The Basics: Bonding and Molecular Structure in Organic Chemistry
Terms for Ch 1: The Basics: Bonding and Molecular Structure
Atom (Sec 1.2)
Smallest unit of matter that retains an element’s properties; composed of protons, neutrons, and electrons.
Element (Sec 1.2)
Fundamental form of matter composed of atoms of only one kind (identical atomic number), that cannot be broken apart into a different form of matter by ordinary physical or chemical means.
Compound (Sec 1.2)
Substance composed of two or more different elements that are chemically bound.
Atomic Number, Z (Sec 1.2)
The number of protons in the nucleus of a particular atom, which determines the identity of that atom.
Mass Number (Sec 1.2)
Sum of the number of protons and neutrons in the nucleus of an atom, which determines over 99.9% of the mass of that atom. Also called atomic mass number.
Atomic Mass Unit
A unit of mass equal by definition to 1/12 of the mass of an atom of carbon-12, which is 1.6605402 × 10-27 kg. Also called Dalton (Da).
Isotopes (Sec 1.2A)
Different atomic forms of an element that have the same number of protons and are chemically identical, but contain different numbers of neutrons, and thus have different atomic mass numbers.
Valence Electrons (Sec 1.2B)
Electrons in an atom’s outermost shell (valence shell), which determine most of the chemical properties of that atom.
Octet Rule (Sec 1.3, 1.4)
Main group elements heavier than boron tend to gain, lose, or share electrons so as to have eight valence electrons, which will achieve the electron configuration of the nearest noble gas.
Electronegativity (Sec 1.3A, 2.2)
A measure of the ability of an atom to attract shared electrons to itself, and thereby polarize a covalent bond.
Ionic Bond (Sec 1.3A)
A chemical bond formed between a cation and anion, due to the electrostatic force of attraction between oppositely charged ions.
Salt (Sec 1.3A)
An ionic compound that is composed of cations and anions, which is often formed by the reaction of an acid with a base.
Covalent Bond (Sec 1.3B)
A chemical bond formed when atoms share electrons.
Molecule (Sec 1.3B)
The smallest uncharged individual unit of a compound that retains the composition and properties of that compound.
Structural Formula (Sec 1.3B, 1.7)
Formula that shows how atoms of a molecule are attached to each other.
Lewis Structure (Sec 1.3B, 1.4)
A representation of a molecule showing each electron pair as two dots ( : ) or a dash ( – ). Also called electron-dot structure.
Lone Pair (Sec 1.5)
A pair of valence electrons that belongs solely to one atom, and does not contribute to bonding in a covalent molecule. Also called nonbonding electron pair, or unshared electron pair.
Formal Charge (Sec 1.5)
The charge on an atom in a molecule or ion, which is determined as the difference between the number of electrons assigned to an atom in a molecule and the number of electrons it has in its outer shell in its elemental state. The formal charge on an atom can be calculated using the formula: F = Z ─ S/2 ─ U, where F is the formal charge, Z is the group number of the atom (i.e., the number of electrons the atom has in its outer shell in its elemental state), S equals the number of electrons the atom is sharing with other atoms, and U is the number of unshared electrons (lone pair electrons) that the atom possesses.
Isomers (Sec 1.6, 5.2)
Different molecules that have the same molecular formula.
Molecular Formula (Sec 1.6)
A chemical formula that gives the total number of atoms of each element present in one molecule of a compound
Empirical Formula
A reduced molecular formula that expresses the kinds of atoms and the relative proportions of elements in a compound as the smallest set of whole numbers, which is the simplest ratio of elements.
Connectivity (Sec 1.6, 1.7A)
The sequence, or order, in which the atoms of a molecule are attached to each other.
Constitutional Isomers (Sec 1.6, 4.2, 5.2)
Compounds that have the same molecular formula, but that differ in their connectivity, i.e., their atoms are connected in different ways. Also called structural isomers.
Condensed Structural Formula (Sec 1.7B)
Organic formula where the atoms that are attached to a carbon are usually written immediately after that carbon, listing hydrogens first.
Bond-Line Formula (Sec 1.7C)
Organic formula that shows the carbon skeleton of a molecule with lines; hydrogen atoms are not written in, but all other non-carbon atoms are written in.
Resonance Structures (Sec 1.8, 13.2, 13.4)
Lewis structures of the same molecule that differ only in the position of their electrons; a single resonance structure will not adequately represent a molecule, and the molecule is best represented as a hybrid of all of the resonance structures. Also called resonance contributors.
Resonance Stabilization (Sec 1.8B, 13.5, 13.8, 14.5)
The extra stability of a molecule that has resonance contributors, since the energy of the actual molecule is lower than the energy that is estimated for any of its resonance structures.
Electrostatic Potential Map (Sec 1.8, 2.2A)
Computer generated structure that uses color to show the relative distribution of electron density at the Van der Waals surface of a molecule or ion; violet shows electron-poor regions that have a positive charge (+); blue to blue-green show regions that have a partial positive charge (δ+); green shows regions of normal electron density with no charge (0); yellow to orange show regions that have a partial negative charge (δ─); red shows electron-rich regions that have a negative charge (─). Also called map of electrostatic potential.
Quantum Mechanics (Sec 1.9)
A theory of atomic and molecular structure that explains bonding in molecules, where the total energy of the system can be described by a mathematical expression called a wave equation, which is used to calculate the energy associated with the state of the electron and the relative probability of an electron residing in a given region of space.
Wave Function (ψ function) (Sec 1.9)
A mathematical expression derived from quantum mechanics corresponding to the energy state for an electron in its orbital.
Electron Probability Density (Sec 1.10)
The probability of finding an electron in a given region of space, which is given by the square of the wave function, ψ2.
Orbital (Sec 1.10)
A region of space around a substance in which there is a high probability of finding an electron, which can be described mathematically by squaring the wave function; each orbital has a characteristic energy and can hold two electrons when their spins are paired.
Atomic Orbital (Sec 1.10 – 1.15)
A volume of space about the nucleus of a single atom where there is a high probability of finding an electron (or two spin-paired electrons). Abbreviated AO.
s Orbital (Sec 1.10)
A spherical atomic orbital; the principal quantum number n ≥ 1; the azimuthal quantum number l = 0; the magnetic quantum number m = 0.
p Orbitals (Sec 1.10)
A set of three degenerate (equal energy) atomic orbitals; the principal quantum number n ≥ 2; the azimuthal quantum number l = 1; the magnetic quantum numbers m are +1, 0, -1.
d Orbitals (Sec 1.10)
A set of five degenerate (equal energy) atomic orbitals; the principal quantum number n > 3; the azimuthal quantum number l = 2; the magnetic quantum numbers m are +2, +1, 0, -1, -2.
Aufbau Principle (Sec 1.10A)
Electrons are added so that orbitals of lowest energy are filled first.
Pauli Exclusion Principle (Sec 1.10A)
No two electrons of an atom may have the same set of four quantum numbers; thus only two electrons can occupy the same orbital, and then only when their spin quantum numbers are opposite (spins are paired).
Hund’s Rule (Sec 1.10A)
Orbitals in a subshell must all be half-filled before any can be completely filled with electrons; when orbitals are degenerate (of equal energy), then electrons with the same spin are added to each orbital until all degenerate orbitals contain one electron, and then electrons are added to each orbital so that the spins are paired.
Heisenberg Uncertainty Principle (Sec 1.11)
Both the position and momentum of an electron (or any very small object) cannot be exactly measured simultaneously.
Molecular Orbital (Sec 1.11 – 1.15)
Orbital that encompasses two or more atoms in a molecule. When atomic orbitals combine to form molecular orbitals, the number of molecular orbitals that result will always equal the number of atomic orbitals that combine. Abbreviated MO.
Bonding Molecular Orbital (Sec 1.11 – 1.15)
The energy of a bonding molecular orbital is lower than the energy of the isolated atomic orbitals from which it arises. When electrons occupy a bonding molecular orbital, they help to hold together the atoms that the molecular orbital encompasses.
Antibonding Molecular Orbital (Sec 1.11 – 1.15)
A molecular orbital whose energy is higher than that of the isolated atomic orbitals from which it is constructed. Electrons in an antibonding molecular orbital destabilize the bond between the atoms that the orbital encompasses.
LCAO Method (Linear Combination of Atomic Orbitals Method) (Sec 1.11)
Wave functions, ψ, for molecular orbitals are obtained by linearly combining (addition or subtraction) the wave functions for the atomic orbitals.
Hybridization of Atomic Orbitals (Sec 1.12 – 1.14)
A mathematical (and theoretical) mixing of two or more atomic orbitals to give the same number of new hybrid orbitals, each of which has some of the character of the original atomic orbitals.
sp3 Orbital (Sec 1.12A)
A hybrid orbital that is derived by mathematically combining one s atomic orbital and three p atomic orbitals; four sp3 hybrid orbitals are obtained by this process, and they are directed toward the corners of a regular tetrahedron with angles of 109.5° between them.
Single Bond (Sec 1.12A)
Chemical bond formed when two atoms share one pair of electrons by forming one sigma bond.
Sigma (σ) Bond (Sec 1.12A)
A single bond formed when electrons occupy the bonding sigma orbital formed by the end-on overlap of atomic orbitals (or hybrid orbitals) on adjacent atoms. In a sigma bond, the electron density has circular symmetry when viewed along the bond axis.
Electron Density Surface (Sec 1.12)
Structure that shows a calculated 3-D surface with the same electron density everywhere on that surface.
Van der Waals Surface (Sec 1.12, 2.2A)
A plot of the furthest extent of a molecule’s electron cloud, and thus its overall shape; when the van der Waals surface is penetrated by another molecule, it experiences strong repulsive forces between the overlapping electron clouds.
sp2 Orbital (Sec 1.13)
A hybrid orbital that is derived by mathematically combining one s atomic orbital and two p atomic orbitals; three sp2 hybrid orbitals are obtained by this process, and they are directed toward the corners of an equilateral triangle with angles of 120° between them.
Double Bond (Sec 1.13)
Chemical bond formed when two atoms share two pairs of electrons by forming one sigma bond and one pi bond.
Pi (π) Bond (Sec 1.13)
A bond formed when electrons occupy a bonding pi molecular orbital (i.e., the lower energy molecular orbital that results from overlap of parallel p orbitals on adjacent atoms).
Superposable (Sec 1.13B, 5.1)
Two objects that can be placed on top of each other so that all parts of each coincide. Also called superimposable.
Stereoisomers (Sec 1.13B, 4.9A, 4.13, 5.2B, 5.14)
Compounds with the same molecular formula and the same connectivity, but are not superposable because they differ in the arrangement of their atoms in three-dimensional space; includes enantiomers and diastereomers, but excludes constitutional isomers.
cis-trans Isomers (Sec 1.13B, 4.5, 4.13, 5.2B, 7.2)
Diastereomers that differ in their stereochemistry at adjacent atoms of a double bond or on different atoms of a ring; the cis-isomer has two substituents on the same side of a double bond or ring; the trans-isomer has two substituents on opposite sides of a double bond or ring. Also called geometric isomers.
sp Orbital (Sec 1.14)
A hybrid orbital that is derived by mathematically combining one s atomic orbital and one p atomic orbital; two sp hybrid orbitals are obtained by this process, and they are oriented in opposite directions with an angle of 180° between them.
Triple Bond (Sec 1.14)
Chemical bond formed when two atoms share three pairs of electrons by forming one sigma bond and two pi bonds.
Valence Shell Electron Pair Repulsion (VSEPR) Model (Sec 1.16)
A model for predicting the shapes of molecules and ions in which valence electron pairs are arranged around each atom to minimize the repulsion of electron pairs by maximizing the distance between them.
Molecular Geometry (Sec 1.16)
The shape of a region of a molecule or ion, which is determined by the arrangement in three-dimensional space of a central atom and the atoms directly attached to it; nonbonding electron pairs occupy spacial positions around that central atom, but only the locations of bonding electron pairs define the name of the shape at that central atom.