Download 1 LS 1a Glossary (Lectures 3 and 4) Fall 2014 This glossary is

LS 1a Glossary (Lectures 3 and 4)
Fall 2014
This glossary is meant to clarify some of the terms that you may hear in lecture, section, or during office
hours during the semester. Many of these terms you do not need to know but they may prove useful in
your studies. If there are additional terms you would like to see added or if you continue to be confused
by a term, please email us at [email protected].
Acid: An acid is a molecule that can lose a hydrogen ion (“H+”) depending on the pH of the solution.
Rather than donating protons, an acid can also be thought of as accepting electrons during chemical
reactions.
Acid Dissociation Constant (Ka): The acid dissociation constant is the equilibrium constant for any
reaction in which an acid (“HA”) donates a proton to water (H2O) to generate hydronium (H3O+) and the
deprotonated acid (“A-”). Large Ka values indicate a strong acid; small Ka values indicate a weak acid.
𝐾𝑎 = (
[𝐴− ][𝐻3 𝑂 + ]
)
[𝐻𝐴]
Alcohol: Alcohols are molecules that contain a “hydroxyl” (X-OH) functional group.
Base: A base is a molecule that can gain a hydrogen ion (“H+”) from solution depending on the pH of the
solution. Rather than gaining protons, a base can also be thought of as donating electrons during
chemical reactions.
Carbonyl: A carbonyl functional group consists of carbon double-bonded to an oxygen (C=O).
Carboxylic acids, amides, anhydrides, and esters are some examples of other functional groups that
include carbonyls (the carbonyls below are highlighted in magenta).
Carboxylic Acid: A carboxylic acid functional group (X-COOH) consists of a hydroxyl group (X-OH)
attached to a carbonyl (carbon double-bonded to oxygen) (C=O). This functional group is found in all
monomeric amino acids and gives amino acids the “acid” part of their name. Carboxylic acids are also
found in the side chains of the amino acids glutamic acid and aspartic acid. When deprotonated,
carboxylic acids are called “carboxylate” groups.
1
Conjugate base: An acid that has lost its proton (“H+”) is called a “conjugate base.” They are often
negatively-charged after having lost the positively-charged proton (“A-”), although they can also be
neutrally-charged if the acid was positively-charged.
Covalent Bond: A covalent bond describes a bond between two atoms in which electrons are shared
between the two atoms. Bonds between atoms with electronegativity differences of less than 1.7 are said
to be covalent. Covalent bonds can be either polar, in which case the electrons are evenly shared
between the two atoms, or nonpolar, in which case the electrons spend more time around one atom than
the other.
Deprotonation: Deprotonation is the process in which an acid loses a hydrogen ion (“H+,” or “proton”).
Dipole: A dipole can be either a bond or a molecule that is positively-charged at one end and negativelycharged at the other end. The positive and negative charges can be either full or partial.
Diprotic Acid: Diprotic acids are acids that can potentially lose two hydrogen ions. Sulfuric acid (H 2SO4)
is an example of a diprotic acid. As pH increases, sulfuric acid is first deprotonated to produce hydrogen
sulfate (HSO4-1) and again to produce sulfate (SO4-2)
Dispersion Force: See “Van der Waals Interactions.”
Electron: An electron is a subatomic particle that is negatively-charged. Electrons carry an electrical
charge that is exactly opposite to the charge of a proton, but electrons are only a tiny fraction of the
mass of a proton. Nearly all chemistry is based on the movement and rearrangement of electrons within
atoms and molecules.
Electron Shell: The electrons surrounding an atomic nucleus are grouped into shells, like the layers of
an onion, according to the energy the electrons possess. An electron shell is a grouping of electrons with
similar energies, and atoms can use several different shells to accommodate electrons of different
energies. Shells nearest the nucleus have the lowest energy and electron shells further away have higher
energies. Each electron shell can only hold a certain number of electrons (shell 1 holds 2 electrons, shell
2 holds 8 electrons, etc.). As a result shells nearer to the nucleus are filled first before electrons are
added to higher level shells. For example the neutral atom lithium has three electrons: the first two
occupy the most-inner first shell and the third occupies the outer second shell.
2
Electronegativity: Electronegativity is the tendency of an atom to attract electrons. Atoms with greater
electronegativity will tend to pull the electrons in a bond closer to itself, giving it a partially-negative
charge and leaving the other atom with a partially-positive charge. Atoms with greater electronegativies
can also more stably sustain a full negative charge (e.g., oxygen or chlorine).
Electrolyte: “Electrolyte” is effectively another word for “salt.” An electrolyte is a molecule that dissolves
into ions when placed in water, such as sodium chloride.
Equilibrium: Equilibrium is the state of a chemical reaction in which the concentrations of products and
reactants do not change. At equilibrium ΔG = 0, the Gibbs free energy of the system is minimized, and
the rates of the forward and reverse reactions are equal.
Equilibrium Constant (Keq): The equilibrium constant, Keq, is the ratio of the concentrations of
products over reactants when a reaction is at equilibrium. Values of K eq that are greater than 1 reflect a
thermodynamically favorable reaction; conversely, values of K eq that are less than 1 reflect a
thermodynamically unfavorable reaction. Keq is a property of the reaction and only changes with
temperature.
Formal Charge: Formal charge is a convention used to express whether an atom in a molecule “owns”
more or less electrons than what is required for the atom to be neutral (given its number of protons).
Formal charge is calculated by subtracting the number of non-bonded (lone pair) electrons and half the
number of electrons involved in bonds from the number of valence electrons found in the free neutral
atom. The convention used to calculate formal charge assumes electrons in bonds are always shared
evenly; therefore, atoms that have a neutral formal charge may still have a partial charge if they are part
of a polar bond.
Full Charge: A full charge is a term used to describe an amount of charge corresponding to the charge
of either an electron (if negative) or a proton (if positive).
Functional Group: A functional group is a portion within a larger molecule that conveys properties
and/or reactivities to the molecule.
Gibbs Free Energy (G): Gibbs free energy is a measure of the energy available to do work. The type of
“work” we typically care about in LS 1a is the net conversion of reactant to product, or vice versa, in a
given chemical reaction. Chemical systems release Gibbs free energy until it is minimized (when ΔG = 0)
and equilibrium is reached. Reactions for which the Gibbs free energy of the reactants is higher than that
of the products (ΔG°rxn <0) are thermodynamically favorable. ΔG°rxn can be related to the equilibrium
constant (Keq) by the equation on the right when the system is at equilibrium. The equation on the left
more generally describes the energy available to the system if the product/reactant ratio does not equal
Keq.
[products]
𝚫G = 𝚫G°rxn + RT ln ([reactants])
𝚫G°rxn = −RT ln(K eq )
@ equilibrium, when ΔG = 0
Hydrogen Bond: A hydrogen bond is a unique type of dipole-dipole interaction because it has a
directional component. Hydrogen bonds can form between a partially-negatively charged “acceptor” atom
3
(usually F, O, or N) and a partially-positively charged “donor” hydrogen atom, which itself is covalently
bonded to a second electronegative atom. There are several conditions that must be met for hydrogen
bonds to form: 1) the partially negative F, O, or N (the “acceptor” atom) must have a lone pair of
electrons; and 2) the partially-positive “donor” hydrogen atom and acceptor atom must be appropriately
oriented relative to one another. Hydrogen bonds have an ideal bond angle of 180°.
Hydroxyl Group: A hydroxyl functional group is a polar, hydrophilic functional group with the formula XOH. Hydroxyl groups are very weakly acidic, but their pKa values are usually too high to be biologically
relevant. This group is found in the amino acids serine, tyrosine, and threonine.
Induced Dipole Interaction: See “Van der Waals Interactions.”
Intermolecular Interaction: An intermolecular interaction is an electrostatic attraction that occurs
between different molecules or between far-away portions of the same molecule. Intermolecular
interactions vary in strength depending upon the magnitudes of the charges involved and the distances
over which they act.
Ion: An ion is any atom or molecule that contains an overall net charge because of an unbalanced
number of electrons and protons.
Ionic Bond: An ionic bond is a bond between a positively-charged ion (a “cation”) and a negativelycharged ion (an “anion”). A cation has fewer electrons than protons; an anion has more electrons than
protons. Ionic bonds can form between two atoms in which the electronegativity difference between the
two atoms is so great (> 1.7) that one atom effectively loses its electron to the more electronegative
atom.
Ionizable: Ionizable molecules and functional groups are those that can dissociate to form a charged
species. This term is most often used to describe acids and bases that can become charged at certain
pHs.
Ka: See “Acid Dissociation Constant.”
Keq: See “Equilibrium Constant.”
Lewis “dot” structure: A Lewis “dot” structure is a style of diagram that represents the arrangement of
atoms and valence electrons within a molecule. Lewis dot structures show the location of all atoms and
4
valence electrons. Valence electrons are shown either as lone pairs or as forming bonds: single bonds are
shown as pairs of valence electrons shared between two atoms; double bonds are shown as four
electrons shared between two atoms; triple bonds are shown as six electrons shared between two atoms.
A valid Lewis dot structure satisfies the octet rule for each atom. An example of a Lewis dot structure of
carbon dioxide (CO2) is shown below:
Lewis structure: A Lewis structure is similar to a Lewis “dot” structure, with the lone difference being that
pairs of electrons between atoms representing covalent bonds are replaced with lines. An example of a
Lewis structure of carbon dioxide (CO2) is shown below:
Macromolecule: A macromolecule is a large molecule—typically a polymer—that is made up of smaller
repeated units (called “monomers”). Proteins, nucleic acids, and many types of carbohydrates are
examples of macromolecules.
Metabolism: Metabolism is the sum total of all the chemical processes that take place within a cell or
organism.
Monomer: A monomer is a small-molecule building block that can be used to construct a larger polymer:
polymers are the result of iteratively attaching monomers together. Nucleotides and amino acids are
examples of biological monomers that comprise nucleic acids and proteins, respectively.
Monoprotic Acid: Monoprotic acids are acids that are only capable of losing one hydrogen ion.
Hydrochloric acid (HCl) is an example of a monoprotic acid.
Nucleus (Atomic): The nucleus, in the context of an atom, is the central portion of the atom that
contains both neutrons (neutrally-charged subatomic particles) and protons (positively-charged subatomic
particles).
Nucleus (Cellular): The nucleus, in the context of a eukaryotic cell, is the membrane-bound organelle
that contains the cell’s genetic material. This organelle is complex and involved in a number of cellular
processes; it is perhaps most notable as the location where DNA replication and transcription occur.
Octet Rule: The octet rule describes the tendency of atoms to form bonds such that their valence shells
of electrons are filled with eight electrons. This rule applies particularly to elements such as C, N, O, and
F, which are in the second row of the periodic table. Sulfur and phosphorus do not always follow this
rule, a phenomenon we call “octet expansion.” Hydrogen (in the first row of the periodic table) is most
stable when it can fill its valence shell with two electrons.
Orbital: An orbital is a probabilistic description of where an electron can mostly likely be located at any
given time. Each orbital holds two electrons. Orbitals form various three-dimensional shapes; s orbitals
are essentially spherical, and p orbitals form a two-lobed shape. The electronic configuration of orbitals is
beyond the scope of this course, so don’t worry about it.
5
Partial Charge: A partial charge refers to any amount of charge density that is greater than zero but
less than the charge of a proton (if positive) or an electron (if negative). Partial charges are indicated
with a lower-case Greek letter “delta” with a superscript + or – indicating the polarity of the charge (e.g.,
δ+ represents a partial-positive charge).
pH: pH is the property of a solution that describes its concentration of hydrogen ions (“H+”) in solution.
When water is solvent, as it will always be in this class, we measure the pH as the concentration of
hydronium ions (“H3O+”).The pH is a measure of the acidity of a solution; low pH values (i.e., <7) denote
an acidic solution and high values (i.e., >7) denote a basic solution. The pH is related to the hydrogen
ion (or hydronium ion) concentration by the equation pH=-log10([H3O+]).
pKa: pKa is a measure of the propensity of an acid to lose a hydrogen ion. The pK a is related to Ka by the
equation pKa=-log10[Ka]. When placed in a solution with a constant pH that is equal to its pK a, an acid will
exist 50% in its protonated state and 50% in its deprotonated state. If the pH > pKa of the of the acid, it
will deprotonate; if the pH < pKa of the of the acid, it will be protonated.
Polar Bond: A polar bond is a type of covalent bond in which electrons are unevenly shared between
the two atoms in the bond. Bonds connecting atoms that have electronegativity differences greater 0.4
but less than 1.7 are polar covalent bonds. These bonds form an electrical dipole due to the uneven
distribution of electrons, and as a result, the more electronegative of the two atoms in the bond tends to
be partially-negatively charged while the less electronegative atom tends to be partially-positively
charged.
Polymer: A polymer is a macromolecule that is comprised of many repeating units (a.k.a. monomers).
Nucleic acids, proteins, and some carbohydrates are examples of biological polymers.
Product (of a reaction): A product is a newly produced chemical species that is created as the result of
a chemical reaction.
Protein: A protein is a macromolecular biological polymer derived from individual monomers called
amino acids. Proteins assume a wide variety of folded shapes that perform varied cellular functions.
Protonation: Protonation is the process in which a base acquires a hydrogen ion, or proton.
Reactant: A reactant is a chemical species that is present at the start of a chemical reaction and is (at
least somewhat) consumed during that reaction.
Salt Bridge: Another name for an ionic bond.
Side Chain (Amino Acid): An amino acid side chain is the variable “R-” group that is attached to the
alpha carbon. The side chain determines the identity and properties of the amino acid.
Small Molecule: A small molecule is a molecule of low molecular mass (generally less than 100 atoms).
Such molecules tend to be highly diverse relative to macromolecules, which tend to be comprised of
repeating subunits.
6
Stability: Stability is a term used to describe the thermodynamic and kinetic reactivity of a reaction or of
a molecule. To be “more stable” is equivalent to being “lower in energy,” or “less reactive” which is
thermodynamically favorable. To be “less stable” is equivalent to being “higher in energy,” or “more
reactive.” To be “kinetically stable” means the reaction is very slow with a high energy of activation; to
be “kinetically instable” means a reaction will proceed rapidly.
Standard Line Drawing: A standard line drawing is a style of diagram that represents the arrangement
of atoms and bonds within a molecule. By convention, the end point of a line or the vertex between two
or more lines in a standard line drawing is assumed to be a carbon atom. Each assumed carbon atom is
assumed to be bounded to an appropriate number of hydrogen atoms such that its octet is fill (e.g., if a
carbon is at the end point of a line, it would need to be bound to three hydrogen atoms in order to have
a full octet). All atoms other than carbon and hydrogen must be shown explicitly on a standard line
drawing. All hydrogen atoms that are bound to non-carbon atoms must also be shown explicitly. Lone
pair electrons do not have to be shown, but they are sometimes shown for clarity. It is like a Lewis
structure, but without explicitly labeling the carbons and the lone pairs of electrons. An example of a
standard line drawing is shown below on the left. To the right is the same molecule with all atoms
labeled.
Starting Material: See “Reactant.”
Steric Clash/Steric Effects: Steric clash or steric effects are repulsive, non-bonding interactions
between atoms and/or molecules that occur as they collide. Atoms take up space and two atoms cannot
occupy the same space at the same time. A molecule tends to adopt a conformation that avoids steric
clash between its atoms.
Spontaneous: Spontaneous describes a thermodynamically favorable reaction that does not require any
additional energy input. (It has nothing to do with the rate of a reaction.)
Thermodynamics: Thermodynamics is the study of the transfer and conversion of energy, particularly
the favorability (or the “spontaneity”) of a chemical reaction.
Valence Electron: A valence electron refers to an electron located in the outer-most electron shell of an
atom. These electrons are nearly always the electrons that are involved in chemical reactions.
Van der Waals Interaction/Force (VDW): Van der Waals interactions or van der Waals forces are
weak electrostatic intermolecular interactions that occur due to transient, instantaneous dipoles that form
within atoms and/or molecules in response to their proximity to other atoms/molecules. A transient dipole
in one molecule can transiently induce a dipole in a neighboring molecule. These “transient” or
“instantaneous” dipoles are due to the random motion of electrons within atoms or bonds which leads to
short-lived areas of positive and negative charge (dipoles). These short-lived charges are electrostatically
7
attractive, allowing non-polar weakly attract one another. These transient dipoles can also be induced by
the presence of a charge (in the form of an ion, a partially charged atom, or even another instantaneous
dipole); this occurs because the charge triggers the motion of electrons via either attraction or repulsion,
leading to polarization in the molecule/atom being affected. Van der Waals interactions are generally
weak, but their strength increases proportionally to the surface area over which they can form; extended
molecules with extensive surface area form more significant van der Waals interactions than more
compact molecules. These interactions are also called “induced-dipole:induced-dipole interactions,” “van
der Waals” interactions, or “London Dispersion Forces.”
8