In an acid-base reaction the reactant where the bond to H is breaking is the acid and the reactant where the bond to H is forming is the base. Likewise, the product formed when the bond to H is broken is called the conjugate base and the product formed when the bond to H is formed is called the conjugate acid. For any group of acids, H-X (where X can be almost any other atom), the strongest acid will have the most stable conjugate base. Since stability is inversely correlated with basicity, it is possible to express the same idea by saying: the stronger the acid, the weaker the conjugate base. The converse is also true the weaker the acid, the stronger the conjugate base.  It is important to make the distinction that not all weak acids are strong bases.  Methane (CH₄) is a weak acid, but it cannot serve as a base as it does not have a lone pair. A better way to make the distinction is weak acids have strong conjugate bases where the conjugate base of CH₄, CH₃^– is an extremely strong base.

While charged species are more unstable than neutral species, an acid is becoming more negative with the loss of a proton so the stability of the new lone pair on the conjugate base is significant in determining how favorable the reaction will be. Generally, the lower the charge density, the more stable a species is. In the same way, high charge densities tend to be less stable than low charge densities. In order to spread out a charge to gain greater stability the more volume/surface area a charge occupies the more stable it will be. So as we go down the periodic table from Fluoride to Iodide anions, the magnitude of the negative charge does not change, but the volume that it occupies does. Iodide ion, being considerably larger than fluoride ion (206 pm vs. 119 pm) is more stable, which means that H-I is a stronger acid than H-F. In addition, adding electron withdrawing groups to an atom can have a similar effect to that of increasing electronegativity. For example, replacing a hydrogen with a chloride stabilizes the negative charge increases.

Resonance is yet another way a negative charge can be dispersed in a molecule. If the conjugate base has a charge which can interact with adjacent double bonds or p orbitals, the stability of the conjugate base will increase. This leads to increased acidity of what becomes the conjugate acid. The closer a negative charge is to the nucleus, the more stable it is. Another way of saying this is when considering sp3 (alkane) to sp2 (alkene) to sp (alkyne) hybridization, the stability of the negative charge increases. Thus, alkynes are remarkably acidic compared to alkanes.

The equilibrium constant Ka, also known as the acidity constant is a measure of how likely an acid is to give up a proton or an H. By taking the logarithm of the acidity constant Ka, multiply it by negative, we obtain the pka. The most common measure of how acidic a substance is. The smaller the pka (as well as the larger and more negative), the stronger or more likely to give up a proton the acid is. If the pH is below the pka, the proton remains on the molecule. If the pH rises above the pka, then the proton ionizes or is removed from the molecule. If the pH equals the pka then according to Henderson Hasselbalch there is 50% of the protonated acid and 50% of the deprotonated conjugate base.

A nucleophile donates an electron pair to an electrophile to form a chemical bond during a reaction. All molecules or ions with a free pair of electrons or at least one pi bond can act as nucleophiles. As nucleophiles donate electrons, they are by definition Lewis bases. The most common features of a nucleophile are electrons that are available to be shared as a formal negative charge, a partial negative charge, usually in conjunction with a polar bond, a pi bond (double bond) or lone pairs. A Lewis base in the reaction shares an electron pair with a Lewis acid to make a new covalent bond. A Lewis base is an electrophile (a molecule that loves electrons). One of the important distinctions to make after saying that all nucleophiles are Lewis bases in that they donate a lone pair of electrons is that a “base” (or, “Brønsted base”) is a nucleophile when it’s forming a bond to a proton (H+). A nucleophile attacks any atom other than hydrogen. Reactions where nucleophiles attack carbon-based electrophiles are significantly more sensitive to steric effects, because empty orbitals on carbon are not as accessible. The medium (solvent) in which a reaction takes place can influence the rate of a reaction. Specifically, the solvent can greatly reduce the nucleophilicity of some Lewis bases through hydrogen bonding.

A carbonyl group (double bond oxygen to a carbon) is found on several functional groups: aldehydes, ketones, amides, and carboxylic acids. In aldehydes, the carbonyl group is on the primary carbon, at end of a carbon chain, while in ketones, it is on a secondary carbon, in the middle of a carbon chain. The double bond in the carbonyl group is very susceptible to chemical reactions, specifically, oxidation and reduction reactions and the formation of hemiacetals and acetals. The names of aldehydes and ketones are simply derived by dropping “-e” from the root and adding “-al” or “-one” respectively. A position number is needed for ketones since the carbonyl group may be on any number of several carbons in the middle of a chain. For example, propanone also known as acetone is primarily a solvent since it dissolves in both water and non-polar organics; however, it may also be present in the urine of diabetics. It is also frequently used in fingernail polish remover. The carbonyl on the aldehyde is always on the number one carbon so no position number is needed. For example, methanal also known as formaldehyde is used to synthesize methanol and many plastics such as Bakelite and Melmac. In addition to its antiseptic properties, formaldehyde has also been used in embalming and preservation of biological specimens.

An amine is an organic compound, similar to ammonia (NH₃), that contains a nitrogen atom bonded to one or more alkyl groups on each molecule. Similar to alcohols, amines can be classified as primary secondary or tertiary. It may be necessary to include a number in the suffix to indicate which carbon group the amine is attached to. Secondary and tertiary amines are named using the locator, N, to indicate the attachment of additional chains to the nitrogen atom. Amines are polar and many can hydrogen bond. Amines have higher melting and boiling points than their corresponding alkanes. Small amines are soluble in water. Amines behave as weak bases in water. Amines can undergo neutralization reactions with acid. Primary amines can be synthesized by reacting an alkyl halide with ammonia. Secondary amines require an alkyl halide and a primary amine. Tertiary amines require an alkyl halide and a secondary amine.

In comparison, an amide is an organic compound that contains a carbonyl group bonded to a nitrogen atom. Amides can be synthesized by the condensation reaction of a carboxylic acid with ammonia or a primary or secondary amine. Amides are weak bases. Low molecular weight amides are soluble in water. Amides that have the ability to hydrogen bond will have higher melting and boiling points. Under acidic or basic conditions, amides can undergo a hydrolysis reaction (the reverse of condensation) to form an amine (or ammonia) and a carboxylic acid. Amines and amides are abundant in nature. They are a major component of proteins and enzymes, nucleic acids, alkaloid drugs (Nitrogen containing, weakly basic organic compounds).

(Functional Groups)

One of the most prevalent intermolecular forces in biochemistry is the attractive force between the hydrogen attached to an electronegative atom of one molecule and an electronegative atom of a different molecule. Usually the electronegative atom is oxygen, nitrogen, or fluorine, which has a partial negative charge. The hydrogen then has the partial positive charge. The hydrogen bond is a type of dipole.  The electronegative atom must have one or more unshared electron pairs as in the case of oxygen and nitrogen, and has a negative partial charge. The hydrogen, which has a partial positive charge tries to find another atom of oxygen or nitrogen with excess electrons to share and is attracted to the partial negative charge. This forms the basis for the hydrogen bond. Hydrogen bonding is usually stronger than normal dipole forces between molecules. Hydrogen bonding is not as strong as normal covalent bonds within a molecule.

Alcohols are organic molecules containing the hydroxyl functional group, where the OH is directly bonded to carbon. The carbon directly attached to OH is technically called the carbinol carbon. The carbinol carbon (carbon attached to OH), however, is the key to understanding the most common classifications we use for alcohols, that being “primary”, “secondary”, and “tertiary” alcohols. If the carbon attached to the hydroxyl is primary, it is attached to one other carbon. If it is a secondary alcohol, the carbon is attached to two other carbons. If the hydroxyl is attached to a carbon attached to three other carbons, it is a tertiary carbon. It is methanol if the hydroxyl is attached to only one carbon. Hydroxyl groups attached to aromatic rings are called, phenols. Not all functional groups containing OH are alcohols. If the OH is attached to a carbonyl (C=O), that functional group is called a “carboxylic acid”. The OH attached to an alkene is called an enol (ene + ol).

Ethers are a class of organic compounds that possess an ether group where an oxygen is connected to two carbons either alkyl or aryl groups. They have the general formula R–O–R′, where R and R′ represent the alkyl or aryl groups. There are two varieties of ethers: if the alkyl groups are the same on both sides of the oxygen atom, then it is a simple or symmetrical ether. However, if they are different, the ethers are called mixed or unsymmetrical ethers. A typical example of the first group is usually a solvent such as diethyl ether also and anesthesia commonly referred to simply as “ether” (CH₃–CH₂–O–CH₂–CH₃). Ethers are common in biochemistry, pervasive linkages in carbohydrates and lignin.

Similar to oxygen, sulfur is also a nonmetal found in organic compounds. The two amino acids containing sulfur are nonpolar and hydrophobic. The amino acid methionine is one of the most hydrophobic amino acids and often found on the interior of proteins. The amino acid Cysteine does ionize to yield the thiolate anion. Cysteines are also rare to find on the surface of a protein for several reasons. First, sulfur has a low propensity to hydrogen bond, unlike oxygen. As a result of this H₂S is a gas under conditions that H₂O is a liquid. Second, the thiol group of cysteine reacts with other thiol groups in an oxidation reaction that yields a disulfide bond. As a consequence, cysteine residues are most frequently buried inside proteins.

Any uncharged group in a molecular entity that is capable of dissociating by yielding an ion (usually an H⁺ ion) or an electron and itself becoming oppositely charged is an ionizable group. Every acidic or basic group on a molecule has a different “pK” (K is the dissociation constant) value. The dissociation constant is a quantity expressing the extent to which a particular substance in solution is dissociated into ions, equal to the product of the concentrations of the respective ions divided by the concentration of the undissociated molecule. The relationship between the pH of the solution it is in and the pK of the ionizable group will determine the predominant form of the ionizable group. Every acidic or basic group has an “acid form” (also known as the “protonated form”) and a “base form” (also known as the “deprotonated form”). For carboxylic acids, the protonated form (acid form) is –COOH and the deprotonated form (base form) is –COO^– . For amines, the protonated form (acid form) is –NH₃ ⁺ and the deprotonated form (base form) is –NH₂. If the pH of the solution equals the pK of the ionizable group, then the acid and base forms of that group will be present in equal amounts. If the pH of the solution is lower than the pK of the ionizable group, then the acid form of that group will be more abundant than the base form. (The predominant form is the protonated form.) If the pH of the solution is higher than the pK of the ionizable group, then the base form of that group will be more abundant than the acid form. (The predominant form is the deprotonated form.) Knowing the pH of the solution and using the previous three possible scenarios, then it is possible to determine if an ionizable group will be neutral, positively or negatively charged. It is important to note that pK values depend on temperature, ionic strength, and the microenvironment of the ionizable group.

Bond energy also known as bond enthalpy is the measure of bond strength in a chemical bond. IUPAC defines bond energy as the average value of the gas-phase bond dissociation energies (usually at 298 K) for all bonds of the same type within the same chemical species. When atoms combine to make a compound, energy is always given off, and the compound has a lower overall energy. When atoms bond together to form compounds they attain lower energies than they would possess as individual atoms. Heat, equal to the difference between the energies of the bonded atoms and the energies of the separated atoms, is released. Thus, the bonded atoms have a lower energy than the individual atoms do. When a bond is strong, there is a higher bond energy because it takes more energy to break a strong bond. This correlates with bond order and bond length. When the Bond order is higher, bond length is shorter, and the shorter the bond length means a greater the Bond Energy because of increased electric attraction. In general, the shorter the bond length, the greater the bond energy. The exact value of a C–H bond energy will depend on the particular molecule, all C–H bonds have a bond energy of roughly the same value because they are all C–H bonds. It takes approximately 100 kcal of energy to break 1 mol of C–H bonds, so the bond energy of a C–H bond is approximately 100 kcal/mol. A C–C bond has an approximate bond energy of 80 kcal/mol, whereas a C=C has a bond energy of about 145 kcal/mol. In order to calculate a more general bond energy find the average of the bond energies of a specific bond in different molecules to get the average bond energy.

The hydrophobic effect occurs when nonpolar substances aggregate in aqueous solutions and exclude water. The word hydrophobic means water-fearing minimizes the contact between water and nonpolar substances. For example, the hydrophobic effect is responsible for the separation of oil and water/ Hydrophobicity also plays a significant role in cellular membranes, formation of vesicles, protein folding, small molecule-protein interactions. Materials with an affinity for water, where water spreads across in order to maximizing contact are known as hydrophilic. Hydrophobic surfaces are where water self-segregates or the surface repels water, causing droplets to form. Hydrophobicity is the association of non-polar groups or molecules in an aqueous environment which arises from the tendency of water to exclude non-polar molecules.

A compound consisting entirely of carbons and hydrogens is a hydrocarbon. As the maximum number of atoms available to bond with carbon is equal to the number of electrons that are attracted into the outer shell of carbon. The outer shell of carbon comprises 4 electrons, and thus has 4 electrons available for covalent Hydrocarbons are classified based on the presence of single, double or triple bonds. Saturated hydrocarbons possess only single bonds and the number of carbons and hydrogens exist in the following ratio: C_nH_2n+2(1-r), where r is the number of rings. Hydrocarbons possessing only one ring are cycloalkanes. Saturated hydrocarbons can be linear or branched. Hydrocarbons with the same molecular formula but different structural formula are called structural isomers. Branched hydrocarbons can be chiral. Chiral saturated hydrocarbons are often found in the side chains of biomolecules such as chlorophyll and tocopherol.

Unsaturated hydrocarbons have one or more double or triple bonds. Those possessing double bonds are called alkenes. Those with double bonds have the formula C_nH_2n (assuming non-cyclic structures). Those possessing triple bonds are called alkynes. Those with triple bonds have the formula C_nH_2n−2. Aromatic hydrocarbons have conjugated double bonds and are also known as arenes. Hydrocarbons can take the form of gases, liquids, or solids.

Methane (CH₄) and ethane (C₂H₆) are gaseous at ambient temperatures and cannot be readily liquefied by pressure alone. While propane (C₃H₈) is easily liquefied, and often exists in ‘propane bottles’ mostly as a liquid, it can also be a gas. Likewise, butane (C₄H₁₀) is also easily liquefied for lighters. Pentane (C₅H₁₂) is a clear liquid at room temperature, commonly used in chemistry and industry as a powerful nearly odorless solvent of waxes and high molecular weight organic compounds, including greases. As a component of gasoline, hexane (C₆H₁₄) is also a widely used non-polar, non-aromatic solvent. The C⁶ through C¹⁰ alkanes, alkenes and isomeric cycloalkanes are the top components of gasoline, naptha, and jet fuel as well as specialized industrial solvent mixtures. With the progressive addition of carbon units, the simple non-ring structured hydrocarbons have higher viscosities, lubricating indices, boiling points, solidification temperatures, and deeper color.