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Chapter 1
- Constitutional isomers have the same chemical formula, but different name, structure, and chemical properties.
- Formal charge is based on the number of electrons an atom should have based on the octet rule. We count the number valence electrons in each atom. If an atom has then it should, then that is the formal charge of the atom. Or group number minus electrons assigned to it (1 per bond and 1 for each electron in a lone pair)
- Aufbau (building) principle is how 4s fills before 3d, like 1s 2s 2p 3s 3p 4s 3d 4p 5s 4d etc.
- Covalent electronegativity >0.
- Polar covalent electronegativity 0.5<x<1.
- Ionic electronegativity >1.
- Positive and negative in relation to bonding and orbital is weird. When positive and negative overlap it is destructive interference causing the solution of electron wave function to get smaller.
- Molecular orbital theory. Highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital will always bond together.
- Pi bonds are weaker then sigma bonds because the orbitals overlap side-by-side instead of end- over-end
- Steric number is how many domains an atom has (lone pairs + bonds) and determines hybridization (4=sp3, 3 =sp2, 2=sp1, 5=sp3d1, etc.)
- The magnitude of a dipole will not be calculated in this course, however a dipole is when a molecule is polar, the electrons are moving towards the anion (negative charge/ more electronegative/
−¿¿) direction of polarity is super important.
- Induced dipoles are the result of the electrons in the orbital changing what side of the molecule it is on, this can happen very rapidly/almost instantaneously. Normally electrons are balanced within their orbitals, but sometimes they aint. This rapid change can induce neighbouring electrons to also become a dipole. This is the theory behind London dispersion
- Protic means it gives off a proton (acid) this ones also engage in h-bonding and called protic solvents. Solvents that do not h-bond are aprotic
- Like-dissolves-like. Polar can dissolve polar, non-polar can dissolve non-polar, phenol can dissolve phenol Chapter 2
- Formal charges other than zero must be indicated on the bond line structure.
- Formal charge = Valence electrons – (Bonds + Lone pair electrons)
- Carbons with a positive formal charge is a carbocation
- Resonance, when it comes to formal charge, a plus just means there is an empty orbital, now if there is a double bond or something in the molecule, the double bond can move from it’s atom to the empty orbital. The delocalized pi-bond is equally stable in both configurations. A three- center two-electron bond.
- When you spread out charge, electrons become more stable
- Curved arrows show the movement of electrons in a resonance structure, pointing to the bond where the electrons are going
- Only pi bonds move in resonance structures, sigma bonds don’t resonate.
- Resonance doesn’t exceed the octet rule.
- Types of bonding patterns
- In a double bond, the carbons that are double bonding are vinylic, carbons attached to the double bonded carbons are allylic. There is only a name for one degree of separation, not two atoms separated.
- Filling the octet in resonance is more important than giving electrons to the most electronegative atom.
- Phenols/benzene is a resonance structure
- The most significant contributor to resonance has all/most of it’s octets filled
- Compounds with an overall formal charge, we focus on the movement/delocalization of that charge, adding additional charges is valid but unnecessary and insignificant in terms of contribution
- Rule 1: fill all octets
- Rule 2: minimize formal charges
- Rule 3: Negative charges sits on most electronegative atom
- Resonance hybrid is the delocalization of the pi bond of allylic carbocations delocalized over all three carbon atoms
- Only delocalized electrons are in resonance and more stable.
- Be careful when determining the hybridization of delocalized electrons in resonance, any lone pair that is delocalized can become a double bond and is only possible through overlapping p- orbitals. Turning sp3 into sp2 hybridization
- Remember to look at the direction of p-orbitals when looking at resonance. If the orbitals aren’t in resonance, they can’t do they thing. Vinylic lone pairs aren’t delocalized, and cant perform resonance. Chapter 3: Bronsted-Lowry: Acids donate protons, Bases accept protons. Lewis: Acids accept electrons, Bases donate electrons
Alcohol vs carboxylic acid. When deprotonated, it is now a base with a delocalized lone pair on an oxygen.. that lone pair can be shared across the two oxygen atoms in the acid, making it more stable, therefore more acidic the acid. Stable base, weak base, strong acid
- Induction Hydrogen is less Electronegative then carbon, pushing it’s electrons towards the oxygens. While Chlorine is MUCH more Electronegative then carbon, pulling the charges away from the carbons and oxygens, helping the hydrogen fall off easier. Less stable acid, stronger acid, weaker more stable base. The more electron withdrawing groups means a more stable conjugate base and a stronger acid. And the closer ones have more of an effect on induction then the further ones. Doesn’t count after about 3 or 4 atoms
- Orbital An sp^3 hybridized orbital has a much wider area then sp^2 and sp hybridized orbitals. The closer electrons are to the nucleus, the more stable they are. So sp orbitals are pulling on the electron more then sp^3 orbitals, therefore the strongest acid and weakest conjugate base which is not as reactive. sp^3 pKa is ~ sp^2 pKa is ~ sp pKa is ~
- the more stable the base means that the molecule is more capable of being a base, not needing the hydrogen to be stable it will freely give it off. LOWEST PKA IS THE STRONGEST ACID AND WEAKEST BASE. HIGHEST PKA IS THE WEAKEST ACID AND STRONGEST BASE. We can predict which of the sides of an acid base is preferred using ARIO, the pKa values of H-A and H-B (the acids) the one with the higher value will be favoured. We can also use the relative stability of the bases, with the more stable one being preferred. This is also appropriate for determining reagents in an acid/base reaction, determing the pKa of what we are trying to de/protonate is very important
The leveling effect, gotta be careful of that. The strongest acid in water is straight hydronium (H 3 O+^ baby) and the strongest base is OH-. If you put a stronger base then OH-^ in water, the water will donate it’s hydrogen to form hydroxide. The same is true for a stronger acid then H 3 O+. so we cannot use these acids and bases in water, we gotta carefully choose the solvent used. COUNTERIONS, aka spectator ions. Present to balance overall charge of solution but do nothing, like how we use sodium all the time to do stuff in biochem. INTRO TO SPECTROSCOPY CHAPTER 14
Wavelength is inversely proportional to E E =
hc
= hv as wavelength increase, energy decrease.
matter have particle-like properties, so waves can interact with particles. Atoms are quantized, as in they have discrete energy levels like the electron can be here_ here – or here ~ but nowhere in between. So if a photon strikes a molecule with the exact necessary amount, the light is absorbed and the molecule will be vibrationally excited. IR causes molecular vibration, different types of bonds absorb different IR energies, resulting in the release of heat. IR aint strong enough to break bonds, but it can make the molecule start to stretch and dance and vibrate. the energy necessary to cause vibration of different types of bonds varies from bond to bond. IR spectrophotometer irradiates the KBr sample or salt plate with all frequencies of IR light, the graph made of the transmittance of the molecules and at which frequencies will tell us the functional group that is present. Each peak of the graph is specific to a functional group/type of bond. Wave number is wavelength/c, and goes form 400 to 4000 cm-.
Carbonyl groups have a much higher intensity then a carbon double of triple bond A lot of identical bonds can and will increase the intensity of the peak of that bond C double bonds are usually moderate intensity, weak stretches only happen in symmetric molecules. OH bonds have very high wave numbers, around 3600 cm-1, hydrogen bonds weakens the bond, resulting in a lower wave number, broadening out the peak a lot lowe. Resulting in a narrow peak at 3600, then a very broad peak around 3400. In a concentrated sample, the O-H peak disappears, giving us only the broad peak. In dilute solution the hydrogen bonding peak disappears, giving us just the sharp peak at 3600. Carboxylic acids dimerize, forming hydrogen bonds between the o-h groups. Forming a very strong and broad peak, with many characteristic peaks at the most intense sections. And another narrow peak around 1700. The hydrogen can move from molecule to molecule, making the peak even more broadened. n-h stretching signal from primary and secondary amines. Bonds follow the same hydrogen bonding principle as the last example since they h-bond. Primary amines have 2 n-h peaks, secondary amines only have one N-H peak. The two stretches are cause by symmetric and asymmetric stretching, secondary amines only have the one since they only have one hydrogen attached, resulting in symmetric stretching.
- Look at 1600-1850 for double bonds
- 2100-2300 for triple bonds
- 2700-4000 for x-h bonds
- Look at wave number, intensity and the shape. In mass spec, a compound is vaporized, ionized and fragmented. Useful for determining the molar mass and formula. The masses of the ions are detected and graphed. When vaporized and ionized, it goes througha tube with a magnet. The lighter particles have less mass, therefore less inertia, and will curve into the tube right away, heavier ions will travel further before curving due to their inertia.
Each of the radicals that are formed from the mass spec are unstable, and break apart into smaller and smaller fragments. Based on the location of where each fragment falls, we know the exact mass of the fragment, telling us exactly what was in the organic molecule like puzzle pieces. Focussing just on the molecular ions. This is the mass spec of methane. The most intense peak is the base peak, from the removal of one electron. Base peak=molecular ion peak, this is not always true but for this course it is. The mass of methane is 16, 12+4*1, the other peaks are each a removal of a hydrogen, and the M+1^ peak is 13 C. Benzene has 6 carbons and 6 hydrogens, mass is 78, so the base peak is at 78. Often but not always the base peak and molecular ion peak is the same. The charge will always be +1 for the base peak. That’s why it’s m+1. The m/z of the parent ion is the molar mass of the compound. Most hydrocarbons end up with an even number of hydrogen, with a mass of one. And since carbon has a mass of 12, we end up with constant even numbered masses. When we have an odd number we know there is at least one nitrogen present since it has an odd number of bonds, changing the mass by one. However when we have 2 nitrogens it is more ambiguous. 1.1% of all carbon atoms are carbon 13. So with each additional carbon we have an additional 1% of carbon 13. Increasing the intensity of that m+1 peak.
Chapter 15: NMR time pretty much exactly an MRI. Involves the reaction of Nuclei with electromagnetic radiation and the nucleus (this is what makes it nuclear). Looking at the spin of a nucleus. We wil focus on doing this to C and H and the molecular structure affects how radiation is spread through the molecule. Protons and neutrons in the nucleus are spinning. Therefore there is a net spin. This net spin means that the nmr only works when nucleus has an odd number of particles. So nmr only works on carbon 13, since these isotopes have an odd number of nuclei, therefore an net spin generating a magnetic field. When a general magnetic field is applied to the space where the molecule exists, it will align with the applied magnetic field (B 0 ). The field can either be aligned with the applied field, and this is the alpha spin state, lower energy. Or it can be opposing the applied magnetic field, this is the beta spin state, or higher energy. Every different bond in the molecule will have a different gap in the energy level. And the change in the energy level will end up releasing light (specifically radio waves). The bigger the magnetic field we use also changes that energy gap, resulting in higher wavelengths being released. Some researchers use the earths magnetic field to do this even lol. Superconducting magnets are typically used for this tho. Think about electrons, they have a charge and spin, bigger nuclei are much more shielded by the magnetic field induced by electrons. Needing less energy to spin flip. The stronger magnetic field increases the gap in the energy level of the two spin states, allowing for more effective signal separation. As the atoms are excited and relax they emit energy, this is called the free induction decay (FID). Do a fourier-transform(complex math algortihtm) to get the NMR spectrum. We use deuterated solvents instead of regular hydrogen to avoid the odd numbered hydrogen. For NMR we look at
- Number of signal
- Signal location (chemical shift)
- Signal intensity (area under the signal)
- Signal shape (splitting pattern) Similar on stuff from IR spec, but here we are quantitative. First we will discuss 1H NMR. Any unique and different kind of hydrogen will generate a peak. These are non chemically equivalent hydrogens. Identical protons are chemically equivalent, either homotopic or enantiotropic. Homotopic protons, imagine that you rotate the molecule along an imaginary axis, both protons will map directly onto each other, without changing the molecule. The protons are just different conformations of that molecule
Enantiotropic protons are able to make a mirror image along a imaginary plane, since the compound as a whole is symmetric but the hydrogens are. Enantiotopic protons are planes of symmetry, homotopic have an axis of symmetry. If we were to replace a proton with a chlorine we are generating a chiral center, and making two chemicals which are enantiomers. Diastereotopic protons are not chemically equivalent. These are generated when the carbon that the carbon we are working with is attached to is also a chiral center, we are making two new diastereomers when we replace a hydrogen with a chlorine. THEY REQUIRE THERE TO BE ANOTHER CHIRAL CENTER PRESENT. Heterotopic protons are those that form structural isomers when a hydrogen is replaced with a chlorine. So for an nmr all enantiotopic and homeotopic protons will produce one signal. All hydrogens in a methyl group are equivalent. Easily all molecules without chiral centers have only chemically equivalent protons. The one on the left will generate only 4 signals from an NMR spectrum. The only on the right will generate 10 different signals since each hydrogen is unique. Chair conformation of cyclohexane is the most stable arrangement of it’s molecules. However it can do a lil flipy flopy dance, shifting it’s whole molecular structure, this shift results in the axial and equatorial hydrogens to move like a lever going from 90 degrees to 0. At room temperature this shift occurs super rapidly, NMR ain’t fast enough to see these changes, but at like -100 C and beyond the ring flipping is observable.
- Chemical shift 1% TMS is added as an internal standard, its methane but with a silicon at the center. This silicon is less electronegative then carbon, so it will be donating density. So the signal for this hydrogen will have the most density. Because these protons will be more shielded. TMS as a result will have the lowest energy waves released, so this will be our standard/zero
Chemical Shift ( δ )= Observed Shift ¿ TMS ∈ hertz ¿
Operating Frequency of theinstrument ∈ hertz
and this would return a constant value for what is coming out, the result is measured in parts per million. Peaks will spread further apart when
We can use this to determine what peaks are attached to. If there are electrons in resonance in a ring like benzene. These bonds will have an effect on the applied magnetic field, causing these hydrogens to shift it to around 7-8, so peaks in the 7-8 range are caused by the benzene ring. But with really big rings, the magnetic field caused by the moving electrons will have a negative effect on any hydrogen attached to the center of the ring. Sometimes for compounds that have a more unstable hydrogen, this one that keeps falling off the molecule might not show up on the nmr. The intensity of the NMR peak is done by taking the integration (area under a curve) of each of the peaks and spitting out a number. If we normalize the intensities and multiple through to get close to whole number, we get the lowest number of hydrogens and what groups they belong too, we are getting the lowest number since the peak of one hydrogen, and of 13 identical hydrogens, will both have the same intensity. Normally we don’t deal with multiples higher then 5. Multiplicity/shape from NMR output.
Info about what is around the hydrogen. The number of hydrogens upto three bonds away that are different from itselfare responsible for the different amounts of peaks. Each hydrogen can either spin with the measured hydrogen, or against it and the field, causing another peak but at the same location. With three protons, there are 2 possibilities where two of the three are spining together and one is opposite, resulting in a ratio of 1:2:1. Equivalent hydrogens cannot spin in opposite ways, and hydrogens up to 4 bonds away can have a coupling effect, like in benzene, but don’t for this course. N+1 rule, the peaks we see are caused by how many different hydrogens are 3 bonds away +1. If we look at the distance between the two unique constants, they will be the same and we will know which hydrogens are close to each other. This constant is called the coupling constant or j value Some characteristic peaks to look out for is a singlet peak with an integration of 9, that’s a tert-butyl (R(CH 3 ) 3 ) group. Or a singlet integration of 6h, and a septet peak with an integration of 1h, that’s an isolated isopropyl group. depending on the chemical, we can see a quartet made of triplets, and we can still use the coupling constant to determine which hydrogens are coupled with what. This coupling tells us that Hc is coupling less then Ha, since the distance between the triplet peaks is much smaller, then we know that the tripling coupled hydrogens have less of an effect. If the two couplings are similar sizes, they may overlap due to how similar they are, resulting in a multiplet. Multiplets with identical coupling constants will end up looking like standard multiplicities, there wouldn’t be a quartet of triplets by example. Think of alcohol, due to the ability for the hydrogen in water to randomly fall off and be deprotonated cause of water, meaning that that hydrogen wont partake in coupling (incel proton). Partakes in any hydrogen that is ionizable, or any hydrogen that can hydrogen bond. But be carefull, if done with a deuterated solvent it can result in the OH becoming OD, and since deuterium wont peak in NMR, there won’t be a peak at all.
Chapter 4 A bicyclic ring is just two rings jammed together We start the naming by going from the bridgehead carbons (Tertiary carbons) and counting each of the fragments from that carbon, or just named by the number of carbons of the chain., and named in the order of the different carbons, so this one is bicyclo[2,2,1]Heptane Constitutional isomers, they completely change the arrangement of atoms within the molecule. Cycloalkanes if it was flat, each carbon in a ring would be undergoing angle strain, since like a triangle has a 60o^ angle, that’s so far from carbons 109.5o. so bigger rings are much more stable, because of angle strain, and torsional strain caused by exlipsing. Cyclobutane for example, is not fully exlipsed, but bends up to relieve pressure. Chair conformation of a benzene is the most stable The twist within the twist boat relieves pressure in the chemical. Functional groups along equatorial are more stable along the axial. the only difference between cis and trans stereoisomers is that two of the substituents are differently located. Cis-isomers have the substituents both either axial or equatorial, trans have one of each.
Stereoisomers have the same molecular formula and shape, just a change in the arrangement of some molecules, specifically a rotation. constitutional isomers have a different structures. Cis has the highest priority group on the same sides. Trans has the highest priority groups on opposite sides. Chiral object is asymmetric, meaning their mirror image do vibe. Chiral molecules may not interact complimentarily to each other, their structure and chemistry might be the same, but pharmacology might differ. Think how specific enzymes are. Sometimes stereoisomers can be enantiomers, these isomers form when we ake a mirror image of the compound. ONLY CHIRAL BITCHES BE ENANTIOMERS. For R and S groups we number them based on priority. Arrange the compound so that the lowest, probably hydrogen, to the highest. Clockwise is R, counter clockwise is S. atomic number determines group priority, if they are bound to the same element then we go to the next one. Double bonds count as 2 bonds when we keep going down the group, Chiral stereoisomers only differ in how they interact with light and with other chiral molecules (like how enzymes only work with one of the isomers), Chiral stereoisomers can rotate light wavelength in different ways then their Chiral stereoisomers. There is no relation between the R/S of the compound, and the + dextrorotary/- levorotary of the compound, just that one isomer will be + and the other will be -. Recemic mixtures have equal amounts of both. If there is an unequal mixture, and one has a different specific rotation, then we can calculate the ratio we have (% enantriomeric excess). It is equal to the
observed specific rotation (observed α ) over the α of the pure enantiomer
Remember stereoisomers are not superimpossible, with the same connectivity. Enantiomer can make a mirror image, stereoisomers cant. Diastereomers can’t form either mirror images or superimpose. Cis and trans isomers are not mirror images, but have the same connectivity, but they have different
physical properties. Number of isomers are a mathematical property, the formula to determine is 2 n
where n is the number of chiral centers. Generally one chiral center means it’s a chiral compound. If there are more then one chiral center, the compound could not be chiral maybe. Think of 1,2-methyl-cyclohexane. Trans cyclohexane is chiral but cis isn’t. because when we flip the cis configuration it is the same molecule, it has a plane of symmetry so it will be superimpossible on its mirror image, making it non chiral. Meso compounds have an even number of chiral centers with a plane of symmetry. We can check this by seeing if a mirror image are identical. Plane of symmetries mean it is achiral, but if there is a point of
Delta S increases when we have more moles of product then reactant, or when a cyclic compounds become acyclic
Δ Stot =(
Δ H sys
T )
− ΔSsys
Gibbs free energy tells us if a reaction will occur or not.
Δ G = Δ H +(− T Δ S )
negative gibbs means reaction will occur/ is spontaneous at room temperature. Positive is opposite solid to liquid to gas will increase. Gonic means gibbs, thermic means temperature.
- Δ G favors products, endergonic favors reactants. The equilibrium constant
Keq =
[ products ] [ reactants ]
[ C ] [ D ]
So we can calculate Δ G with
Δ G =− RTln Keq
All these terms are only thermodynamic, they tell us nothing on the rate of reactions. If delta G is like above ten in either direction, the equation goes one way. But we do not now the rate of reaction, like how all diamonds will turn into graphite since it is favourable, but it is slow. Explosions are fast. Rate law, more reactants means more reactions means faster reactions. Rate=k(reaction contant)[K] First order, one thing is reacting, probably breaking Rate=k[A][B] Second order, when one is doubled, then the reaction rate is doubled, and this pattern just keeps going. Rate= [A]^2 [B] Third order, a doubles, rate quadruples. But since three molecules need to be orientated in a specific way, and hit spontaneously, it is super unlikely to happen. Activation energy, the initial variable, not all molecules have enough energy to do the reaction. Lower activation energies mean faster reaction since more molecules have sufficient energy. Temperature, increases the temperature of the compound. Making more molecules have enough energy to go and do they thing. Steric considerations, like if the place where the reactions are not nearby, they wont react.
Catalysts work by taking a different path of reaction and not being used, in essence lowering the activations energy. Reactions with catalysts are multistep with much lower activation reactions. Kinetics is a rate of reaction, Thermodymics is equilibrium. Kinetics work faster then thermodynamics. Like sure one product is more thermodynamically stable, but the other product has a lower activation energy, it happens faster, so unless something changes about the environment, we get kinetically favored product. We control by temperature, so like if high temp we get the more thermodynamically stable product, and lower temp is kinetic favored. Transition states are the top of the energy graph, where the bonds are being broken and formed, intermediate states are more easily observable, and are between two transition states. Hammond postulate allows us to predict which transition state we see, depending where we are on the energy graph the bonds can be closer to the product or reactant. Endothermic have transition states closer to the product, exothermic is closer to the reactant. Nucleophiles and electrophiles. Positive and negatives attract, electron rich species attracted to electron deficient species. Nucleophiles are lewis bases (electron donor), they have extra electrons and can donate. Bigger electrons tend to be more nucleophilic, since they are more easily polarized. Electrophiles are lewis acids (electron acceptors) ALWAYS LOOK AT RESONANCE TOO TO DETERMINE ELECTRO/NUCLEOPHILISM Nucleophiles are negatively charged, resonance will make it less nucleophilic. Electrophiles are positively charged, ARROW PUSHING
- Nucleophilic attack, nucleophile attacking an electrophile a. Tail starts where electron is, b. Head shows result c. Electrons are shared, not transferred. d. MAKE SURE WE DON’T EXCEED THE OCTET e. So we show resonance with another arrow to prevenet this
- Loss of leaving group
