax]sp^3[/mathjax]. This is because rather than a light hydrogen, an R-group is far bulkier, and dominates over the [weaker] repulsion of electrons, which therefore has less effect in reducing the bond angle, and so therefore, increases this bond angle.

© 2014 MR. SHUM

The hydroxyl group ([mathjax]-OH[/mathjax]) in alcohol is polar and therefore water-soluble. However, the carbon chain is nonpolar, and therefore water insoluble. Therefore, lower molecular mass alcohols are water soluble, but higher molecular mass alcohols have a dominating nonpolar carbon chain, thereby decreasing its solubility. Lower molecular mass alcohols are less dense than water (i.e. float on water). Like alkanes, boiling point increases with molecular mass, and decrease with branching (discussed ).

Alcohols can behave as acids, although they are slightly weaker acids than [even] water. This is possible despite water is neutral, because pH provides information about the level of [mathjax]\ce{[H]+}[/mathjax] ions present at any point in time, rather than the ability to donate [mathjax]\ce{[H]+}[/mathjax] ions. Therefore, the equilibrium [mathjax]pK_{a}[/mathjax] is a better measure. Water has a [mathjax]pK_{w}[/mathjax] of 14, in contrast with alcohols, which have a [mathjax]pK_{a}[/mathjax] of between 16-19, indicating they are weaker acids than water. This is so because the R group is electron donating, therefore decreasing the polarity of the [mathjax]-OH[/mathjax] bond [in contrast with water], thereby creating a weaker acid. Because each R group is electron donating, the more R groups, the less the polarity [and therefore the weaker the acid]. Therefore, the strongest acids are primary alcohols, followed by secondary, then tertiary. In contrast to electron donating R groups [which decrease polarity], electron withdrawing R groups increase polarity.

Given phenol is a benzene with an alcohol group attached, remember first that benzene is electron withdrawing [apart from when attached to itself, discussed ].

However, when an alcohol is attached to benzene [called phenol]; the polarity of the [mathjax]-OH[/mathjax] bond is increased, which increases acidity. In fact, it has a [mathjax]pK_{a}[/mathjax] between 10-12, and therefore more acidic than water.

The conjugate base of an alcohol, is an alkoxide ion.

Alcohols are synthesized by:

  • Hydration of an alkene, already mentioned
  • Reacting carbonyl groups ([mathjax]C=O[/mathjax]) with a Grignard reagent (organometallic compound, which is where a slightly negative carbon and slightly positive metal are compounded together; this is so because metals like losing electrons, and will leave the carbon therefore, slightly negative). Because of the slightly negative carbon of Grignard reagent, it is therefore a good nucleophile (donates an electron pair). It therefore attacks the partially positive carbonyl carbon [of the carbonyl group], thereby removing the double bond, and attaching its [own] carbonyl group, onto the reactant carbonyl group. The oxygen group is then protonated in the presence of acid, to form an alcohol

© 2014 MR. SHUM

There are also reactions where alcohol is a reactant, including:

  • Oxidation
    of alcohols, which would be a reverse reaction of the
     of aldehydes, ketones, or carboxylic acids. Primary alcohols can be oxidized either to aldehydes or carboxylic acids, and secondary alcohols are oxidized to a ketone. Tertiary alcohols are resistant to oxidation

© 2014 MR. SHUM

Ethers ([mathjax]R-O-R'[/mathjax]) are compounds containing an oxygen bonded to two alkyl groups. They look similar to, but should not be confused with, alcohols. Ethers are good organic solvents, because it is polar, however [unlike most polar substances, it is] aprotic (i.e. cannot donate hydrogen, and therefore unable to hydrogen bond with itself), and of low chemical reactivity. Ethers therefore dissolve a range of solutes, without reacting. Ethers react with hydrogen halides (a strong acid, mentioned ), which splits the ether into an alkyl halide, and an alcohol.

© 2014 MR. SHUM

Epoxide is a type of ether, that is more reactive than other ethers. Like the standard ether model, it has an oxygen bonded to two carbons, but the distinction is that these two carbons are bonded to another, creating a triangle. The reactivity of epoxide is due to high angle strain.

© 2014 MR. SHUM

Formative learning activityMaps to RK5.A
What are alcohols, and how are they distinct?

2 Aldehydes, ketones

Carbonyl are functional groups with a carbon atom double bonded with an oxygen atom ([mathjax]C=O[/mathjax]). They include:

  • Aldehydes, discussed
  • Ketones, discussed 
  • Esters, discussed 
  • Carboxylic acids, discussed 
  • Amides, discussed  

Like alkene, carbonyl has one double bond and two single bonds, meaning there are three [initial] sigma bonds, and one [subsequent] pi bond. Since the pi bond is not counted [when calculating orbital hybridization], carbonyl is [mathjax]sp^2[/mathjax], and thus has an [expected] bond angle of [mathjax]120^{\circ}[/mathjax], giving a trigonal planar (flat) shape. Because the oxygen is more electronegative, it draws electron density away from the carbon, increasing the bond’s polarity, hence the carbon has a partial positive charge, is thus often initialed with [mathjax]\delta^+[/mathjax]; and the oxygen has a partial negative charge, and is thus often initialed with [mathjax]\delta^-[/mathjax].

© 2014 MR. SHUM

Its partial positive charge and flat shape, make carbonyl carbon a good electrophile (likes to accept electrons), opening it to nucleophilic attack (attack by a substance that likes to give electrons). The question that remains [for carbonyls], is whether it prefers nucleophilic addition, or nucleophilic substitution, of which the latter requires good leaving groups.

Aldehydes ([mathjax]R-CHO[/mathjax]) are compounds with an alkyl group and hydrogen on either side of a carbonyl group, or alternatively, can be thought to have a formyl [mathjax]-CHO[/mathjax] group.

© 2014 MR. SHUM

The simplest aldehyde has a hydrogen as the R group, and is known by the common name formaldehyde, or the IUPAC name methanal. The “-al” suffix is indicative of an aldehyde.

Ketones ([mathjax]R-CO-R'[/mathjax]) are compounds with alkyl groups on either side of a carbonyl group. Aldehydes and ketones are chemically similar.

© 2014 MR. SHUM

The simplest ketone has methyl groups as both R groups, and is known by the common name acetone, or the IUPAC name propanone. The ‘-one” suffix is indicative of a ketone.

Aldehydes and ketones have higher boiling points than [similar molecular mass] hydrocarbons and ethers, due to their partial charges [whereas the others only have dispersion forces]. However, they have lower boiling points than [similar molecular mass] alcohols, because they are unable to hydrogen bond to another [as they do not have a hydrogen]. Nevertheless, aldehydes and ketones are able to hydrogen bond with compounds that can hydrogen bond, because the carbonyl oxygen has a partial negative charge that can accept a hydrogen proton. Because of their polarity, short chained aldehydes and ketones are water soluble, and hence, good solvents for alcohols.

The reactions where aldehydes and ketones are a reactant, depend on the mode in which they react, and include:

  • Undergoing nucleophilic addition, because as stated , they are subject to nucleophilic attack. They do not undergo nucleophilic substitution, because neither a negatively charged alkyl group [of ketones], or a hydride ion [of aldehydes], are good leaving groups. Therefore, aldehydes and ketones undergo nucleophilic addition
    • Aldehyde and ketone reacted with alcohols, as aldehydes and ketones are good electrophiles, and alcohols are good nucleophiles. A lone pair of electrons on [and with its] alcohol, attacks and bonds to the partially positive carbonyl carbon [of aldehyde or ketone]. The hydrogen [of the alcohol] drops off, and protonates the carbonyl oxygen [in another zone of the aldehyde or ketone]. The resulting compound is a hemiacetal or hemiketal, derived from an aldehyde and ketone respectively. This reaction occurs in the presence of acid

      © 2014 MR. SHUM

      Hemiacetals and hemiketals can then be reacted with more alcohol, again in the presence of acid, which protonates the hydroxyl group of hemiacetal or hemiketal, permitting a water-leaving group. The [just added] alcohol, acting [again] as a nucleophile, has its lone pair of electrons attack and attach on to the carbonyl carbon, forming an acetal or ketal

      © 2014 MR. SHUM

      To reverse this reaction, the opposite will need to be encouraged, namely, hydrolysis (adding water) in the presence of acid.

      The advantage of acetals and ketals is that they be used as protecting groups, as the aldehyde/ketone is not present, so a reaction (e.g. hydrolysis by base, and many oxidizing and reducing agents) that affects other groups, will not affect the aldehyde/ketone. [In contrast, aldehydes and ketones may be subject to reaction.] After the targeted reaction has completed, hydrolysis in the presence of acid, can help regain the original aldehyde or ketone, unaffected

  • As water can be considered the simplest alcohol, it interacts with aldehydes and ketones analogously. When dissolved in water (hydrated), aldehydes and ketones react to form germinal diols, which is where the carbonyl’s double bonded oxygen is replaced with two single bonded hydroxyl groups

© 2014 MR. SHUM

  • Aldehydes and ketones can also act as a Bronsted-Lowry acid, meaning that it donates [mathjax]\ce{H+}[/mathjax] ions (discussed ), specifically, the alpha hydrogen, which is the hydrogen attached to the alpha carbon. Starting at the functional group (carbonyl carbon) and counting either side, they are named alpha, beta, gamma, delta, epsilon, and so forth [down the Greek alphabet]

    © 2014 MR. SHUM

    By removing this [alpha] hydrogen, what is left is a carbanion (group with negatively charged carbon), which is therefore a Lewis base [as it is an electron pair donator, discussed ]. This is why carbanion is the conjugate base of aldehyde and ketone. Note from  however, that the carbonyl carbon has a partial positive charge, which is therefore offsets the carbanion’s negative charge, thereby weakening the base [as an electron pair donator]. Remember from  that a weak conjugate base is linked with a strong acid. As the oxygen is able to take on a partial negative charge (from ) [effectively, converting the [mathjax]C=O[/mathjax] double bond into a single bond], this then permits the carbonyl carbon to take on the carbanion’s electron [effectively, converting the [mathjax]C-C[/mathjax] single bond into a double bond]. The resulting carbanion is known as an enolate ion, which is stabilized by resonance, resonating between a structure with the negative charge sometimes on the alpha carbon, and sometimes on the oxygen

    © 2014 MR. SHUM

    Despite its ability to act as an acid, it is less acidic than alcohol [which is in turn less acidic than water, mentioned ]
  • Behaving as both an electrophile and acid, namely:
    • Aldol condensation, where the aldehyde/ketone reacts with itself, or another aldehyde/ketone. There are 2 parts to the reaction:
      • Aldol addition: The reaction can be catalyzed by either acid or base. Since aldehydes/ketones can become enolate ions [by donating their alpha hydrogen, covered just ], the negatively charged carbon on the enolate ion can attack the [positively charged carbon] carbonyl on the other aldehyde/ketone, thereby forming an alkoxide ion ([mathjax]RO^-[/mathjax]). The hydrogen returns to protonate the enolate ion [portion of the new alkoxide ion], thereby forming an aldol

© 2014 MR. SHUM

  • Aldol condensation: A second alpha hydrogen, along with the hydroxyl group, is removed, thereby forming an enol

© 2014 MR. SHUM

Tautomers are structural isomers [bonded differently, discussed ], where a proton shifts. Aldehydes/ketones exist in equilibrium with its enol tautomer (an alcohol), the alpha hydrogen shifting from the alpha carbon to the oxygen, creating this alcohol. Keto-enol tautomerism is an equilibrium [and not resonance], which favors the keto form.

© 2014 MR. SHUM

Conjugated system is where there are alternating single and double bonds. They have increased stability, over systems with isolated double bonds [separated with more than, rather than just, one single bond]. This increased stability can alter already said rules, such as Markovnikov’s [which attempts to create the most stable carbocation].

For example, a double bond between the alpha and beta carbons of a carbonyl, is a conjugated system.

Normally, if an electrophile (electron lover) is added to an alkene, by Markovnikov’s rule, the electrophile will add on the carbon with least alkyl substituents [discussed ]. However, in the just said conjugated system, the electrophile may add to the carbonyl oxygen.

Another example, in the just said conjugated system, a nucleophile (likes to donate electrons) may add directly to the beta carbon, instead of adding to the carbonyl carbon [which is partially positive], as expected.

© 2014 MR. SHUM

Formative learning activityMaps to RK5.B
What are aldehydes? What are ketones?

3 Carboxylic acids

Carboxylic acids are compounds with the carboxyl [mathjax]-COOH[/mathjax] group, which is a carbonyl attached to a hydroxyl group.

© 2014 MR. SHUM

The simplest carboxylic acids include formic acid ([mathjax]H-COOH[/mathjax]), acetic acid ([mathjax]\ce{CH3-COOH}[/mathjax]) and benzoic acid ([mathjax]Benzene-COOH[/mathjax]).

Aliphatic acids are where alkyl groups attach to carboxylic acid. Aliphatic acids with long carbon chains as their alkyl groups, are known specifically as fatty acids (refer ).

The conjugate base of carboxylic acids are carboxylate ions, and end with the suffix “-ate”.

The conjugate base of acetic acid, is the acetate ion, which can be abbreviated as [mathjax]OAc^-[/mathjax].

Carboxylic acids are one of the strongest organic acids, but is weak compared to inorganic acids.

For instance, it is less acidic than the hydronium ion [mathjax]\ce{H3O^+}[/mathjax], having a positive [mathjax]pK_{a}[/mathjax], compared with hydronium which has a negative [mathjax]pK_{a}[/mathjax] [specifically, -1.74].

The increased resonance of the carboxylate ion increases its acidity. When carboxylic acid is deprotonated, both oxygens can take on some of the negative charge. As the negative charge is spread over a larger area, there is increased stability of this conjugate base, meaning its acid will be more acidic.

© 2014 MR. SHUM

As the molecular mass of carboxylic acid increases, its acidity and water solubility decreases, because of the dominance of the nonpolar alkyl (R) group. Carboxylic acids follow the melting and boiling point trends of hydrocarbons, but have far higher melting and boiling points, due to hydrogen bonding. Although shorter carboxylic acids are liquids, carboxylic acids with longer alkyl groups are usually solid, unless containing double bonds. Because of the presence of two oxygens, carboxylic acids can double hydrogen bond [forming 2 hydrogen bonds per molecule]. It can also hydrogen bond with itself, creating a dimer. Dimers effectively double the molecular weight of carboxylic acid, thereby further increasing its boiling point. Carboxylic acids also exist in dimers in nonpolar solvents, through self-association.

© 2014 MR. SHUM

The reactions where carboxylic acids are a reactant, include:

  • Although carboxylic acids have a strong acidic function, like the other carbonyl groups, they are also good electrophiles (electron lovers). The distinction with aldehydes and ketones however, is whereas they like to undergo nucleophilic addition; carboxylic acids [as well as their derivatives, discussed ] like to undergo nucleophilic substitution [because water is a great leaving group]. An example of this is:
    • Reaction [of the carboxylic acid] with an alcohol, where the alcohol [as usual] acts as a nucleophile (electron donating), and the carboxylic acids acts as an electrophile. The acid protonates the hydroxyl group, releasing water. The remaining product is the ester [mathjax]R-COO-R'[/mathjax], which are carbonyls between a carbon and an oxygen (in turn bonded to another carbon). Esters are formed in the presence of a dehydrating agent

© 2014 MR. SHUM

  • Reaction with thionyl chloride ([mathjax]SoCl_{2}[/mathjax]), where the chlorine substitutes the hydroxyl group [on the carboxylic acid], leaving an acyl chloride (aka acid chloride)

    © 2014 MR. SHUM

    Acyl chlorides are acidic, for reasons analogous to the aldehyde (discussed just , namely, by donating an alpha hydrogen). Since chlorine [in the acyl chloride] is electron withdrawing (being highly electronegative), this makes the carbonyl carbon even more positive, stabilizing the conjugate base [which has lost a hydrogen, and hence positive charge]. Therefore, acyl chloride is more acidic than aldehyde. Like other carbonyl groups, acyl chloride [in and of itself] is a good electrophile, and therefore undergoes nucleophilic attack. Because the chloride ion is an excellent leaving group, acyl chlorides like to undergo nucleophilic substitution. In fact, reacting an acyl chloride with alcohol yields an ester; reacting an acyl chloride with carboxylate ion yields an acid anhydride, which is where two carbonyl carbons are separated by an oxygen

© 2014 MR. SHUM

© 2014 MR. SHUM

Formative learning activityMaps to RK5.C
What are carboxylic acids?

4 Acid derivatives


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Chapter 5: Oxygenic compounds - Organic chemistry - Pre-med science - MR. SHUM'S CLASSROOM