Codex @codex  0

Here an amide means a carbonyl group whose carbon is bonded directly to nitrogen; each of $R$, $R^{\prime }$ and $R^{\prime \prime }$ may be hydrogen or a group attached through carbon. A peptide bond contains this linkage. Chemical resonance distinguishes its nitrogen from that of an amine. ^[ref] and ^[ref]

An amido ligand contains an anionic nitrogen donor, such as $\mathrm{N}{\mathrm{R}}_2^{-}$. A neutral secondary amine retaining its N–H bond is a different donor type; confusing them changes formal metal oxidation state.

A simple neutral amine has nitrogen bonded to one, two, or three groups attached through carbon, with hydrogen filling the remaining positions in the neutral three-bond form. These are the primary, secondary, and tertiary forms respectively. An amide has different connectivity to a carbonyl group. ^[ref]

An amino acid combines carboxylic acid and amine functionality in the same molecule; the name alone does not specify their separation. An alpha-amino acid has its amino nitrogen attached to the carbon immediately adjacent to the carboxyl carbon, the amino acid alpha carbon. For example, ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ is glycine, whereas ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ has an extra intervening carbon and is not an alpha-amino acid. These chemical formulas describe connectivity, not the predominant protonation state in water.

Most common proteinogenic amino acids share the skeleton ${\mathrm{H}}_2\mathrm{N}-\mathrm{CH}(R)-\mathrm{COOH}$, with $R$ the amino acid side chain. In glycine, $R$ is hydrogen; in alanine, $R=\mathrm{C}{\mathrm{H}}_3$. Proline is a useful exception to the displayed primary-amine skeleton: its amino nitrogen is part of a ring and has a second carbon substituent. The shared backbone permits assembly into polypeptides, while different amino acid side chains give the resulting proteins diverse chemistry. ^[ref]

In a chemical solution, protonation changes the electric charges without changing this backbone. Free glycine near neutral pH is predominantly ${\mathrm{H}}_3{\mathrm{N}}^{+}-\mathrm{C}{\mathrm{H}}_2-\mathrm{CO}{\mathrm{O}}^{-}$, a zwitterion. Its positive and negative groups are joined within one molecule; zero net electric charge does not mean absence of local electric charges, nor does it mean the uncharged drawing ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ predominates. Glycine protonation explains how lowering or raising pH changes the balance. ^[ref]

Building a protein joins the carboxyl carbon of one amino acid to the amino nitrogen of another through a peptide bond, an amide linkage. The formal net condensation loses the elements of water; cellular translation uses activated substrates at a ribosome, rather than simply mixing free amino acids in water. Incorporated units are amino acid residues. The interior amide groups no longer have the same acid/base behavior as the two free terminal groups of glycine, so its free-molecule glycine titration cannot be copied independently at every chain position. ^[ref]

Chirality distinguishes most common proteinogenic amino acids from glycine. The other nineteen members of the conventional twenty have a stereocenter at their amino acid alpha carbon; ordinary translation incorporates their L forms. Glycine's two identical hydrogen substituents make it achiral. Thus being an amino acid, or even an alpha-amino acid, does not by itself imply chirality. ^[ref]

A tert-butoxycarbonyl group used to protect an amine as a carbamate. Acid-promoted cleavage releases carbon dioxide and restores the amine.

Diisopropylethylamine is a sterically hindered tertiary amine base. It can remove protons and trap acid while competing relatively weakly as a nucleophile.

A hydrogen bond donor is the $X-\mathrm{H}$ group supplying the attached hydrogen in a hydrogen bond $X-\mathrm{H}\cdots Y$. The donor atom $X$, or the whole molecule containing it, may also be called the donor. The terminology does not imply transfer of a free proton: in the ordinary water pair, the O–H covalent bond remains. Familiar donors include O–H groups in water and N–H groups in Ammonia. See Andrew Glasfeld, Intermolecular Attraction, pp. 12–13: donor and acceptor roles.

The attached hydrogen is essential to this role. At the nitrogen site, an unprotonated amine $R_3\mathrm{N}$ can be a hydrogen bond acceptor, but has no N–H hydrogen bond donor. Protonation gives $R_3{\mathrm{NH}}^{+}$: the new N–H group can donate, while that nitrogen no longer has the accepting lone pair. This is a change of chemical form, not a permanent label attached to a chemical element. Here $R$ denotes a group attached through carbon; the statement concerns the nitrogen site and does not rule out weaker C–H associations elsewhere. See McMurry, Organic Chemistry, 24.3: amine protonation and Glasfeld: protonated amines as donors.

An amide with an N–H covalent bond can donate even though its nitrogen is ordinarily not an accepting site. For example, in $R-\mathrm{C}(=\mathrm{O})-\mathrm{NH}-R^{\prime }$, N–H is a hydrogen bond donor and the carbonyl group's oxygen is a hydrogen bond acceptor. Replacing the remaining N–H by another group attached through carbon removes this N–H donor without removing the accepting oxygen. The analogous division of roles in a peptide bond helps explain protein structure. See Glasfeld: amide roles and biological interactions. The useful question is therefore which site supplies the hydrogen, rather than whether the whole substance is simply “hydrogen bonding”.

A compound containing a carbon–nitrogen double bond. Reversible condensation of an aldehyde with a primary amine gives an imine and water under suitable conditions.

$\mathrm{LiAl}{\mathrm{H}}_4$, a strong hydride donor capable of reducing ketones to alcohols and amides to amines, with oxygen removal in the latter transformation.

A monomer is a chemical substance whose molecules can undergo polymerization and contribute units to the essential structure of a polymer. A monomer molecule is the individual reactant; its incorporated monomeric unit is the portion identifiable as derived from that reactant. Incorporation can change chemical bonds and release small byproducts, so the unit in the chain need not have the complete molecular formula of the feed molecule. See IUPAC: monomer molecule and IUPAC, A brief guide to polymer terminology: monomeric units.

Three different counts answer three different questions. Monomer molecules describe the feed; monomeric units trace that feed's contributions to the product; a constitutional repeating unit describes the smallest chemical pattern repeating along a regular chain. In Nylon 6,10, two different monomers supply one interior constitutional repeating unit,Its molecular formula is ${\mathrm{C}}_{16}{\mathrm{H}}_{30}{\mathrm{N}}_2{\mathrm{O}}_2$. The diamine feed is ${\mathrm{C}}_6{\mathrm{H}}_{16}{\mathrm{N}}_2$, and the diacid-chloride feed is ${\mathrm{C}}_{10}{\mathrm{H}}_{16}\mathrm{C}{\mathrm{l}}_2{\mathrm{O}}_2$; subtracting two $\mathrm{HCl}$ gives the interior-repeat budget. For a finite linear chain made from $n$ of each reactant, there are $2n-1$ joining connections, hence $2n-1$ formal $\mathrm{HCl}$ eliminations, rather than $2n$. One amine end and one acid-chloride end remain in that ideal unmodified chain. This is a stoichiometry check on the depicted reaction, not a claim that the washed experimental thread retains those ends. The reacting end-group chemistry is documented in Hammond, lecture 5, p. 4; the specified Nylon 6,10 reactant pair is reported in Polymer Day, nylon demonstration.

Ethene shows the reverse counting mismatch. One $\mathrm{C}{\mathrm{H}}_2=\mathrm{C}{\mathrm{H}}_2$ monomer molecule contributes a two-carbon $-\mathrm{C}{\mathrm{H}}_2-\mathrm{C}{\mathrm{H}}_2-$ monomeric unit to ideal linear polyethylene, without a small byproduct in that growth step. But the smallest constitutional repeating unit of its uniform backbone is just $-\mathrm{C}{\mathrm{H}}_2-$: a chain containing $m$ incorporated ethene monomeric units contains $2m$ such interior one-carbon repeats. End groups are additional bookkeeping. The frequently drawn $[-\mathrm{C}{\mathrm{H}}_2-\mathrm{C}{\mathrm{H}}_2-{]}_m$ is useful for tracing the feed, although it is not the smallest constitutional repeat. The minimum-pattern definition is given in IUPAC: constitutional repeating unit; the ethene growth chemistry is described by ^[ref].

A segment of a freely jointed chain or Gaussian chain instead belongs to a statistical model. It can represent many chemical bonds and several constitutional repeating units; its length and the segment count are chosen to describe chain conformation at the intended scale. The three-repeats-per-segment drawing in Figure "From two liquid layers to a Nylon 6,10 thread: monomers, a constitutional repeating unit, and statistical segments" is a deliberately arbitrary coarse-graining example, not a measured Kuhn length. Always state the counting convention before substituting a segment count for a degree of polymerization. This separation lets chemistry track which chemical atoms entered the material while statistical models track how the material bends and extends.

Use ionic electron counting, counting each ordinary donor atom once and keeping ligand charge distinct from denticity. A is 16-electron, B is 14-electron and C is 16-electron, so none is an 18-electron complex under this convention.

A contains a modified, monoanionic PNP pincer: the exocyclic double bond and altered pyridine-ring bond pattern in the drawing matter. Its two phosphines and its central N donor provide six electrons altogether, while neutral N${}_2$ provides two. Neutrality then gives Co(I), $d^8$, and $8+6+2=16$. Treating the modified pincer as a neutral intact pyridine ligand would incorrectly produce Co(0) and a 17-electron count. A four-coordinate approximately square planar molecular geometry in a $d^8$ complex can leave the strongly sigma-antibonding orbital empty and be stable at 16 electrons. The underlying modified-pincer chemistry has been examined using structure, spectroscopy and electronic-structure calculations.^[ref]

B has a neutral tertiary amine donor at the centre of its tripod and three anionic amido arms. Their combined charge is $-3$, so Re is Re(III), $d^4$. The four N donors give eight electrons and N${}_2$ gives two: $4+8+2=14$. Such an electron count is not inherently unexpected in an amido-supported complex: strong amido pi donation and the imposed five-coordinate geometry alter the orbital energies, and the empty orbitals are not nine equivalent slots that must all be filled. Steric protection and chelation also help stabilize this coordinatively restricted structure. The 14-electron figure uses the usual two-electron ionic count for each amido donor; pi bonding should not be appended to it inconsistently.

C has an anionic acyl carbon donor and a neutral phosphine in the chelate, together with two neutral PMe${}_3$ donors. Thus Co(I), $d^8$, receives $2+2+4=8$ ligand electrons, giving $8+8=16$. This is again a reasonable four-coordinate $d^8$ structure. The acyl C=O is part of a carbon-bound acyl ligand, not an additional free CO donor.

A and C are chiral; B is achiral. In A, a quaternary ammonium stereocenter occurs because nitrogen has four different substituents: phenyl, methyl, ethyl, and the sulfinylethyl chain. It has no nitrogen lone pair available for ordinary pyramidal inversion of an amine. The sulfoxide sulfur is also stereogenic: its pyramidal arrangement distinguishes oxygen, methyl, the nitrogen-containing chain, and the lone-pair direction. There are two independent stereocenters and no internal symmetry, giving four configurations in two pairs of enantiomers. This is chirality of the cation; a bromide counterion does not remove it.

B can adopt a trans-1,4-dimethylcyclohexane chair with both methyl groups equatorial. An inversion centre at the chair centre exchanges its opposite carbon atoms and methyl groups. Its mirror image is therefore superposable: trans substituents in a flat ring drawing do not by themselves prove chirality. ring inversion gives the less favourable diaxial conformer without changing the trans configuration.

In C, tetrahedral phosphorus has four different substituent directions: oxo, methoxy, ethoxy, and phenoxy. C has a phosphorus stereocenter. Delocalization in the P–O bonds does not make these four ligand environments identical. A tetrahedral drawing and its mirror cannot be superposed without exchanging two ligands.

Transfer is favourable when new water–solute interactions compensate the cavity and reorganization costs of accommodating the solute. The Gibbs energy also includes the loss of solute–alkane interactions; it is not simply a count of hydrogen bonds. isobutane cannot compensate those costs with strong directional interactions, explaining its positive transfer Gibbs energy. acetone and both amines can accept hydrogen bonds from water and have favourable electrostatic solvation, making their transfer moderately favourable. isopropylamine can additionally donate to water, consistent with a somewhat greater preference for water than trimethylamine.

acetamide combines a strong carbonyl acceptor with N–H donors and has the most favourable hydration in the group, accounting for its much more negative transfer Gibbs energy. Its pure solid lattice is not an extra sublimation penalty to insert here: the stated process starts from a dilute alkane solution and ends in dilute water, rather than dissolving the pure crystal. The nonmonotonic relationship between hydrogen-bond acceptor parameter and transfer Gibbs energy is expected because donor strength, nonpolar surface, solvent cavity formation, and all other solvation contributions also enter.

For matched standard states, $\Delta G_{\mathrm{tr}}^{\circ }=-RT\ln K_{\mathrm{tr}}$, with $K_{\mathrm{tr}}$ the water-to-alkane activity ratio. As an illustrative 298 K calculation, the hydrocarbon value implies $K_{\mathrm{tr}}\simeq 7.0\times 10^{-4}$, whereas the amide value implies approximately $3.6\times 10^4$. These are standard-state partition preferences, not absolute aqueous solubilities. amine protonation could introduce an additional pH-dependent contribution to an experimentally measured distribution coefficient, but no such speciation information is supplied and it is not needed for the molecular comparison.

The clearest comparison is between the two amines, which have the same molecular formula and molar mass. isopropylamine can donate N–H hydrogen bonds to neighbouring nitrogen lone pairs; trimethylamine has no N–H donor. The resulting intermolecular association raises the primary amine's boiling point, allowing it to remain liquid at room temperature, whereas trimethylamine is gaseous. Independent phase-change data place their normal boiling points on opposite sides of room temperature.^[ref]

acetone has a substantial carbonyl dipole and London dispersion forces sufficient for a room-temperature liquid, even though it cannot build a strong donor–acceptor hydrogen bond network by itself. isobutane has mainly London dispersion forces and a compact shape and remains gaseous. acetamide combines carbonyl acceptors with two N–H donors, allowing an extended, directionally bonded crystal lattice; favourable packing as well as intermolecular association stabilizes its solid state.

These compounds have similar molar masses, so mass alone cannot explain the differences. The hydrogen-bond acceptor parameter also cannot predict the phase on its own: a pure substance needs complementary donors to exploit strong acceptor sites, and freezing additionally depends on crystal packing and entropy. A stronger acceptor does not automatically imply a higher melting point for arbitrary molecules.

The acceptor-strength trend is amide oxygen and amine nitrogen strongest, ketone oxygen weaker, hydrocarbon essentially nonaccepting. trimethylamine and isopropylamine each provide a relatively available nitrogen lone pair; adding N–H bonds changes donor ability much more conspicuously than it changes the acceptor ranking in this comparison. Alkyl substitution and solvation modify the precise values, so the matching amine parameters should be read as the stated empirical strengths rather than a universal equality of all amines.

In acetamide, nitrogen lone-pair donation contributes an ${\mathrm{O}}^{-}-\mathrm{C}={\mathrm{N}}^{+}$ form contributing to resonance in chemistry, increasing electron density at oxygen and making it a strong hydrogen bond acceptor. The amide acceptor is oxygen, not nitrogen: the nitrogen lone pair is delocalized into the carbonyl. acetone also accepts at oxygen, but lacks this nitrogen-to-carbonyl donation and has the smaller hydrogen-bond acceptor parameter. isobutane has neither a heteroatom lone pair nor a comparable acceptor site; its zero value is consistent with the absence of an ordinary directional hydrogen bond acceptor.

Ammonia and cyclohexylamine are sigma-donor ligands; chloride and acetate are sigma- and pi-donor ligands. The nitrogen lone pair of each amine points toward the metal and forms the donor interaction. These saturated amines have no low-lying conjugated acceptor system that would make them conventional pi-acceptor ligands.

chloride uses a lone pair for sigma donation and has additional occupied $p$ orbitals perpendicular to the bond that can donate with pi symmetry. An oxygen-bound acetate similarly has occupied oxygen-centred orbitals available for sigma and pi donation, although its carboxylate resonance in chemistry changes their energies and distribution. Neither should be classified as a pi acceptor merely because its bonding can be drawn with multiple bonds or resonance in chemistry contributors. None of these four is a standard sigma-donor/pi-acceptor ligand.

The alcohol oxygen attacks sulfur of methanesulfonic anhydride. Cleavage of the anhydride S–O bond releases methanesulfonate, and the amine base removes the O–H proton, giving the corresponding mesylate. This activation preserves the substrate C–O bond while replacing the poor hydroxide leaving group by $\mathrm{OS}{\mathrm{O}}_2\mathrm{Me}$.

The base then removes a hydrogen from the adjacent methylene on the side toward the vinyl chloride. In a favorable antiperiplanar arrangement, C–H electrons form the new C=C bond while the C–OMs bond breaks. An E2 elimination creates the alkene between the former alcohol carbon and that methylene. It links the two neighboring unsaturated regions into the extended conjugated triene segment, while the pre-existing carbon skeleton and vinyl chloride are retained.The left-hand polyenoate portion is unchanged. The base is diisopropylethylamine; it accepts acid during mesylation and promotes elimination. The product's E/Z mixture concerns the newly formed alkene, and no single geometry needs to be assigned.

4-Fluorophenol probes acceptor strength because it donates its OH hydrogen. The qualitative order is C $>$ D $>$ B $>$ A: the electron-rich lactam oxygen is the strongest acceptor here, the secondary amine is next, pyridine nitrogen is intermediate, and aldehyde oxygen is weakest. Resonance donation from amide nitrogen increases the lactam oxygen's basicity relative to an ordinary aldehyde or ketone oxygen. The N-methylpyrrole site in A does not add an independent amine-like acceptor.

N-Methylpyrrolidin-2-one is a carbonyl acceptor without N–H, so it instead probes the solute's donor ability. B $>$ C $\gg$ A and D: B's phenolic OH is a strong donor, the lactam N–H of C is appreciable, A lacks a conventional donor, and D's neutral secondary-amine N–H is weak. The amine can be a good acceptor and a poor donor at the same time; the two properties are not opposites on one scale.

These are association equilibria in cyclohexane, where solvent competition for hydrogen bonds is weak. The quoted constants should be compared within each probe series, not treated as solvent-independent measures. At 298 K, as an illustrative common temperature, a tenfold increase in $K_a$ corresponds to a binding free-energy advantage $RT\ln 10\simeq 5.7\mathrm{kJ}\mathrm{mo}{\mathrm{l}}^{-1}$. This does not imply the experiment's temperature was specified, nor that every difference is the energy of one isolated hydrogen bond.

A: aldehyde oxygen is the best acceptor; there is no conventional strong O–H or N–H donor. The N-methylpyrrole nitrogen contributes its lone pair to aromatic bonding and is not an ordinary amine acceptor. A formyl C–H or ring C–H can participate in weak contacts, but is not comparable to the donors in B and C.

B: pyridine nitrogen is the best acceptor and the phenolic OH is the best donor. Its oxygen can accept more weakly, but nitrogen provides the primary basic site in the depicted hydroxypyridine form.

C: lactam carbonyl oxygen is the best acceptor and the amide N–H is the donor. amide nitrogen is not a useful acceptor because its lone pair is delocalized toward the carbonyl.

D: the secondary amine nitrogen is the best acceptor, and its N–H is the only conventional donor, but a weak one here. Its ketone oxygen is also an acceptor, although weaker than the amine site in this comparison. These assignments distinguish functional-group identity and lone-pair availability, rather than counting heteroatoms.

In $A$, the tridentate ligand contains one anionic phenoxide ligand, a neutral secondary amine with its N–H bond intact, and a neutral phosphine ligand. The three chloride ligands contribute another three negative charges. Consequently the neutral complex has Ti(IV), $d^0$, and 12 valence electrons:The N–H label is essential: counting this nitrogen as an anionic amido ligand would give the wrong oxidation state. A six-coordinate early-metal complex need not obey the 18-electron rule.

In $B$, the substituted cyclopentadienyl ligand is ${\eta }^5$ and anionic, while the three-carbon bent ligand is an anionic ${\eta }^3$ allyl ligand, a four-electron donor in ionic counting. The pendant pyridine nitrogen is uncoordinated. Therefore Mo(II), $d^4$, 18 electrons follows fromThe curved delocalization mark across the three-carbon ligand must not be read as a separate alkene or alkyne.