In the case of the terminology, there is the type of chemical structure based on the saturation of carbon atoms, and then the shape of the molecule (in which are the pairs of terms that identify the names of isomeric compounds that are compounds) that have more than one shape or structure.
Atoms, Molecules, Compounds and Solutions:
The building blocks of all organic and inorganic materials is the atom, contained within the atom is the nucleus, made of the protons and neutrons, and the electron clouds (made of electrons orbiting the nucleus at various energy levels). Atoms link together to form molecules; these linkages are formed via sharing pairs of electrons (termed covalent bonding) or by one atom letting a second atom take away an electron (termed ionic). Covalent bonds are stronger than ionic bonds since the covalent bonds are “held together” by the shared electrons, while the ionic bonds are weaker since the atoms are “held together” by electrostatic charge between the atoms (a positive and a negative). Covalent bonds are formed by elements with a valence count between 3 and 6, remember that the valence electrons are the electrons in the outermost energy level. In some covalent molecules, electrons are not evenly shared within the electron cloud develop poles, termed polar molecules, atoms that have the electrons within the orbits of the cloud for a longer period of time are referred to as partially positive (δ+) while the atom with the shorter period of time for the electron with the orbits are referred to as partially negative (δ-). These polar molecules form special bonds referred to as hydrogen bonds (because most of the molecules exhibiting polarity due to the hydrogen contained within the molecule.
For the body there are a host of important elements and molecules, but the five most important elements are: Carbon (C), Oxygen (O), Hydrogen (H), Nitrogen (N) and Phosphorus (P). These five are followed by Calcium (Ca), Iron (Fe), Chlorine (Cl), Sodium (Na), Sulfur (S) and Magnesium (Mg). These elements form number of molecules, the most important of these are the macromolecules that act as the building blocks for the cells and tissues of the body, these include: carbohydrates (C, H, O), lipids (C, H, O), amino acids (C, H, O, N, S), nucleic acids (C, H, O, N), adenosine triphosphate (C, H, N, O, P) and water (H, O). Since a majority of the body is made of fluid, the behavior of these molecules will vary with interactions with water.
When compounds are placed into water, the mixture is deemed a solution; the type of solution depends on the several characteristics that establish the bonding principles forming covalent and ionic molecules, and polar and nonpolar molecules. This interaction forms solutions where the solid elements are dispersed throughout evenly, in clumps and clusters (colloids), or where the elements remain as solid particles within the liquid (suspensions). Generally speaking: polar and nonpolar molecules do not interact and the non-polar molecules form micelle (balls) that suspend within the liquid, while ionic molecules dissociate (separate) when exposed to water forming ions within the water that either increase the concentration of hydrogen ions, and hydroxide ions, within the solution forming acids or bases.
Table 5. Summary of mixture classifications based on chemical properties of the solutes within with solution.
Figure. Generalized atomic structure, covalent, ionic and hydrogen bonds showing the sharing and movement of electrons and the attractive force between polar sides of the molecule.
Figure. The periodic table of elements. Note that the columns of the table ROMAN-Numeral (I-A to VIII-A) group elements based on type classification in ascending order of atomic nuclei (size of the element) along each of the rows of the table ARABIC-Numeral (1-to-7), furthermore the atomic number is the indication of number of protons or electrons, while the atomic mass is the indication of the mass of the nucleus (essentially number of protons plus neutrons).
Molecular shapes and isomers:
Molecules of the same principle elements and components can form a variety of shapes based on the principles of bond angles and orientation of components of the molecules around the central structure that form different molecules. This ability to have multiple structures for the same molecule is deemed isomers (or isomerization). There are a variety of reasons for isomeric formation including but not limited to exposure to ultraviolet light, enzymatic activity, polar and hydrogen bonding interactions. When discussing isomers, they can be structural isomers, e.g., chain isomer (pentane vs. 2-methylbutane), position isomer (butan-1-ol vs. butan-2-ol), or functional group isomer (ethanol vs. methoxymethane); or geometric isomers (stereoisomer), e.g., diastereomers (cis-but-2-ene vs. trans-but-2-ene) and enantiomers (L-glyceraldehyde vs. D-glyceraldehyde or R (+) -lactic acid vs. S (-) -lactic acid).
Figure. Differences between isomer configurations based on being structural isomers or stereoisomers. Note the difference in the chain structure between Pentane and 2-methylbutane and the positional shift of the –OH within the molecules of Butan-1-ol versus Butan-2-ol. Also, notice how the position of the –OH within the Glyceraldehyde and the Lactic Acid molecules distinguishes the isomer type.
The interaction of molecules within an aqueous solution produces a reaction that dissociates (breaks) a portion of the water (H2O) molecules in the solution into the ionic components of hydrogen (H+) and hydroxide (OH-) ions that we measure along a continuum known as the pH scale.
Table. Summary of pH based on concentration of the hydrogen ions within the solution and example of common substances contained within that pH.
Functional Groups: Alkane, Alkene, Alkyne
This is the indication of the type of bonding that exists between the carbon atoms within a molecule
Alkane: only single bonds between carbon atoms (leads to a “saturated” molecule)
Alkene: at least 1 double bond between carbon atoms (leads to an “unsaturated” molecule)
Alkyne: at least 1 triple bond between carbon atoms (leads to an “unsaturated” molecule)
Additionally there are a group of structures that are identified as “functional groups” that atoms or small groups of atoms (two to four) that exhibit a characteristic reactivity when treated with certain reagents. A particular functional group will almost always display its characteristic chemical behavior when it is present in a compound. Because of their importance in understanding organic chemistry, functional groups have characteristic names that often carry over in the naming of individual compounds incorporating specific groups.
Table. Identification of the functional groups based on the organic chemistry of the molecule that impacts the reactivity of the molecule that contains the functional group based on the type of functional group and the organization of bonds within the molecule. Note molecules that show an “R”, the “R” is an indication for placement of carbon chain and those that show an “X”, the “X” indicates a halogen atom.
Isomers
cis- and trans-
Geometric identification of the isomers
Trans isomer: Latin meaning "across" indicates that the molecule has side-chains (branches of the molecule) are on opposite sides of the molecule from each other
Cis isomer: Latin meaning "on this side" indicates that the molecule has side chains (branches of the molecule) are on the same side of the molecule with each other
L- and D-
Optical isomers
Designated with the letters (D) and (L) to indicate the absolute configuration. In an absolute configuration the position of the groups is compared to a commonly agreed upon standard molecule. In amino acids, this molecule is serine and for carbohydrates, it is glyceraldehyde.
l- and d- (not to be confused with L- and D-)
Polarization optical isomers:
The isomer that rotates the plane of polarized light to the left (counterclockwise) is called levorotatory (l). The other isomer that rotates the light to the right (clockwise) is called dextrorotatory (d)
R- and S-
Enantiomer and Stereoisomer
Mirror-image configurations via optical analysis of enantiomers as "right-handed" (R), indicating orientation in the clockwise fashion, and "left-handed" (S), indicating orientation in the counter-clockwise fashion, that is based on counting organization of elements (in ascending order) around the Chiral center of the molecule following the nomenclature rules:
The higher the atomic number of the immediate substituent atom, the higher the priority, i.e., H– < C– < N– < O– < Cl–.
Different isotopes of the same element are assigned a priority according to their atomic mass.
If two substituents have the same immediate substituent atom, evaluate atoms progressively further away from the chiral center until a difference is found, i.e., CH3– < C2H5– < ClCH2– < BrCH2– < CH3O–.
If double or triple bonded groups are encountered as substituents, they are treated as an equivalent set of single-bonded atoms, i.e.,
C2H5– < CH2=CH– < HC≡C–
Types of Reactions for Organic Molecules:
Reactions: Alkanes
Oxidation
Halogenation
Reactions: Alkenes
Halogenation
Hydrohalogenation
Addition of hydrogen bromide in the presence of peroxide
Hydration (direct addition of water)
Hydroboration-oxidation (indirect addition of water)
Hydrogenation
Epoxide formation
Oxidation
Ozonolysis
Cationic polymerization
Free-radical polymerization
Addition of halogens and water (hypohalous acid)
Reactions: Alkynes
Hydrogenation
Hydrohalogenation
Halogenation
Hydration (keto-enol tautomerization)
Reaction of acidic terminal hydrogen (acid-base reaction)