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Ammonia is $\mathrm{N}{\mathrm{H}}_3$, a pyramidal molecule with a nitrogen lone pair. The lone pair can accept a proton to form ammonium or coordinate a Lewis acid.

In water, the Ammonia-ammonium equilibrium affects pH. Molecular Ammonia and the ammonium ion therefore have different charge states and should not be treated as interchangeable species.^[ref]

Ammoniacum is a plant gum-resin historically associated with Dorema ammoniacum. The name refers to a mixed plant product, distinct from an ammonium salt.

Ammonification converts nitrogen in organic compounds to Ammonia or ammonium during their breakdown. For example, microbial degradation of dead organisms can release the nitrogen that had been incorporated in amino acids.

Ammonification differs from nitrogen fixation, which begins with molecular nitrogen, and from nitrification, which oxidizes reduced inorganic nitrogen. Separating these transformations explains how decomposers reconnect living material to the nutrient pools used by primary producers.^[ref]

Ammonium is protonated Ammonia, $\mathrm{N}{\mathrm{H}}_4^{+}$. Its abundance relative to Ammonia depends on pH.

Ammonium acetate solution is an aqueous pharmaceutical preparation containing the ammonium salt of acetic acid. Its name specifies the principal solute but not, by itself, a concentration. Composition and strength must therefore be distinguished.

A salt containing ammonium and nitrate. Its thermal decomposition has condition-dependent pathways; the familiar nitrous oxide pathway is not universal.

Deamination removes an amino group from a compound. In amino acid metabolism, oxidative deamination of glutamate can release ammonium and regenerate a carbon skeleton for further reactions. This differs from transamination, which transfers nitrogen between molecules without directly releasing free ammonium. Coupling the two processes helps channel nitrogen from many amino acids toward common assimilation or disposal pathways. ^[ref]

Glutamate synthase transfers the amide nitrogen of glutamine to 2-oxoglutarate with coupled reduction, producing two glutamate molecules. It works with glutamine synthetase in nitrogen assimilation: the first enzyme captures ammonium into glutamine and the second distributes that nitrogen into glutamate. Different forms use different electron donors, so the enzyme name alone does not specify whether NADPH, NADH or reduced ferredoxin supplies reducing power. ^[ref]

Glutamine synthetase incorporates ammonium into glutamate to form glutamine, coupled to ATP hydrolysis. Glutamine can then supply nitrogen for other biosynthetic reactions, including the reaction catalysed by glutamate synthase. Coupling nitrogen incorporation to ATP consumption helps explain why nutrient assimilation depends on energy availability as well as the supply of ammonium. ^[ref]

Hydrolytic deamination replaces an amino group using water, releasing Ammonia or ammonium according to pH. Adenosine deaminase introduces solvent oxygen at the C6 position of adenosine.

Mistura Ammoniaci is an ammoniacum gum-resin mixture. The botanical gum-resin name must not be confused with an ammonium salt.^[ref]

Nitrite reductase catalyses reduction of nitrite. Assimilatory forms can produce ammonium for incorporation into cellular material; other forms produce nitric oxide in respiratory nitrogen metabolism. These are distinct reactions with different electron requirements and biological purposes. The generic name therefore needs a specified product and electron donor before it identifies a precise catalytic activity. ^[ref][ref]

Nitrogen assimilation incorporates inorganic or organic nitrogen into the compounds of a biological cell. In plants, absorbed nitrate must be reduced before its nitrogen can enter amino acids, whereas ammonium can enter the assimilation pathway more directly. These reactions require energy and carbon-containing precursors, linking nutrient acquisition to photosynthesis and metabolism.

Assimilation differs from nitrogen fixation, which converts atmospheric nitrogen into biologically accessible reduced forms. A plant may assimilate nitrogen supplied by a symbiotic partner without itself catalysing nitrogen fixation.

The nitrogen cycle connects the movement and chemical transformation of nitrogen in the atmosphere, organisms, soils and water. Nitrogen fixation converts molecular nitrogen into reduced forms; nitrogen assimilation incorporates available nitrogen into cellular compounds; ammonification returns organic nitrogen to ammonium during breakdown.

Nitrification and denitrification connect further oxidized and reduced forms under different environmental conditions. The distinction matters because a large atmospheric reservoir does not make all of its nitrogen directly available to every plant: biological access depends on the chemical form and on transformations carried out by other organisms.^[ref]

Warm C with dilute aqueous acid to hydrolyse the iminium ion to the second ketone. water attacks the iminium carbon, proton transfers give a carbinolamine, and C–N cleavage releases pyrrolidine, present predominantly as its ammonium salt in the acidic medium. The two carbon–carbon bonds constructed in the preceding Michael additions remain intact. This replaces the iminium nitrogen substituent by oxygen and gives the diketone D; neither oxidation of the skeleton nor reduction of the original ketone is required.

The reactive fragment is the C6 amidine-like portion of the purine ring; the N9–ribose attachment is retained. Write it locally as $N1=C6(\mathrm{N}{\mathrm{H}}_2)-$, with the rest of the fused ring understood. One productive acid catalysis route protonates N1, making C6 more electrophilic. water then adds at C6 while the C6=N1 pi electrons move onto N1. Subsequent proton transfers generate a carbinolamine and then a protonated amino leaving group:These are local bonding fragments: C6 retains its bond to the adjoining ring carbon at every step. In the addition step, an oxygen lone pair forms C6–O and the C6=N1 pi bond opens. During collapse, an oxygen lone pair reforms C6=O and the C6–N6 bond breaks toward the departing nitrogen. Solvent mediates each proton transfer; no direct unsupported transfer across a long distance is required.

water supplies the new C6 oxygen, and Ammonia is expelled after protonation of the leaving group. Final deprotonation gives the lactam form of inosine. In acidic bulk solution the released Ammonia is largely trapped as ammonium. The catalytic proton transfers regenerate acid around the substitution cycle; ammonium trapping separately affects the net proton balance. This is hydrolytic deamination, not cleavage of the glycosidic bond.

For the ordinary ester, the carbon nucleophile of a grignard reagent attacks the carbonyl carbon and moves the C=O pi pair onto oxygen. Collapse of the tetrahedral intermediate expels ethoxide, transiently giving ${\mathrm{R}}^1\mathrm{COR}$. This ketone is more electrophilic than the starting ester because it lacks an alkoxy group's stabilizing resonance donation. A second equivalent of the grignard reagent therefore adds to it before isolation:The negatively charged intermediates are associated with magnesium counterions. Merely reducing the amount of reagent to one equivalent does not generally trap the ketone selectively; it can leave unreacted ester together with the double-addition product.

In the first successful preparation, magnesium insertion into the primary C–Br bond gives n-butylmagnesium bromide. The carbon chain has four carbons, so its acetylation produces hexan-2-one, $\mathrm{C}{\mathrm{H}}_3\mathrm{CO}(\mathrm{C}{\mathrm{H}}_2{)}_3\mathrm{C}{\mathrm{H}}_3$, not pentan-2-one. Attack on acetic anhydride forms $\mathrm{C}{\mathrm{H}}_3\mathrm{C}({\mathrm{O}}^{-})(\mathrm{nBu})\mathrm{OCOC}{\mathrm{H}}_3$. Coordination of the anhydride-derived oxygens to magnesium can stabilize this tetrahedral addition complex. Under suitably cold, controlled-addition conditions it survives sufficiently to delay release of the free ketone until aqueous work-up has destroyed the remaining grignard reagent. Protonation followed by collapse releases acetate/acetic acid and the ketone.

This interpretation has direct experimental precedent: Melvin S. Newman and William T. Booth Jr. obtained methyl ketones by cold addition of grignard reagents to acetic anhydride, attributing selectivity to a persistent addition complex. The temperature and reagent-addition regime are genuine conditions on the explanation, rather than proof that an anhydride can never undergo overaddition; the exam scheme omits them.^[ref]

For the benzonitrile route, n-butyl attacks the nitrile carbon and one C≡N pi pair moves to nitrogen, producing the magnesium ketimine salt $\mathrm{PhC}(\mathrm{nBu})={\mathrm{N}}^{-}\mathrm{MgB}{\mathrm{r}}^{+}$. This anionic nitrogen-containing intermediate resists a second nucleophilic addition much more than a neutral carbonyl does. The ketone $\mathrm{PhC}(=\mathrm{O})\mathrm{nBu}$ appears only during acidic aqueous work-up, after organomagnesium has been quenched. Protonation gives the iminium ion; water attacks its carbon, proton transfers give a carbinolamine, and C–N cleavage from its nitrogen-protonated form produces the protonated ketone and Ammonia, followed by deprotonation. In the acidic mixture Ammonia is present largely as ammonium. This sequence explains why nitrile addition stops at a ketone without requiring the ketone itself to be resistant to grignard reagents.

The atom-labelled hydrolysis sequence isWater's lone pair attacks the iminium carbon while its C=N pi pair moves to nitrogen; the carbinolamine oxygen then reforms C=O while the C–N pair moves to the departing protonated amino group. Final deprotonation gives the neutral ketone. The arrows involving protonation and hydrolysis also exchange protons with the acidic aqueous reservoir; the condensed sequence tracks the carbon–nitrogen and carbon–oxygen transformations rather than displaying every solvent molecule.

The target is 5-Aminohexanoic acid, $\mathrm{H}{\mathrm{O}}_2\mathrm{C}(\mathrm{C}{\mathrm{H}}_2{)}_3\mathrm{CH}(\mathrm{N}{\mathrm{H}}_2)\mathrm{Me}$. Disconnect its terminal amine/carboxylic-acid relationship through hydrolysis of 6-methylpiperidin-2-one. This six-membered lactam follows from a regioselected Beckmann ring expansion of 2-methylcyclopentanone oxime.

Start with cyclopentanone. Form its enolate with lithium diisopropylamide in dry THF at low temperature, add methyl iodide, then quench to obtain 2-methylcyclopentanone. Control the methyl iodide/base stoichiometry to suppress a second alkylation. React the ketone with hydroxylamine to form its oxime and select the geometrical oxime isomer in which the bond to the methyl-substituted adjacent ring carbon is anti to the departing oxime oxygen group.

Activate the oxime, for example under appropriate acid-promoted Beckmann conditions. The anti methyl-bearing C–C bond migrates onto nitrogen as the N–O-derived leaving group departs, inserting nitrogen between the original carbonyl carbon and the methyl-substituted ring carbon. Hydration/tautomerization gives 6-methylpiperidin-2-one. The opposite oxime geometry would insert nitrogen on the other side and ultimately place methyl at a different position in the amino acid; oxime geometry is therefore an essential part of this proposal.

Hydrolyse the lactam with aqueous acid and heat, then adjust the work-up to the desired acid/ammonium form. Cleavage of its acyl–nitrogen bond opens the ring to $\mathrm{H}{\mathrm{O}}_2\mathrm{C}(\mathrm{C}{\mathrm{H}}_2{)}_3\mathrm{CH}(\mathrm{N}{\mathrm{H}}_2)\mathrm{Me}$ after suitable neutralization. All five original cyclopentanone carbons are retained, and the one methyl carbon comes from methyl iodide. A racemic mixture product is appropriate to the stereochemically unspecified target. The reaction sequence is an organic ring-expansion synthesis and requires no biological transformation.

Plants generally incorporate combined nitrogen into organic compounds, whereas animals eliminate the surplus nitrogen of metabolized compounds chiefly as Ammonia, urea or uric acid. The two processes connect nitrogen chemistry to the organism's carbon supply, water economy and environment.

Roots take up nitrate and ammonium from their surroundings. Nitrate must be reduced before its nitrogen can be incorporated in the usual amino form: nitrate reductase produces nitrite, and nitrite reductase produces ammonium. The balanced reduction, written without implying a single elementary reaction, isReducing equivalents and energy must be supplied by metabolism; nitrate is not simply deposited unchanged inside every protein.

In the modern biochemical account, glutamine synthetase incorporates ammonium into glutamine, using ATP; glutamate synthase transfers that nitrogen to a carbon skeleton derived from 2-Oxoglutarate, producing glutamate. Further transfer and synthesis distribute nitrogen into other amino acids, proteins, nucleotides and other cell constituents. Carbon metabolism therefore provides both energy and skeletons for nitrogen assimilation. These named enzymes and reactions explain the process today; they were not a completed molecular scheme in 1864.^[ref]

Ordinary higher-plant cells do not themselves reduce atmospheric molecular nitrogen merely because the gas surrounds the leaves. Biological nitrogen fixation is performed by particular microorganisms; symbiotic associations can supply fixed nitrogen to a host plant. The later elucidation of root-nodule symbiosis should be distinguished from what the examiner could have expected. Organic nitrogen can also be taken up in suitable circumstances, so nitrate and ammonium are important routes rather than an exhaustive prohibition on every other source.^[ref]

A useful assimilation experiment grows comparable seedlings in a defined medium containing all required minerals except combined nitrogen, with parallel nitrate- or ammonium-supplied cultures. Initial seed reserves, contaminating nitrogen, water and microbial growth must be allowed for. Growth and final nitrogen content are more informative than green appearance alone. A plant initially growing in a nitrogen-free solution may simply be consuming seed reserves; that observation does not demonstrate fixation of atmospheric nitrogen.

Animals obtain most of their nitrogen from organic food. Amino acid metabolism separates nitrogen handling from oxidation or reuse of the carbon skeleton. Free Ammonia is toxic at high concentrations, and mammals convert much of their waste nitrogen into urea in the liver; the kidneys then eliminate it in urine. Uric acid is also produced from purine breakdown. Renal ammonium excretion has a separate important connection with acid-base balance. Urea formation and urinary excretion are different processes in different organs.^[ref]

Many aquatic animals can release Ammonia directly into abundant surrounding water. Birds, many reptiles and many insects eliminate much nitrogen as relatively insoluble uric acid, conserving water; mammals generally depend more on soluble urea. These are broad physiological strategies with exceptions, not a rule that all animals have human urine. Faecal nitrogen includes unabsorbed food as well as endogenous material, while smaller losses can occur through skin and secretions. For a stated interval the accounting identity isPositive retention during growth and negative balance during tissue loss need not be errors of excretion. Nitrogen is redistributed or lost in compounds; it is not simply breathed out as all the atmospheric nitrogen passing through the lungs.

Ammonia is the volatile nitrogen–hydrogen chemical compound ${\mathrm{NH}}_3$, obtained historically from ammoniacal salts and from the decomposition of nitrogen-containing organic matter. Sources include the decay of animal and vegetable material, the conversion of urea in stale urine, and the destructive distillation of coal, bones or horn. In gasworks, much of the Ammonia was captured in the aqueous ammoniacal liquor during cooling and washing of crude coal gas. These sources do not mean that nitrogen-free constituents of coal spontaneously produce nitrogen.

An ammonium salt releases Ammonia when heated with a suitable chemical base. For ammonium chloride and slaked lime,The ionic principle is ${\mathrm{NH}}_4^{+}+{\mathrm{OH}}^{-}\to {\mathrm{NH}}_3+{\mathrm{H}}_2\mathrm{O}$. A generating vessel supplies a drying stage and then an inverted dry collecting vessel in which the lighter Ammonia displaces air. It is unsuitable for ordinary collection over water because it dissolves so readily. Quicklime can serve as a drying agent; a strongly acidic drying material would instead consume the Ammonia.

Ammonia is a colourless gas with a penetrating, irritating odour. Its approximate relative density against air is $17.03/28.97\simeq 0.59$. It is readily liquefied under suitable cooling or pressure, and its dissolution in water releases heat. It is toxic and corrosive at sufficient exposure; direct smelling is not an analytical requirement.^[ref]

The aqueous chemical equilibriumexplains the alkaline reaction and the change of moist red litmus to blue. The historical name “ammonium hydroxide” for the solution should not imply that every dissolved molecule has become a discrete molecule of ${\mathrm{NH}}_4\mathrm{OH}$. With hydrochloric acid, Ammonia forms ammonium chloride:The familiar white cloud where the gases meet consists of fine solid salt particles, rather than liquid water alone. In solution, Ammonia also acts as a ligand; an excess can produce a deep-blue copper–ammine coordination complex from suitable copper(II) solutions. Although Ammonia does not readily sustain an ordinary flame in air, it is not intrinsically incapable of combustion; sufficiently favourable mixtures burn.