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Chapter 1: Structure and Bonding
Part of OCHEM Test 1
242
Organic Chemistry
Undergraduate 2
06/05/2017

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Term
the one distinguishing characteristic of all organic compounds
Definition
they all contain the element carbon
Term
organic chemistry
Definition
the study of carbon compounds
Term
Why is C special? Why do most presently known chemical compounds contain C?
Definition
because of its structure and its consequent position on the periodic table
Term
why C is able to form so many compounds
Definition
because of its ability to bond

-can share 4 ve's and form 4 strong covalent bonds
-C atoms can bond to each other, forming long chains and rings
Term
some elements commonly found in organic compounds
Definition
-C
-H
-O
-N
-F
-P
-S
-I
-Cl
-Br
Term
the color used to represent H
Definition
some kind of dull yellow
Term
the color used to represent C
Definition
gray
Term
the color used to represent N
Definition
blue
Term
the color used to represent O
Definition
red
Term
the color used to represent F
Definition
some kind of pale turquoise color
Term
the color used to represent P
Definition
purple
Term
the color used to represent S
Definition
yellow
Term
the color used to represent Cl
Definition
green
Term
the color used to represent Br
Definition
brown
Term
the color used to represent I
Definition
looks magenta to me
Term
the general composition of an atom
Definition
-small, dense nucleus with protons and neutrons
-electrons circling it at a relatively large distance
Term
the electron density in an atom
Definition
denser closer to the nucleus than towards the outer edge
Term
isotopes
Definition
atoms with the same atomic number but different mass numbers
Term
the behavior of a specific electron in an atom can be described by...
Definition
the wave equation
Term
the solution to a wave equation
Definition
an orbital
Term
orbital
Definition
the solution to a wave equation
Term
Ψ
Definition
this is the Greek letter psi

this denotes the orbital, which is the solution to a wave function
Term
how an orbital describes the volume of space around a nucleus that an electron is most likely to occupy
Definition
by plotting the square of the wave function, Ψ2, in 3D space
Term
the 4 types of orbitals
Definition
-s
-p
-d
-f
Term
the orbitals we're primarily concerned with in OCHEM and biochem
Definition
s and p because they're the most common
Term
the shape of an s orbital
Definition
spherical
Term
the shape of a p orbital
Definition
dumbbell
Term
the shape of a d orbital
Definition
4 of the 5 are shaped like a 4-leaf clover

the other one is shaped like a dumbbell inside a donut
Term
the atoms in an orbital are organized into...
Definition
different electron shells
Term
electron shells
Definition
a group of an atom's electrons with the same principal quantumn number
Term
each orbital in a shell can be occupied by how many electrons?
Definition
2
Term
composition of the first energy level in an atom
Definition
a 1s orbital, thus just 2 electrons
Term
composition of the second energy level in an atom
Definition
a 2s orbital and 3 2p orbitals, thus 8 electrons
Term
composition of the third energy level in an atom
Definition
a 3s orbital, 3 3p orbitals, and 5 3d orbitals, thus 18 electrons
Term
the types of p orbitals
Definition
-px -py -pz
Term
how the p orbitals are arranged
Definition
along mutually perpendiculat directions, denoted px, py, and pz [image]
Term
the lobes of an orbital are separated by...
Definition
an area of zero electron density called a node
Term
node
Definition
an area of zero electron density between the nodes of an orbital
Term
how the lobes of the orbital are denoted in the wave function
Definition
with the algebraic signs + and -
Term
ground-state electron configuration
Definition
the orbitals occupied by an atom's electrons at its lowest energy arrangement (its ground state)
Term
the 3 rules for listing the orbitals occupied by an atom's electrons (WRITE THIS DOWN!)
Definition
1: Aufbau principle; the lowest energy orbitals fill up first, according to the order 1s --> 2s --> 2p --> 3s --> 3p --> 4s --> 4d. Note that the 4s orbital lies between the 3p and 3d orbitals.
2: Pauli exclusion principle; electrons act in some ways as if they were spinning around an axis, somewhat like how the Earth spins. This spin can have different orientations, denoted as up (/|\) and down (\|/). Only 2 electrons can occupy an orbital, and they must be of opposite spin.
3: Hund's rule; if 2 or more orbitals of equal energy are available, one electron occupies each with spins parallel until all orbitals are half full.
Term
Aufbau principle
Definition
The lowest energy orbitals fill up first, according to the order 1s --> 2s --> 2p --> 3s --> 3p --> 4s --> 4d
Term
Pauli exclusion principle
Definition
Only 2 electrons can occupy an orbital, and they must be of opposite spin
Term
Hund's rule
Definition
If 2 or more orbitals of equal energy are available, one electron occupies each with spins parallel until all orbitals are half full
Term
the orbitals that fill up first
Definition
the lowest energy orbitals
Term
how many electrons can occupy an orbital?
Definition
2
Term
how must the electrons in an orbital spin?
Definition
they must be of opposite spin
Term
what electrons do when 2 or more orbitals of equal energy are available
Definition
one electron occupies each with spins parallel until all orbitals are half full
Term
how to predict ground state electron configuration:
Definition
[image]
Term
the valency of carbon in organic compounds
Definition
tetravalent; always forms 4 bonds when it joins other elements to form stable compounds
Term
tetravalent
Definition
always forms 4 bonds when it joins other elements to form stable compounds
Term
the spatial orientation of a carbon atom's bonds
Definition
a regular tetrahedron (basically a trigonal pyramid)
Term
how bonds coming out of the page toward the viewer
Definition
[image]

heavy, wedge-shaped line
Term
how bonds on the same plane as the page are represented
Definition
[image]

solid line
Term
how bonds receding back behind the page away from the viewer are represented
Definition
[image]

dotted line
Term
why do atoms bond together?
Definition
because the the compound that results is more stable and lower in energy than the separate atoms
Term
flow of energy when a bond is formed
Definition
energy, usually as heat, always flows out of a chemical system when a bond is formed
Term
flow of energy when a bond is broken
Definition
energy must be put into a chemical system to break a bond
Term
why do atoms want an octet?
Definition
to obtain noble gas configuration
Term
ionic bond
Definition
electrostatic attraction between an anion and a cation
Term
covalent bond
Definition
sharing of electrons between atoms
Term
molecule
Definition
neutral collection of atoms held together by covalent bonds
Term
Lewis structures aka...
Definition
electron-dot structures
Term
a stable molecule results when...
Definition
a noble gas configuration is achieved for all the atoms
Term
Kekulé structures aka line-dot structures
Definition
kinda like Lewis structures, but the bonds are represented with lines instead of electron pairs
Term
lone-pair electrons
Definition
valence electrons that are not used for bonding

aka nonbonding erlectrons
Term
2 models that have been developed to describe covalent bonding
Definition
-valence bond theory
-molecular orbital theory
Term
valence bond theory
Definition
According to this theory, a covalent bond forms when 2 atoms approach each other closely and a singly occupied orbital on one atom overlaps a singly occupied orbital on the other atom. The electrons are now paired in the overlapping orbitals and are attracted to the nuclei of both atoms, thus bonding the atoms together.
Term
sigma (σ) bond
Definition
covalent bond formed by head on overlap of atomic orbitals

this is basically what happens in a single bond
Term
why molecules are more stable than the free atoms
Definition
because the product molecule has less energy than the starting free atoms
Term
1 kJ = ______ kcal
Definition
0.2390 kcal
Term
1 kcal = ______ kJ
Definition
4.184 kJ
Term
bond length
Definition
the distance between 2 nuclei that leads to maximum stability; this is at the minimum energy point between the 2 nuclei
Term
rxn coordinate diagram
Definition
see if you can find it in the video
Term
sp3 hybrid orbital
Definition
hybrid of an s orbital and three p orbitals
Term
depiction of unhybridized s and p orbitals
Definition
[image]
Term
depiction of sp3 hybrid orbitals
Definition
[image]
Term
why there's directionality in a tetrahedral molecule
Definition
because the sp3 hybrid orbitals have 2 lobes and are unsymmetrical about the nucleus, giving them directionality and allowing them to form strong covalent bonds when they overlap with orbitals from other atoms
Term
why sp3 hybrid orbitals form stronger bonds than unhybridized s and p orbitals
Definition
because one of the 2 lobes is larger and can therefore overlap more effectively with an orbital from another atom to form a bond
Term
why sp3 hybrid orbitals are asymmetrical
Definition
because the 2 lobes of the p orbital have different algebraic signs (+ and -). Thus, when a p orbital hybridizes with an s orbital, the positive p lobe adds to the s orbital but the negative p lobe subtracts from the s orbital, making the orbital strongly oriented in one direction
Term
the bond length between C and H
Definition
109 pm
Term
the bond angle in a tetrahedral molecule
Definition
109.5°
Term
chemical formula for methane
Definition
CH4
Term
chemical formula for ethane
Definition
C2H6
Term
the simplest molecule with a C-C bond
Definition
ethane
Term
the overlap between the C atoms in an ethane molecule
Definition
sigma
Term
the hybrid orbital that comes from each C atom in an ethane molecule
Definition
sp3
Term
length of the C-C single bond
Definition
154 pm
Term
the bond angles when an atom has 4 electron domains
Definition
about 109.5°
Term
sp2 hybrid orbitals
Definition
this occurs when an s orbital hybridizes with the px and py orbitals, but not the pz orbital; it remains unchanged
Term
the orientation of sp2 hybrid orbitals
Definition
trigonal planar with the 3 lobes 120° apart from each other and the unchanged p orbital perpendicular to the sp2 plane
Term
pi (π) bond
Definition
covalent bond between 2 p orbitals
Term
the regions occupied by the sigma (σ) bond
Definition
the region centered between nuclei
Term
the regions occupied by the sigma (π) bond
Definition
the regions above and below a line drawn between the nuclei
Term
length of the C-H single bond
Definition
108.7 pm
Term
length of the C=C double bond
Definition
134 pm
Term
why a double bond is less than twice as strong as a single bond
Definition
because the sideways overlap in the pi (π) part is not as much as the head on overlap in thew (σ) sigma part
Term
sp hybrid orbital
Definition
this happens when an s orbital hybridizes with the px orbital, but not the py and pz orbitals; they remain unchanged
Term
how a triple bond occurs
Definition
sp-sp bond between the sp orbitals and py-py pi bond between the py orbitals and pz-pz pi bond between the pz orbitals
Term
length of then C-C triple bond
Definition
120 pm
Term
length of the C-H bond
Definition
often 109 pm, but sometimes 106 pm
Term
electron domain alignment associated with sp hybrid orbitals
Definition
linear
Term
electron domain alignment associated with sp2 hybrid orbitals
Definition
trigonal planar
Term
electron domain alignment associated with sp3 hybrid orbitals
Definition
tetrahedral
Term
bond angle associated with sp hybrid orbitals
Definition
180°
Term
bond angle associated with sp2 hybrid orbitals
Definition
120°
Term
bond angle associated with sp3 hybrid orbitals
Definition
109.5°
Term
why P can form 5 covalent bonds
Definition
due to its position on the Periodic Table, it can expand its outer shell octet and form more than the typical number of covalent bonds
Term
why S can form 4 covalent bonds
Definition
due to its position on the Periodic Table, it can expand its outer shell octet and form more than the typical number of covalent bonds
Term
organophosphate
Definition
com[pounds that contain a P atom bonded to 4 O, with one of the O bonded to a C
Term
thiol
Definition
compound with a S atom bonded to one H and one C
Term
sulfide
Definition
compound that has a S atom bonded to 2 C
Term
molecular orbital (MO) theory
Definition
describes covalent bond formation as arising from a mathematical combination of atomic orbitals (wave functions) on different atoms to form molecular orbitals, so called because they belong to the entire molecule rather than to an individual atom
Term
the 2 ways for a molecular orbital to occur
Definition
-the additive way
-the subtractive way
Term
the additive way for molecular orbitals to occur
Definition
this combination leads to a molecular orbital that is lower in energy and is roughly egg-shaped
Term
the subtractive way for molecular orbitals to occur
Definition
this combo leads to a molecular orbital that's higher in energy and has a node between nuclei
Term
bonding molecular orbital (MO)
Definition
molecular orbital that's lower in energy than the atomic orbitals from which it is formed
Term
antibonding molecular orbital (MO)
Definition
molecular orbital that's higher in energy than the atomic orbitals from which it is formed

can't contribute to bonding because the electrons it contains can't occupy the central region
Term
condensed structures
Definition
shorthand method for writing structures in which C-H and C-C single bonds aren't shown, but instead understood example: propane being written as CH3CH2CH3
Term
skeletal structures
Definition
shorthand way of writing structures in which C atoms are assumed to be at each intersection of 2 lines (bonds) and at the end of each line
Term
rules for drawing skeletal structures (WRITE THIS DOWN!)
Definition
1: C atoms aren't usually shown. Instead, a C atom is assumed to be at each intersection of 2 lines (bonds) and at the end of each line. Occasionally, a C atom might be indicated for emphasis or clarity.
2: H atoms bonded to C aren't shown. Because C always has a valence of 4, we mentally supply the correct number of H atoms for each C.
3: Atoms other than C and H are shown.
Term
what the end of the line in a skeletal structure represents
Definition
CH3
Term
what a 2-way intersection in a skeletal structure represents
Definition
CH2
Term
what a 3-way intersection in a skeletal structure represents
Definition
CH
Term
what a 4-way intersection in a skeletal structure represents
Definition
C
Term
bonds that have a circular cross-section and are formed by head-on interaction
Definition
sigma (σ) bonds
Term
bonds formed by sideways interaction of p orbitals
Definition
pi (π) bonds
Term
shape of a hexagonal benzene molecule
Definition
planar
Term
hybridization of C+ ion when it forms 3 single bonds
Definition
sp2
Term
geometry of C+ ion when it forms 3 single bonds
Definition
trigonal planar
Term
electronic relationship refers to...
Definition
# of valence electrons
Term
singlet (spin-paired) orbital
Definition
has pair of electrons, opposite spin
Term
triplet (spin-unpaired) orbital
Definition
has one electron
Term
how the chemical symbols in an organic compound's molecular formula are ordered
Definition
first C, then H, then alphabetical from there
Term
why the 4 bonds of C can be arranged in a variety of ways
Definition
because of differences in hybridization
Term
bond angle of tetrahedral bonds
Definition
109.5°
Term
hybridization of tetrahedral
Definition
sp3
Term
hybridization of trigonal planar
Definition
sp2
Term
bond angle of trigonal planar
Definition
120°
Term
where the p orbital is in trigonal planar
Definition
perpendicular to the sp2 orbitals on the trigonal planar
Term
hybridization of linear
Definition
sp
Term
bond angle of linear
Definition
180°
Term
some other elements that are often found in organic compounds
Definition
-H
-O
-N
-S
-P
-halogens
Term
functional group
Definition
small collection of atoms that gives a molecule specific properties
Term
volume of an atom has to do with...
Definition
the electron cloud
Term
the most common C isotope
Definition
C-12

99% of the C in mature
Term
distance between energy layers vs. distance from nucleus
Definition
the further you get from the nucleus, the closer and closer those energy layers get
Term
s orbitals always cone ______ at a time
Definition
1
Term
p orbitals always cone ______ at a time
Definition
3
Term
shape of an s orbital
Definition
spherical
Term
shape of a p orbital
Definition
dumbbell (2 lobes)
Term
node
Definition
point of zero electron density between the nodes of an orbital
Term
the difference between the p orbitals
Definition
the orientation; they're the same except for the axis
Term
degenerate
Definition
exactly the same in energy
Term
d orbitals always cone ______ at a time
Definition
5
Term
f orbitals always cone ______ at a time
Definition
7
Term
why the 1st energy level can have only 2 electrons
Definition
because it has only 1 s orbital
Term
stability of orbital vs. distance from nucleus
Definition
the further from the nucleus, the less stable the orbital
Term
where the node is in a p orbital
Definition
nucleus
Term
the most common elements we will deal with in OCHEM
Definition
CHON
Term
electronegativity
Definition
an atom's affinity for electrons
Term
general trend for electronegativity
Definition
northeast
Term
what causes polarity in bonds?
Definition
diff in enegativity
Term
some elements that have the same electronegativities as C
Definition
H
S
I
Term
why the C-O bond is more polar than the C-Cl bond
Definition
because O is 2 elements to the right of C and Cl is just 1 element to the right of S
Term
# of nodes vs. energy of orbital
Definition
the more nodes, the higher the energy
Term
the difference between a 1st energy orbital (such as 1s) and a 2nd energy orbital (such as 2s)
Definition
an extra node
Term
the type of node in an s orbital
Definition
spherical node
Term
why the valence electrons are so special
Definition
because the define the chemistry and size of the element
Term
trend in size of atoms as you go down the columns of the PTable
Definition
size increases, but by increasingly smaller increments
Term
trend in size of atom as you go right along the rows of the PTable
Definition
size of the atom decreases
Term
electronegativity vs. size of atom in the same row
Definition
inverse relationship
Term
the 2 main types of bonds
Definition
-ionic
-covalent
Term
ionic bond
Definition
bond created by attraction of electric charge
Term
the elements that typically yield anions
Definition
nonmetals
Term
the elements that tend to form anions are the ones that are more...
Definition
electronegative
Term
covalent bond
Definition
sharing of electron density between 2 separate nuclei
Term
polar covalent bonds
Definition
covalent bonds with unequal sharing of electrons
Term
is bond formation endothermic or exothermic?
Definition
exothermic
Term
which is more stable? molecule or individual atoms?
Definition
molecule
Term
is bond breaking endothermic or exothermic?
Definition
endothermic
Term
bond dissociation energy
Definition
the energy input needed to break bonds apart
Term
rxn coordinate diagram
Definition
[image]

the bond length is nominal bond length
Term
nominal bond length
Definition
average length of bond
Term
what happens to the energy of the bond as the nuclei get further apart?
Definition
increases
Term
how wavelength is related to energy
Definition
ΔE = hv

ΔE = change in energy
h = Planck's constant
v = wavelength (nm)
Term
Planck's constant
Definition
6.626 × 10-34 m2 kg / s
Term
bond length vs. bond strength
Definition
inversely related
Term
1 nm = ______ m
Definition
1 / 1 billionth 1 x 10-9 meter
Term
1 pm = ______ m
Definition
1 / trillionth 1 x 10-12 meter
Term
frequency of vibration of bonds vs. length of bond
Definition
inversely proportional
Term
why the length and strength of bonds between atoms is important for chemistry
Definition
because it helps predict reactivity
Term
length of bond between atoms vs. reactivity
Definition
directly proportional
Term
how size of atom affects reactivity
Definition
affects internuclear distance, thus affecting bond length and frequency
Term
is the covalent bond between 2 atoms static?
Definition
no
Term
how a covalent bond between 2 atoms vibrates
Definition
at a specific frequency characteristic to that bond
Term
depiction of where this equation, ΔE = hv, fits into internuclear bonds
Definition
[image]
Term
Heisenberg's uncertainty principle
Definition
you can know either the location or energy of the electron, but not both
Term
the amount of time an electron spends in its specific orbital
Definition
about 95%
Term
the spin of an electron
Definition
+ or - 1/2
Term
depiction of how to draw a p ordital
Definition
[image]
one lobe is shaded to indicate that one of the numbers is positive
the horizontal line is a plane where the node is
Term
the 2 key types of orbitals you gotta pick up on in molecular orbital theory
Definition
sigma and pi
Term
energy vs. # of nodes
Definition
as you increase the energy, you increase the # of nodes
Term
depiction of how s orbitals interact in covalent bonding
Definition
[image]

the one on top shows antibonding orbitals as a result of destructive interference at high energy and the one on bottom shows bonding molecular orbitals as a result of constructive interference at low energy
the arrows at the bottom represent the opposite spins of paired electrons
Term
what a theory is used for
Definition
it's used to make predictions
Term
example of how to characterize a bond (ON TEST!)
Definition
[image]

this shows the orbitals involved in forming the bond
Term
depiction of how electron configuration contributes to covalent bonds when bonding atoms are tetrahedral
Definition
[image]
Term
how to characterize double bonds when the bonding atoms are trigonal planar
Definition
[image]
Term
why the bond angles that are assumed are often approximations
Definition
because of the molecule not being entirely symmetrical
Term
the orbitals that are relevant in VSEPR theory
Definition
only s orbitals
Term
the type of orbitals used by sigma bonds
Definition
hybrid orbitals
Term
how to characterize triple bonds when the bonding molecule is linear
Definition
[image]

remember, a triple bond contains 1 sigma bond and 2 pi bonds
Term
what a triple bond contains
Definition
1 sigma bond and 2 pi bonds
Term
depiction of unhybridized s and p orbital overlapping
Definition
[image]

the shaded area of the p orbital is positive
everything unshaded is negative
Term
depiction of sp hybrid orbital
Definition
[image]

the shaded area is positive
Term
the effect of hybridization on the sp orbital
Definition
destructive interference causes the positive lobe to decrease in amplitude and the negative lobe to increase in amplitude

[image]
Term
the orbitals that define shape of an atom
Definition
hybrid
Term
σ (sigma) system
Definition
the electrons that are in the hybridized orbitals
Term
what causes π (pi) bonds?
Definition
overlap of p orbitals
Term
the symmetry a sigma bonding orbital has
Definition
cylindrically symmetrical (cross section along any point in the bond is circular)
Term
if a bond is cylindrically symmetrical, it's a ______ bond
Definition
sigma
Term
if a bond is not cylindrically symmetrical, it's a ______ bond
Definition
pi
Term
π (pi) system
Definition
the electrons in the unhybridized π (pi) bonds
Term
which electrons are more energetic? those in the sigma system or those in the pi system?
Definition
those in the pi system
Term
why are the electrons in the pi system more energetic than those in the sigma system?
Definition
further from nucleus
Term
which electrons are most likely to be reactive in a chemical reaction?
Definition
the more energetic ones; those in the pi system
Term
can electrons that influence shape of an atom be part of the pi system?
Definition
no, they're part of the sigma system
Term
principal quantum number (n)
Definition
this defines the energy level of an electron
Term
angular momentum quantum number (l)
Definition
this defines the shape of the orbital
Term
subshell
Definition
set of electrons that have the same n and l values
Term
how a subshell is designated
Definition
by a letter and a number, such as s1, s2, and p2
Term
magnetic quantum number (ml)
Definition
describes the orientation of the orbital in space

can have values of l to -l, including 0
Term
value of l for the s orbital
Definition
0
Term
value of l for the p orbital
Definition
1
Term
subshell designation for the s orbital
Definition
ns

n = principal quantum number
Term
subshell designation for the p orbital
Definition
np

n = principal quantum number
Term
possible values of ml for the s orbital
Definition
0
Term
possible values of ml for the p orbital
Definition
1, 0, -1
Term
the elements with their valence electrons in the s orbital
Definition
He and the Group 1A and 2 A elements
Term
the elements with their valence electrons in the p orbital
Definition
Group 3A to 8A elements
Term
the elements with their valence electrons in the d orbital
Definition
transition metals
Term
the elements with their valence electrons in the f orbital
Definition
inner transition metals
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