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[under construction] analytical chemistry methods

I won’t be going into how they work, since that tends to be more of a class. I’ll be covering instrumentation, what it’s used for and maybe units and other notes.

Fluorescence spectroscopy

used for measuring compounds in solution

can examine structural changes or binding of two molecules by changes in fluorescence intesity

EPR spectroscopy

used to study materials with unpaired electrons in liquid solutions

like NMR but electron spins instead of nuclei spins

Spectra are used to identify molecules within a sample and more importantly, to characterize the environment of the unpaired electron 

gas chromatography quantitative!! three main pieces of information: (1) number of components in mixture, (2) how much of each compound is in mixture, (3) retention time

atomic absorption spectroscopy can quntitatively extrapolate concentration of a substance by its absorption

Infrared spectroscopy observes vibration of bonds tells what functionalities exist

mass spec mass of molecule may give info on structure

NMR info on environment and number of H (or C) in a molecule

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ideal gases under certain conditions

gases are kind of fun because you often can hold certain aspects of a system constant and see what it does then. this is a short, nonmathematical derivative summary of those situations’; you can try to work through it using the equations on the undergrad thermodynamic page, substituting Δ  for d. I highly recommend taking the time to understand the math behind them, but for the purposes of the GRE, these are what you should know--descriptions and the “math” conclusions.

isothermal processes the system stays at constant temperature. this tends to be for slow, reversible reactions. Holding the temperature constant means dT = 0/ ΔT = 0. additionally, because temperature is a state funciton [insert link to state functions later] of internal energy  ΔU, we know that it is also equal to 0 dU = 0/ ΔU = 0

Adiabatic processes this tends to be a tricky concept. at first glance it seems like isothermal processes; however, the important fact is that heat cannot be transferred in or out, so rather the temperature inside the system itself will change. mathematically, it is a constant q, so  Δq/dQ = 0

isobaric processes pressure is constant;

isochoric processes volume is held constant; so think a rigid container with a lid. dV/ ΔV = 0

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electrochemistry [under construction]

In combining cell potentials, the potential is indepedent of nmber of moles present, unlike within free energy calculations. So even when you change the coefficients for a half-reaction, the potential stays the same!

E° reduction = - E°    oxid

If a half-reaction has a high positive value of  E°, it will most likely to be reduced and act as best oxidizing agent. 

ΔE° > 0  reaction occurs readily as written. ΔE° < 0 reaction only occurs under extreme situations as written.  

 E =  ΔE° - nlogQ, where Q = reaction quotient (aq)

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quick notes: gibbs free energy [under construction]

ΔG° =   ΔH° - T ΔS° 

ΔG°  = -nFE° n = number of moles of electrons exchanged F = faraday constant value E° =   standard electrode potential, aka measure of individual potential of reversible electrode (volts) [link to page on standard electrode potential)

ΔG°  = -RTln(Keq)

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First Year “Physical” Chemistry Constants: An Incomplete List [under construction]

rate constants:

equilibrium constants value of equilbium constand and equilibrium concentrations affected by temp

acid dissociation constants

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[under construction] reaction coordinate diagrams

A few un-obvious tips.

To find deltaH(rxn) from a reaction coordinate, subtract the FINAL part from the INITIAL. ignore the activation energy.

it’s all energy... same units and can find all from it. 

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in a container of water boiling that is open to environment:

ΔH cannot be zero -> the energy required to overcome equilibrium of condensation and evaporation is large and more than accounted for in  ΔU

ΔS cannot be zero -> the “chaos” of water molecules in vapor is different than that of liquid.  ΔS cannot be zero

HOWEVER,   the understanding here is that: boiling = at boiling point at boiling point = liquid and vapor states coexist = in equilibrium  SO  ΔG = 0

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experiments list [under construction]

A list of experiments that may be asked on the ACS test/GRE subject test. Know generally what the experiment was, but most importantly, what it meant:

Rutherford:  Shot alpha particles at a metal foil target. Most of the particles passed without any deflection in path HOWEVER some particles were deflected at large angles. he did this to examine the structur eof the atom this result told him that the atoms of the metal were mostly empty space. 

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alkyne reduction with cataysts [quicknotes]

h2/pd or h2/pt: reduced to alkanes deactivatd catalysts (ie., lindlar catalyst) : reduced to alkenes

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The first step is often the hardest… but also the most important. You won’t regret starting something beautiful :)) 

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studyblrs aren’t all straight rich white girls pass it on

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Hydroboration-oxidation: long story short

This is one of the big reactions; professors love it and asking questions about it. You’ll likely need to know the mechanism for an undergraduate test. Thankfully, I’m not really expected to draw that out on the GRE, though it’ll be good to be familiar with it. So here are some fast facts:

Overall transformation: Alkene into an alcohol; alkyne into an enol into an aldehyde via tautomerization. 

type of reaction: a two-step electrophilic additon. technically a hydration--net gain of water. IT IS NOT A REDUCTION OR AN OXIDATION (the “oxidation” part of the name comes from an internal oxidation of the hydroborated step).

It is anti-Markovnikov and you’ll likely need to know that. 

RETENTION OF STRUCTURE!!!!!!!!! 

syn addition--the OH and H will add to the same side

reagents: To an alkene or alkyne, add in the first step BH3/THF. second step, add base and peroxide. 

interesting notes about mechanism: the big deal here is that the hydrogens on BH3 all get displaced by the alkene (specifically on the less sterics side-->that’s why it’s antimarkovnikov). the base in the second step then comes in to steal that R group. (look at the mechanism will be more helpful tbh)

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OsO4: the oxidant

what it is: osmium tetroxide what it does: it is an oxidizing agent. important characteristics: expensive, toxic. doesn’t work with alkynes. has a ring intermediate

Reactions with pi bonds: alkenes: it will form 1,2-diols, always in the syn formation. 

[list of oxid/red reagents in ochem]

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CrO3: the oxidant

what it is: chromium trioxide what it does: it is an oxidizing agent. In fact, if you see this anywhere as a reagent, already start thinking about oxidizing! important characteristics: normally used under basic conditions, unlike chromium (vi) reagents. extremely powerful!! usually overoxidizes!! is also dangerous in labs Notes: CrO3 is a subset of crvi reagents that specifically include three “mixes”-- Jones reagent (CrO3/H2SO4) - can overoxidize collins reagent (CrO3/CH2Cl2) - good for acid sensitive; more selective Sarrett reagent (CrO3/2pyridine) - more selective; wont affect C=C

Reactions with alcohols: Jones: 1deg alcohol -> carboxylic acid; 2deg -> ketones Collins: 1 deg alcohol -> aldehyde; 2deg -> ketone (W/O OVEROXID at all) Sarrett: 1deg alcohol -> aldehyde; 1deg alcohol -> ketone

Reactions with aldehydes: aldehydes -> carboxylic acid

Reactions with pi bonds: alkenes: in general, CrO3 with alkenes will cleave the double bond in neutral or acidic environments; will oxidize each of the C=C carbons to the highest oxidation state consistent with their substitution patterns So, in “easy to think of” terms, but NOT ACTUAL MECHANISTIC TERMS, the double bond in C=C is broken and an O put at each C (C=O), and any other carbonyl  hydrogens

[list of oxid/red reagents in ochem]

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O3 as an oxidant

what it is: o3; the mechanism is called ozonolysis what it does: this is a large question and goes into niche fields of chemistry, so for genreal ochem purposes, it is an oxidant notes: work-up is either zinc in acetic acid or dimethyl sulfide (which reduces any h2o2 made) or h2o2 to further oxidize and get carboxilyc acids

reactions with alkenes: alkenes -> 2 carbonyl groups

reaction with alkynes: alkyne -> 2 carboxylic acids

[list of oxid/red reagents in ochem]

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HIO4: the rundown

what it is: periodic acid what it does: it is an oxidizing agent. I’ve only seen this in an oxidizing context, specifically used for the oxidative cleavage of alkenes and diols. BUT APPARENTLY periodic acid can be used to cleave various 1,2-difunctional compounds.   for our purposes, it changes a 1,2-diol to two carbonyl compounds. It cleaves the bond between the original hydroxy groups by cleaving vicindal diols important characteristics: 

seems to be used in analysis of carbohydrates, especially structure determination because they can open saccharide rings.

Selectively reacts with 1,2 diols

reaction occurs via cyclic periodate ester formation

can be used as functional group test for 1,2-diols(This can be useful in determining the structure of carbohydrates as periodic acid can be used to open saccharide rings.)

[list of oxid/red reagents in ochem]

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just a literal list of common/need to know oxidizing and reducing agents in organic chemistry

**add hyper links to individual reagent pages later

oxidizing: increasing oxygen content and/or decreasing hydrogen content of a compound

MOST WIDELY USED: chromium (VI) : CrO3, K2CrO7, K2CrO4, PCC, PDC, CrO3-2pyridine manganese(VII): KMnO4 Periodic acid: HIO4 Ozone: O3 Halogens Peroxy acids OsO4

reducing: converse of oxidation

MOST WIDELY USED: complex metal hydrides: LiAlH4, NaBH4 catalytic hydrogenation alkali metals in ammonia clemmenseen reduction wolf-kishner reduction raney nickel

if reactions occurs in which numbers of hydrogen and oxygen atoms change in manner corresponding to addition/net elimination sof water, it is not oxidation or reduction