Language of Chemistry Flashcards
(300 cards)
1
Q
What can you tell from the line structure of a molecule?
A
Bonding, Stereochemistry, Functional Groups, Acidity
2
Q
What is a heteroatom?
A
Any atom in an organic molecule that is not C or H
3
Q
What is a functional group?
A
An atom/group of atoms that have similar chemical properties whenever it occurs
- Defined the characteristic chemical and physical properties of
4
Q
What are the new functional groups to learn?
A
Thiols
Acetals
Carbonates
Ureas
Imines
Azides
Nitro
Lactones
Epoxide
Lactams
5
Q
Are oxidation levels and states the same?
A
No they are not
6
Q
How can you further distinguish FG’s apart from names?
A
Using primary secondary and tertiary
7
Q
How can you name alcohols using primary secondary and tertiary?
A
Depends on the number of other C atoms attached to the C with the alcohol
8
Q
How can you name amines using primary secondary and tertiary?
A
Depends on number of C groups attached to the nitrogen
9
Q
What is a covalent bond?
A
A region of electron density positioned between atomic nuclei that arises through sharing of electrons
10
Q
What is the Lewis Octet rule?
A
2nd row elements C,N,O,F can’t have more than 8 electrons in the valance shell
11
Q
What is the best way to draw diagrams?
A
Using line diagrams (skeletal) as quicker to draw and FG’s can be identified
12
Q
What is the specific thing to remember about line diagrams?
A
There are certain implicit things such as H and lone pairs, unless important
H atoms are shown when attached to heteroatoms or defining stereochemistry
Lone pairs are added to suit occasion (if involved in reaction)
13
Q
What do you use to draw 3D structures?
A
Hashed lines - pointing away
Wedged lines - pointing towards
Solid line - in the plane
Wiggly line - undefined stereochemistry or mixture of enantiomers
14
Q
What do you need to be careful of when drawing 3D diagrams?
A
Drawing the tetrahedral structures as correct rotations
15
Q
What is important to know about drawing lone pairs?
A
They are often missed out but still need to know they’re there
We draw them explicitly when using them in mechanisms
16
Q
What is a formal charge?
A
The charge an atom would have if all the electrons in the covalent bonds are shared equally - not always the case
17
Q
How to assign formal charge? Formally!!
A
No electrons the atom should have - No of electrons the atom actually has
Valence electrons - 1/2(bonding e-) - all non bonding electrons
18
Q
How can formal charges be thought of?
A
They are a ‘bookkeeping tool’ to track electron count of an atom compared with an isolated neutral atom
19
Q
What do formal charges not mean?
A
That the area of the molecule has that charge (e.g. from dipoles)
20
Q
What does electronegativity mean?
A
Tendency for an atom to attract a pair of electrons in a covalent bond
21
Q
What happens when there is a difference in electronegativity?
A
They contain a dipole and the shared electron pair is distributed unevenly
22
Q
Why don’t formal charges always accurately represent electron density?
A
We need to understand why a group carries a specific charge and remember about electronegativity
23
Q
What do formal charges not necessarily tell you?
A
Dipoles and electron density
24
Q
What are the limitations of line structures?
A
They imply electrons are confined to a region of space between two atoms which isn’t always true e.g. in benzene
25
When does delocalisation occur?
Occurs when pi electrons are spread across more than two atoms
1. Where pi bonds are conjugated - alternating pi bonds
2. Empty or filled p orbitals that are next to pi bonds - like in carbocations or lone pairs
26
How does delocalisation work?
Each atom has a p orbital which can all overlap with each other
The lowest energy bonding orbital extends across all four atoms Where pi
27
How do you represent delocalisation?
We use ‘resonance forms’
28
What are resonance forms?
Several different localised structures with in reality a weighted average of these being the ‘true’ form
29
What are the key points about ‘resonance forms’?
They are not interconverting structures
- Not in equilibrium
- Not considered to actually exist
- No actual resonance process
30
What are the key points about drawing resonance forms?
The connectivity of atoms always remains the same as we are only ever talking about p orbitals (don’t break a single bond)
Curved arrows used do not represent a real flow of electrons
Never exceed the octet for 2nd row elements
Retain the overall charge
31
What do the most significant resonance forms have?
Greatest number of filled orbitals
Fewer formal charges
If these are equal it is the negative charge on the more electronegative atom
32
Which form of benzene is significant?
Neither as they are equivalent and contribute evenly
33
What are resonance forms used for?
To help represent delocalisation in drawings
34
How can you easily tell if a formal charge will be positive or negative?
If an atom has one more bond than normal, it’ll be a positive charge
If an atom has one less bond than normal, it’ll be a negative charge
35
What will delocalisation impact?
Stability
Reactivity of compounds
Properties e.g. bond lengths and NMR shifts
36
What is the difference between trivial names and systematic names?
Trivial names are nothing to do with chemical structure e.g. ibuprofen
Systematic names allow you to uniquely identify the structure by its name
37
How do you use Systematic (IUPAC) Nomenclature?
1. Identity the principle functional group using order of precedence
2. Identify longest continuous hydrocarbon chain containing the principle functional group
3. Number the chain and identify numbering for the principle functional group and substituents
38
How do you number your chain?
Numbered from one end of longest chain
Numbered so principle FG gets lowest possible number
If multiple numbered schemes possible, choose lowest possible number at first point of difference
39
What else is key to know about systematic naming?
Any other groups attached to the chain are called substituents
Substituents are listed alphabetically
di, tri etc doesn’t affect the alphabetical order
40
What is important to note about naming alkenes or alkynes?
If second group it doesn’t go as a prefix but it goes in the middle
41
How do you include info about stereochemistry in naming?
Add it to the start e.g. E if it is an E isomer
42
How do Chemists usually communicate?
Communicate primarily by drawing structures
In speech trivial names or acronyms are often used for common compounds
43
How do you refer to structures in lab reports or papers?
Structures are usually given a number
While also making reference to the most relevant FG for that section of the paper
44
How can you name 2 substituents together in benzene rings by relative position?
1,2 - ortho-
1,3 - meta-
1,4 - para-
45
What can the shape of the molecule give rise to?
Shape of a molecule can give rise to isomers
46
What is an isomer?
Different molecules with the same molecular formula
47
What is a stereoisomer?
Same atom connectivity but different arrangement of atoms in space
48
What is the difference between enantiomers and diastereomers?
Enantiomer - non superimposable mirror images (optical)
Diastereomer - non superimposable non mirror images
49
What is the difference between configuration and conformation?
Configuration - change in arrangement in space that involves bond breaking/making
Conformation - change in spacial arrangement by bond rotation
50
What does interconversion by bond rotation mean?
Rotation around an actual bond not space
51
What is the difference between chiral and achiral?
Achiral - Molecule with superimposable mirror images (have symmetry)
Chiral - Molecule with non-superimposable mirror images
52
When is a molecule achiral?
When there is symmetry
53
What are the key things about chirality?
It is a property of symmetry (or lack of) and shape
It applies to a molecule not atoms
Can cause different biological effect and different smells and tastes
54
What do you call the atom in the centre of symmetry
Sterogenic or asymmetric centre
NOT chiral centre as no such thing
55
What is hybridisation?
Mixing atomic orbitals to form new hybrid orbitals
56
How does molecule shape arise?
From bonding
57
What are the different methods to predict shape?
VSEPR theory
Crystal field
Hybridisation
58
What are hybrid orbitals?
A result of mixing atomic orbitals
59
What percentages of s and p atomic orbitals make up each type of hybridisation?
s 50% p 50% = sp
s 33.3% p 66.6% = sp2
s 25% p 75% = sp3
60
Mathematically what happens in sp3 carbon atoms?
1x2s and 3x2p orbitals are equivalent to 4xsp3 degenerate hybrid orbitals
61
What is the resulting shape of sp3 hybridisation?
Distorted dumbbells that point towards the vertices of a tetrahedron forming a tetrahedral shape
62
What are MO’s?
Molecular orbtials
63
How do hybridised orbitals form their shapes?
By being overlaid on each other
64
What can sp3 carbons cause?
Stereoisomers as they will always remain tetrahedral
65
Mathematically what happens in sp2 carbon atoms?
1x2s and 2x2p atomic orbitals are equivalent to 3xsp2 degenerate hybrid orbitals
66
What is the resulting shape for sp2 hybridisation?
They are distorted dumbbells which have a trigonal planar arrangement. Forming a trigonal planar shape
67
What happens to the remaining unhybridised p orbital/s?
They are perpendicular to the hybridised orbitals
68
Mathematically what happens in sp carbon atoms?
1x2s and 1x2p atomic orbitals are equivalent to 2xsp degenerate hybrid orbitals
69
What is the resulting shape in sp carbon atoms?
Linear arrangement of distorted dumbbells - Linear shape
70
Why do benzene and cyclohexane look different in space?
Benzene is planar as is sp2 hybridised whereas cyclohexane is tetrahedral as is sp3 hybridised
71
What are enantiomers referred to as?
being chiral
72
What can a sample of a chiral molecule be?
Racemic mixture = 50:50 mix of enantiomers (racemate)
Scalemic mixture = non 50:50 mix (scalemate)
Homochiral or enantiomerically pure = 100% of single enantiomer
73
What is it called when a sample of a chiral molecule is 100% of a single enantiomer?
Homochiral or enantiomerically pure
74
Does the stereogenic centre need to be carbon?
No it does not, e.g. Si can be a stereogenic centre
75
What might be the problem with non-carbon stereogenic centres?
They may not be configurationally stable so may rapidly convert
76
Do enantiomers need stereogenic centres?
No they do not, e.g. in allenes
77
What is axial chirality? What is point chirality?
Chirality where an axis of chirality is used rather than a stereogenic centre
Chirality with a stereogenic centre
78
Other than tetrahedral, what other shapes can have chirality?
Planar and octahedral
79
How do you assign configuration?
Using CIP rules
80
What is the notation for designating configurations of enantiomers?
R and S
81
What is the order of priority for assignment?
1. Atoms of higher atomic number take precedence - lone pairs have lowest priority
2. Isotopes of higher atomic weight take precedence - 3H>2H>1H
3. The lowest priority group needs to point backwards (hashed bond) so may need to rotate molecule
82
How do you go about assigning enantiomers?
Go through each rule one at a time assigning priority 1 to 4 with 1 being the highest priority
If order of priority decreases clockwise then it is R, if anticlockwise it is S
83
What is the principle of outward exploration?
If priority is equal we need to look at atoms in term along the rest of the chain
The first difference decides what group takes priority
84
How do you decide priority in principle of outward exploration?
Find the first difference, then assign priority as normal to those two groups/atoms
85
What is the sequence rule and how can you use it to assign priority?
Unsaturated pi-systems become hypothetical saturated sigma bonds
Brackets are used to donote (ghost) atoms
Ghost atoms are equivalent priority to real atoms
86
What is a Newman Projection?
Another chemical representation that involves looking at molecules from a certain direction (down a specific bond)
87
How do you draw a Newman Projection?
Draw skeletal formula with wedges/dashes
Look down a bond and draw a sawhorse projection
Use that to draw the NP by superimposing the front and back central carbons
88
How do you show conformation using NP?
You can rotate it
89
When are molecules/atoms antiperiplanar?
When they are opposite each other in the NP
90
How to convert from Newman to 2D?
Look at your NP from the side so some groups point forward and some back
Draw sawhorse projection from that
Then use both NP and sawhorse to draw your 2D structure
Remember some are pointed in different ways
91
What does the free rotation around the C-C bond allow for?
Significant changes in shape as molecules are not static
92
What is the difference between a staggered conformation and a eclipsed conformation?
Staggered - All atoms are antiperiplanar (180 away from each other)
Eclipsed - Atoms are on top of each other
93
Are all conformations equivalent in energy?
No eclipsed conformations are higher in energy compared to staggered conformations
Eclipsed are less stable
94
What does a dihedral angle refer to?
Refers to the angle between C-X from nearest carbon and C-X from back carbon
95
What is the barrier to free rotation termed?
Torsional strain
96
Why do the energies of eclipsed and staggered differ?
Van der Waals radius
Hydrogen Clash
Electron Clash
Hyperconjugation
97
What is Van der Waals radius?
Half of the internuclear (between nuclei) separation of two non bonded atoms of the same element before you get a destabilising effect
98
What does hydrogen clash tell us about energies?
It shows that in some molecules, the hydrogens are too close together (compared to van der Waals radius) so they experience a steric clash and are destabilised (in the eclipsed formation)
99
What does electron clash tell us about energies?
The electron pairs can be considered to repel in the eclipsed formation
100
What must you not fall into the trap of doing for explaining differing energies for differing conformations?
Only ever thinking about destabilising interactions
Also need to consider stabilising interactions, ones that stabilise staggered more than eclipsed
101
What stabilising effect do we get in staggered conformations?
Hyperconjugation - bonding sigma orbital of C-H is filled with electron density whereas the anti bonding orbital on adjacent C-H has no electron density. (antiperiplanar relationship)
- Overlap causes stabilisation
102
Why do we not get hyperconjugation in eclipsed conformations?
sigma and sigma star orbitals are on opposite sides of the molecule so do not interact
103
When can bonds partake in hyperconjugation?
When they are 180 degrees to each other meaning they are antiperiplanar
104
What is an axial vs equatorial group?
Axial - R group that is pointing up/down from central atom
Equatorial - R group that is in the same plane as the central atom
105
What are the possible Newman projection shapes called?
Anticlinal
Synperiplanar
Synclinal/Gauche
Antiperiplanar
106
What is Berry Pseudorotation?
When ligands exchange between axial and equatorial sites (fluxonality)
Meaning all ligands end up being in the same environment
e.g. PF5
107
What is ring strain?
Total amount of strain energy
Addition of angular strain and torsional strain
108
What tells us how much ring strain there is?
Internal angles of the equivalent flat polygon relative to 109.5 degrees
109
When we burn carbon rings what would we expect to happen?
The higher ΔH would have the higher ring strain as ring strain releases energy when burnt
110
Out of C3 to C7 ring systems what would you expect the highest and lowest ΔH to be?
Highest C3 as 109.5-60=49.5
Lowest C5 as 109.5-108=1.5
111
What actually happens when we burn carbon rings?
Experimental evidence doesn't follow the trend
Cyclohexane has the lowest ΔH
112
Why does cyclohexane have the lowest ΔH?
As in actuality it has 109.5 degree angles between atoms. It exists as a chair conformation.
113
What is important to note about the strain in cyclohexane?
No torsional, angular or ring strain
114
What are the two types of hydrogens that exist in a chair conformation?
Axial - Up and down
Equatorial - In the plane
115
What does the double NP show?
Lack of torsional strain as all hydrogens are staggered
116
What is ring flipping?
A conformational change where the axial and equatorial positions interconvert
Bonds get rotated
Not an actual flip - more like an inside out thing
117
What are the different stages between the two chair conformations?
Half-chair
Half-boat
Boat
Half-boat
Half-chair
118
Why is the boat conformation of a higher energy?
Suffers from torsional strain
H atoms are eclipsed in the double NP
Steric 'flagpole' interactions of hydrogens across the ring
119
What happens to substituents in ring flipping?
Axial becomes equatorial
Equatorial becomes axial
120
In monosubstituted cyclohexanes which conformer is higher in energy?
Axial conformal as it is less stable due to suffering from 1,3-diaxial repulsions
121
When do destabilising interactions apply to cyclohexane?
When at least one H has been replaced
122
What happens when the substituted group on cyclohexanes increases?
The compound will have a higher percentage of being equatorial
Apart from OMe compared to Me as the lone pair overlaps with anti bonding orbital so is more axial
123
How do you name carbons when converting between 2D and chair conformations?
Numbers can start anywhere but need to go clockwise
124
What is strain energy often a mix of?
Torsional and angular strain
125
Why are small carbon rings highly strained?
Cannot achieve the 109.5 degree angle so suffer from angular strain
126
What happens to straining as we increase carbon ring length above 6?
Additional max around 10 due to transannular strain - interacting H across the ring
Large rings are flexible enough to avoid strain
127
What are the key differences between conformation and configuration?
Conformation -
- Rotating bonds
- Readily interconvert
- Still the same molecule
Configuration -
- Breaking bonds
- Different molecules
- Change in stereochemistry
128
How do you assign CIP rules for axial chirality?
Look at front carbon first to assign 1 and 2 priority
Look at back carbon separately to assign 3 and 4 priority
Direction to get from 2 to 3 tells you if it is S or R
129
What are the new rules for assigning R/S in axial chirality?
Need to view molecule along chiral axis
Near groups take precedence over far groups
130
What is a biaryl group?
Group containing two aromatic rings
131
What is the ideal dihedral angle between the two rings?
Around 45 degrees
If 0 - Greatest conjugation but greatest steric clash
If 90 - Less conjugation but also less steric clash
132
Do conjugation and steric clash work together?
In alkanes or stereogenic centres they work together
But in biaryls they work against each other
133
What does the angle of 45 degrees mean for biaryls?
Minimum energy conformation minimises repulsion between H atoms while retaining some conjugation
134
How can you use CIP rules for alkenes?
If highest priority groups are on the same side it is a Z isomer. If on different sides it is an E isomer.
135
How do the physical properties of enantiomers vary?
They don't they are identical
136
How do the optical properties of enantiomers vary?
The rotate the plane of light equally but in opposite directions
Clockwise rotation are + isomers and dextrorotatory (d)
Anticlockwise rotation are - isomers and levorotatory (l)
137
What is the separation of enantiomers called?
Resolution - exploiting chiral-chiral interactions
138
What else do enantiomers exhibit?
Circular dichroism - an interaction with chiral light
139
What type of isomers are E/Z alkenes?
Diastereomers
140
When do diastereomers often occur?
In molecules with multiple stereogenic centres
141
How do you find max number of stereoisomers from number of stereogenic elements?
If n stereogenic elements then max 2^n stereoisomers
142
What causes there to be less than the max number of stereoisomers?
Symmetry operations
Make the molecules achiral (superimposable) and are given the description meso
143
What happens if the two stereogenic centres have the same groups attached?
We get 3 stereoisomers instead of 4
- One pair of dissymmetric enantiomers and one meso isomer
144
What does an internal mirror plane in a molecule cause?
Symmetry so it is not chiral
145
What are the physical and spectroscopic properties of diastereomers?
Different chem and phy properties as essentially different molecules
Electrons on different groups react differently
Gives rise to different energies/shape etc
Meaning intermolecular interactions differ and spectroscopy can tell them apart
146
What is the difference between absolute and relative stereochemistry?
Absolute is based on space whereas relative is relative to atoms in the molecule
147
What are the descriptors for relative stereochemistry?
cis/trans
148
What are symmetry operations and elements?
Symmetry Elements - A point, line or plane to which the symmetry operation is performed
Symmetry Operation - An action (rotation, reflection etc) that moves a molecule into a new orientation equivalent to its original one
149
What are the different symmetry operations?
E - Identity element - leaves object unchanged
Cn - Rotational axis - rotation about the axis by 360/n
σ - Plane of symmetry - reflection in plane of symmetry
i - Centre of inversion - projection through point of inversion
Sn - Improper rotation axis - Rotation about an axis followed by a reflection in the plane perpendicular to the axis
150
Can molecules have multiple symmetry elements?
Yes
151
What are dissymmetric enantiomers?
Enantiomers that contain one or more Cn rotational axis in additional to C1 axis as the only symmetric operations
Not all enantiomers are devoid of symmetry operations
152
What are intermolecular interactions (IMI's)?
The attractive interactions between molecules - sometimes called non-covalent interactions
153
What kind of interactions are IMI's and what are they responsible for?
Stabilising interactions responsible for coagulation and self assembly etc
154
What is the addictive effect?
Although individually weak in 'bulk' they are quite strong due to large number of interactions
155
What does the phase a substance exists in depends on?
Depends on the relative extents of its IMI's and kinetic energy
156
What are most intermolecular forces also?
Electrostatic in nature
157
What does Coulomb's law state?
Two charged particles will exert a force on each other
158
Where do IMI's arise from?
Attraction between oppositely charged species
- Opposites attract, like repel
159
What do we use to measure electronegativity?
The Pauling scale
Magnitude between 0-4
160
What is the difference between polar and non polar bonds?
Polar - bond with unequal sharing of electrons
Non polar - bond with equal sharing of electrons
Electron density is greater around atom of higher electronegativity
161
What are partial charges?
Charges that are smaller in magnitude than a full charge and represented by δ
162
What are bond dipoles?
A pair of opposite partial charges separated from each other
163
How does the difference in electronegativity affect partial charges?
As difference in electronegativity increases, charge separation increases, bonds are more polar and atoms carry greater partial charges
164
How do you predict partial charges?
If no difference in electronegativity it is non polar
If difference in electronegativity it is polar
If large difference in electronegativity then an ionic bond is formed
165
What are molecular dipole moments (μnet)?
Vector sum of individual bond dipole moments
Need correct geometry to work it out
166
What does it mean if a molecule has a molecular dipole moment?
It is polar - neutral overall but uneven charge distribution
167
What is the electric dipole moment (μ)?
Measure of the separation of positive and negative charges in a system
μ = Qr where Q is magnitude of two opposite charges and r is distance between them
168
What is the unit for electric dipole moment?
Debye (D) = 3.34x10-30 Cm
169
What happens if ligands are symmetrically distributed?
The compound is non polar - so long as dipoles cancel out
170
How can lone pairs affect molecular dipole moment?
Lone pairs localise negative charge
Can either enhance or diminish the contribution to overall polarity - need to consider directionality
171
What are the steps to determine molecular dipole?
Determine geometry
Identify atoms and electronegativites
Determine bond dipoles
Consider Symmetry
Consider lone pairs
Determine net molecular dipole (vector sum)
172
What are inductive effects?
Effect on electron density away from the dipole due to close proximity to polar bonds
173
What factors affect molecular dipole moments?
Relative magnitudes and directions of bond dipoles
Inductive effects
Shape
Lone pairs
174
What do surface electrostatic potential maps show you?
How charge is distributed across a molecule
175
What are van der Waals surfaces?
Molecular surfaces that show atoms as hard spheres through union of atomic vdW surfaces
176
What is the minimum distance that two atoms that aren't covalently bonded can get to?
Can't get closer than the addition of vdWs radii
177
What do surface electrostatic potential maps show you?
Shows attractive/repulsive forces felt by a point positive charge at various equidistant points from the surface
If attraction area of molecule is negative
178
What are all the IMI's?
Ion-ion
Ion-dipole
Dipole-dipole
Dipole-induced dipole
London dispersion forces (induced dipole dipole)
179
What do the strengths of electrostatic interactions depend on?
Charge and distance
180
How do the strengths of bonding and non bonding interactions differ?
Non bonding much weaker than bonding
Only ion-dipole forces can be decently strong
181
When can you detect intermolecular interactions?
When distance between atoms is less than addition of vdW radii
182
How do you represent IMIs?
Hashed bonds |||| between molecules
In text use middle dots ••••
183
Where are dispersion forces present and where do they result from?
Present in all molecules and result from formation of instantaneous dipoles due to electrons being distributed unevenly due to fluctuation in arrangement
184
What are the properties of dispersion forces and what can they cause?
Weak and transient
Can induce a dipole in another molecule
185
What do the strength of dispersion forces depend on?
Polarisability and surface area (contact with neighbouring molecules)
186
What is polarisability and when does it change?
Refers to how readily the electron density of an atom or molecule can be distorted by an electrical field (e.g. a charged molecule)
Larger molecule means great polarisability and stronger dispersion forces
Explains why increasing chain length increasing dispersion forces
187
How is the shape of a molecule important when thinking about strengths of dispersion forces?
It influences contact surface with other molecules so you may get more or less dispersion forces
Explains why increasing branching decreasing dispersion forces
188
What are dipole-dipole interactions?
Attraction between polar molecules with permanent dipoles
189
What do you need to know about dipole-dipole interactions?
Need to be orientated correctly
Much stronger dispersion forces than above
Molecules align themselves to favour attractive interactions and minimise repulsion
190
What happens if you increase polarity?
Increasing strength of dipole-dipole forces
191
What are dipole-induced dipole interactions?
IMI between polar and non polar
192
How do dipole-induced dipole interactions occur and how strong are they?
Occur when a polar molecule approaches and induces a dipole on a non polar molecule
Weaker than dipole-dipole interactions
193
What is hydrogen bonding?
Attractive interaction between a lone pair of electrons and a hydrogen atom with a delta positive
194
What does hydrogen bonding look like?
D-H•••:A
195
What is D-H called and what is A called in hydrogen bonding?
D-H is called the hydrogen bond donor
where D is more electronegative than H
A is called the hydrogen bond acceptor (a lewis base)
196
What angle are weak vs strong hydrogen bonds?
Weak are 90-150, Strong are 170-180 - Should try and indicate the 180 angle when drawing them
197
What makes hydrogen bonding different to other dipole interactions?
Although mostly electrostatic in nature they also have partial electron sharing that resembles the formation of a covalent bond
- Important directional consequence
198
What happens to hydrogen bond length when the bond gets stronger?
Distance decreases
199
Where else can hydrogen bonding occur?
Intra-molecular - between non bonded atoms of the same molecule
200
What are ion-ion interactions?
Ionic bonds!!!
Use coulomb forces
Operate over relatively long distances compared to other IMIs and are non directional
201
What are ion-dipole interactions?
Interactions that exist between a charged ion and a polar molecule
202
What is a solvent?
Substance that dissolves a solute - focusing on molecular solvents
203
What is the relationship between solvents and solutes?
Polar compounds dissolve in polar solvents and other way around
204
What is solvent polarity?
Doesn't refer to bonds or molecules but rather a bulk property that is the dominant factor in dissolving molecular substances
Continuous scale around how polar it is
205
How can we study solvent polarity?
By finding the solvents dielectric constants (ε)
206
What is a solvents dielectric constant?
A physical property that measures the substances ability to insulate charges from each other
Higher of this equals higher polarity
207
What is the difference between polar protic and polar aprotic?
Polar aprotic solvents lack acidic hydrogens (no H bond donors) e.g. ketone
Polar protic solvents can act as H+ donors and participate in H bonds e.g. alcohol
208
What is Gibbs Free energy equation?
ΔG = ΔHsoln - TΔS
209
What are we thinking in terms of energy about when referring to why compounds can dissolve?
Breaking of initial solute-solute and solvent-solvent interactions and forming new solute-solvent interactions
And then if that means ΔG is negative
210
If a molecule has a polar functional group can it dissolve?
No as we need to think about proportion of non-polar regions in the molecule
211
What do reactions involve?
Transfer of atoms and/or electrons
Most involve several bonds being formed or broken
212
What is the difference between intermolecular and intramolecular?
Intermolecular - between molecules
Intramolecular - within the same one
Reactions can be either one
213
What are features of energy diagrams?
Energy of system and surroundings change during a reaction
Transition states, local energy maxima - cannot be isolated (‡)
Intermediates, local energy minima - may be possible to isolate
214
Kinetics vs thermodynamics
Kinetics - about rate of reaction
Thermodynamics - about equilibrium concentrations
215
What helps molecules come together to react?
Charge interactions
- dipoles/permanent charges
Interactions between filled/empty orbitals
216
Different parts of a curly arrow?
Tail - source of electrons
Head - where electrons end up
217
What are simple reaction steps?
Bond breaking to form lone pair
Lone pair forming a bond
Bond breaking to form new bonds
218
What is a nucleophile?
What is an electrophile?
Nucleophile - a reagent that forms a bond to its reaction partner by donating both bonding e- - electron pair donor
Electrophile - a reagent that forms a bond to its reaction partner by accepting both bonding e- - electron pair acceptor
219
What to think about when thinking about likely arrows?
charge/partial charge/electron density
220
What should you always check with a mechanism?
Has overall charge been preserved?
Do atoms have correct valency?
221
What are electrophiles and nucleophiles when referring to orbitals?
Electrophile - accepts electrons into unoccupied (empty) orbital
Nucleophile - donates electrons from an occupied orbital
222
How do you identify nucleophiles?
Negatively charged or neutral species with a pair of electrons in a high-energy orbital
223
Best nucleophiles to worst nucleophiles
Lone pair (negatively charged species)
Lone pair (neutral species)
pi bond
sigma bond (only nucleophiles in certain situations)
224
Key things about pi bonds for nucleophiles
Bonding orbitals act as nucleophiles if sufficiently high in energy
Substituents affect how nucleophilic alkene is
225
Key things about sigma bonds on nucleophiles
Bonding orbitals act as nucleophiles if sufficiently high in energy
Lower in energy than pi bonds so less nucleophilic
Generally only on electropositive atoms
226
How do you identify electrophiles?
Neutral or positively charged species that can accept electrons
227
Types of electrophiles
Positively charged species with empty AO
Neutral species with empty AO
- Not many species with empty AOs
Double bonded electronegative atom
Single bond to electronegative atom
228
What is the general approach to drawing mechanisms?
1 - What bonds have been formed/broken
2 - Identify elec/nucs
3 - Draw reagents in appropriate orientation with charges
4 - Draw curly arrow from nucleophile to electrophile
5 - Carefully draw product (is it stable)
6 - Repeat until stable product obtained
229
What is nucleophilic substitution?
Substitution where arrow starts from nucleophile
- need to make sure its clear which bonds forming/breaking and which carbon is being attacked so direction of attack is correct
230
What is electrophilic addition?
What is nucleophilic addition?
Breaking a pi bond
One arrow starts from pi bond (electrophile) and one arrow starts from nucleophile
231
What is elimination?
Forming a pi bond, making sure the arrow goes to the middle of the sigma bond
232
What are radical reactions?
Reaction involving a radical (species with unpaired e-)
Use half headed arrows
233
What is the key to reactivity?
Electron flow
- Curly arrows are drawn in order starting from source of electrons
234
What things do you need to consider when asked why a reaction is happening?
Charges and orbitals
235
What happens when two atoms come together?
AOs overlap to form MOs
n AOs form n MOs
Each overlap creates one bonding and one anti-bonding MO
236
What is the difference between bonding and anti-bonding MOs?
Bonding MO lower in energy than anti bonding MO
Electrons in bonding MO form a chemical bond
The electrons are lower in energy than respective AO's
237
What is the interaction between bond making/breaking and MOs?
Bond making - filled bonding MO
Bond breaking - putting electrons in anti bonding MO
238
When is overlap most effective?
When AOs have similar energy
Large interaction causes more change in bonding/anti-bonding MO energy
239
What is a way of telling the difference between diastereoisomers and enantiomers?
All chiral centres must change for a molecule to be an enantiomer
240
If a pair of molecules are achiral what can they not be?
Enantiomers
241
What does in phase and out of phase mean when talking about orbitals?
In phase both are of same sign
Out of phase they are different signs
242
What happens when there is an end to end overlap of sp3 orbitals?
They interact in phase and out of phase to form sigma and sigma star MOs
243
What happens when p orbitals overlap side on?
Interact in phase and out of phase to form pi and pi star MOs and therefore pi bonds
244
What happens if AOs are really far apart in energy?
They are too far apart to interact and form MOs
245
What is the difference between a large interaction and smaller interaction between AOs?
Large interaction - both bonding and anti bonding MO are much lower/higher in energy than AOs
Less interaction - different contributions to bonding and anti bonding for each AO involved - less stabilisation
246
What are some factors affecting orbitals and MO theory?
More electronegative an atom - the lower in energy its AO
Orientation of how AOs overlap affects strength of interaction
end on > side on
Orbitals of similar size overlap better
247
What does a molecule contain?
Many different MOs
248
What is the HOMO?
What is the LUMO?
What is important about them?
HOMO - Highest Occupied Molecular Orbital
LUMO - Lowest Occupied Molecular Orbital
Mainly the only MOs we are interested in for reactions
249
To consider reactivity what do you need to consider?
Reactive parts of molecules and frontier MOs (HOMO/LUMO)
250
Why do bonds between nucleophiles and electrophiles arise?
From overlap of two orbitals and a filled and an empty orbital
Energetically stable to form the bond as two e- end up in bonding MO that is lower in energy
251
When is stabilisation greater for Nu/E bonds?
When the empty orbital on the electrophile is closer in energy to the filled orbital in the nucleophile
252
What do the relative orbital energies of Nu/E tell us about what we should consider?
Usually only consider HOMO a nucleophile and LUMO an electrophile as they are typically close in energy
253
How can we narrow the HOMO-LUMO gap and make reaction more favourable?
Raising HOMO energy and lowering LUMO energy
254
What do electron withdrawing groups and electron donating groups do to orbital energies?
EWG lower orbital energies - e.g. on electrophiles this lowers LUMO energy and increases electrophilicity
EDG raise orbital energies
255
What does delocalisation do to the HOMO?
Causes stabilisation so lowers HOMO energy
256
Why should we care about orbitals when talking about reactivity?
Most organic reactions involve aspects of both interactions of orbitals and charge interactions
257
When two molecules collide what three main forces act?
1. Occupied orbitals on each molecule repel
2. Any positive charge attracts negative charge
3. Occupied orbitals of one molecule interact with unoccupied orbitals of the other - causing attraction
258
What impact can conjugation have on reactivity?
Can cause atoms to become less nucleophilic/electrophilic due to electrons being distributed around
Can cause reactions to only happen on parts of the molecule - meaning some parts won't react as expected
259
Does orientation of orbital overlap matter?
Yes effective overlap can dictate orientation of how Nu/E interact
- Sometimes nucleophiles must approach from rear side to overlap with correct sigma star LUMO
- Sometimes nucleophiles can approach from both above and below the plane of molecule due to two empty orbitals
260
What is a bronsted acid?
What is a bronsted base?
Bronsted acid - proton donor
Bronsted base - proton acceptor
261
What is a lewis acid?
What is a lewis base?
Electron pair acceptor - related to electrophile
Electron pair donor - related to nucleophile
262
What happens when you react an acid and a base considering bronsted?
You get a conjugate acid and a conjugate base
- Means they can be interconverted with their original acid/base by transfer of a proton
263
How close are lewis acid/bases and electrophiles/nucleophiles?
More or less interchangeable
But lewis acidity/basicity are different from electrophilicity and nucleophilicity
264
What is pKa and how do you calculate it?
Measure of acidity
pKa = -log(Ka)
Ka = [H+][A-]/[HA]
265
Why is pKa used?
Used as Ka is often a small number and has a huge range of values (10^10 to 10^-50)
266
How do you express Ka in terms of Keq?
Ka = Keq[H2O]
267
What is pKaH?
pKa of the conjugate acid of a base
e.g. conjugate acid of A- is HA so pKa(HA) = pKaH(A-)
268
What are the key ideas around pKa?
The lower the pKa the stronger the acid (think pH scale)
The stronger the acid the weaker the conjugate base
269
Why is knowing values useful?
Useful for understanding and predicting reactivity as well as approximating unknown pKa values
270
What does a high value of pKaH suggest?
A good base
271
What determines how acidic a compound is?
Factors that stabilise the conjugate base (decrease the pKa) make acid stronger
272
How does charge on A affect acidity?
Acidity increases with increasing positive charge on A
273
How does atom A's electronegativity affect acidity?
Across periodic table - acidity increases with electronegativity
Down periodic table - acidity increases as size increases
274
How does delocalisation of charge affect acidity?
Delocalisation of negative charge in the conjugate base will stabilise it, hence increases acidity
275
How does inductive stabilisation of A- affect acidity?
Electron withdrawing substituents can stabilise A- and increase acidity
Effect increases with electronegativity of X
Effect decreases with increasing distance to e-neg atom
276
What is the inductive effect?
Effect of transmission of charge through a chain of atoms
277
How does orbital hybridisation of A- affect acidity?
Higher proportion of s character stabilises A- and increases acidity of HA
Due to s orbitals having significant probability of being found very close to the nucleus - increasing attraction
278
What does remembering some pKa values and the factors affecting acidity allow for?
Determining most acidic protons
Identify likely reaction sites
Compare relative acidity
Choose appropriate reagents
Assess leaving group ability
279
What is needed to choose a good base for a reaction?
pKa of compound being protonated
How strong the base is
280
What do we use to quantify basicity?
pKaH or pKa of conjugate acid
281
How can you tell if something is a strong or a weak base?
Strong base has a weak conjugate acid so high pKaH
Weak base has a strong conjugate acid so low pKaH
282
What factors affect basicity?
Same ones as for acidity except not opposite reasons
Factors that stabilise the electron pair on basic atom with weaken the base (lower its pKaH)
283
What is important about choosing an acid/base in a reaction?
It will affect the position of equilibrium
We may want to irreversibly deprotonate a compound or just want a reversible reaction
284
How can you use pKa to predict position of equilibrium?
If pKaH of the base is higher than pKa of the acid - equilibrium with shift towards products
If acid is stronger than the conjugate acid - equilibrium shifts towards products
285
How can you use pKa to predict position of equilibrium? (Simple)
Look at both acids
Lower pKa = Stronger acid = More dissociation = Shift to opposite side
286
What happens if there is a large difference in pKa?
Far to one of the sides
287
What can you do to change position of equilibrium?
Change the strength of the base/acid to switch it to the left/right
288
What is the effect of solvents on pKa?
Different solvents stabilise species different amounts so will allow different reactions to go ahead
289
Why do most reactions in organic chemistry use organic solvents?
So reactants are soluble
And you can use a stronger base than hydroxide
- If you use water as a solvent anything with a pKa greater than water would cause the water to react in the reaction first
290
Why do pKa values in DMSO and water differ?
Due to different solvation properties towards ions
- Water is a protic solvent so can solvate both cations and anions well
- DMSO is a aprotic solvent so can strongly stabilise cations and solvates anions less effectively
291
What does knowing pKa values allow us to understand?
Charge state of compounds at particular pH
- Impact on solubility
- Potential to separate compounds
292
How can pKa be used to decide what charge compounds should have?
Acid - If more A- than HA it will be negative
Base - If more B+-H than BH is will be positive
Look at pH value - Compare it to pKa/pKaH values in compound
Decide where equilibrium lies
293
How can pKa be used for separation?
You can add two organic products to a base/acid - if only one of them is soluble in it it will become an aqueous layer that can be separated out
294
How can pKa be used to see leaving group ability?
Species with a low pKaH value tend to be better leaving groups
(lower pKa of HX, better leaving group X-)
295
What is a leaving group?
An atom or group of atoms that can be expelled from a molecule, taking both bonding electrons
296
How does charge affect basicity?
Basicity increases with increasing charge
297
How does conjugation affect basicity?
Basicity decreases with conjugation
298
How do EWG and EDG affect basicity?
EWG - Decrease basicity
EDG - Increase basicity
299
How does hybridisation affect basicity?
Basicity increases with decreasing s character
300
How does the relationship between pKa and pH tell us whether our compounds will be charged at a certain pH?
If pH is greater than pKa then more of your compound is deprotonated so will be charged
If pH is less than pKaH then more of your compound is protonated
If pH is lower than pKa then more of your compound is not dissociated
If pH is lower than pKaH then more of your compound is neutral
If pH=pKa there is a 50% dissociation
