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The following Table Covers Chemistry topics from the simplicity of atoms to the complexity of Organic Systems. An attempt was made to maintain a vertical rule in increasing complexity of the system, that is atoms are before molecules, before organic molecules and before thermodynamic reactions. Thermodynamics. Although not strictily enforced the hierarchy will make searching for terms more easily. SF will be updating the table format as we work to improve site navigation. SSFF hopes the table will help people find useful information by association. All input is greatly appreciated! Write to, we'll gladly answer any questions or take feedback to improve your experience within The Forest.

Atomic Structure
What is an Atom?

Return Home

Does anybody know? Has anybody seen an atom?

How big is it? How do we know? Is there Similitude between Atoms and Galaxies?

Are there more Atoms in the Periodic Table that we do not know of?

Where did you see your first atom?

Is the atom a particle? Is it a wave? Is a Photon an atom?

Electronic Structure, VSEPR

n: principal quantum number: 1,2,3,4

l: 0s, 1p, 2d, 3f orbital. S: 0, P: -1,0,+1

m: for p subshell (-1, 0, 1)...

s: spin: angular momentum

s p d f


2 2

3 3 3

4 4 4 4

5 5 5 5

6 6 6

7 7

Effective nuclear charge

#protons - nonvalence electrons.

Higher nuclear charge = smaller atomic radius.


Periodic Trends

The Periodicity of Elemental Structure:

Electron Affinity vs Electronegativity vs Ionization Energy

The Periodic table is not a square table ;

Atomic Radius increases down a column and to the left in a period.

Ionization Energy increases to the right in a period and up in a column. Helium has highest ionization energy.

Electron Affinity: Increases to the right in a period and up in a column. Generally it increases up in a column, ex Cl vs F

Electronegativity: Increases up a column and to the right. FOClNlBrISCH:decreasing order of electronegativity

Electron Affinity follows trend of Electronegativity, generally increasing as a more stable structure is formed when an electron is gained. Ionization energy is the energy required to remove an electron from an atom. Electronegativity with respect to an atom in a molecule.

Lattice energy is the energy released when a crystal is formed from its constituting ions. e.g. Na+ Cl- -> NaCl(s). The ionic bond is stronger as the charges between atoms is larger. Al(OH)3 is insoluble in water because of large lattice energy

Acidity increases to the right in a period and down a column. Is related to the stability of the anion. As the size of the anion is increased charge can become delocalized easier.

Periodic Exceptions

Cl has higher electron affinity but lower Electronegativity than F because of electron pair repulsion in the valence shell.

Transition metal: When d-block elements form ions, the 4s electrons are lost first.

Vanadium has a higher melting point than Cr. Generally melting point is increased to the right within a period because of london/induced dipole forces.

V:[Ar] 4s2 3d3; V3+[Ar] 3d2

Cr has a half filled d level [Ar] 4s1 3d5

Cu: [Ar] 4s1 3d10

Au: has only one valence electron:

Ag: [Kr] 5s1 4d10


21Scandium and 22Titanium:

1s2 2s2 2p6 3s2 3p6 4s2 3d1 ,

1s2 2s2 2p6 3s2 3p6 4s2 3d2


Charge, Ionic and Polyatomic Ions, Ionic Strength; Hydrogen Bond, Electronegativity, NH4+, PO4-3, SO4-2, ate-ite

Covalent Bonding Hybridization, Geometries sp3, sp2, sp Carbocation has sp2, trigonal planar geometry
Hydrogen Bonding: Dipole Moments

FON: A hydrogen bonded to a electronegative halogen can Hydrogen bond with another electronegative halogen. This can occur intramolecularly within short distances, around 1 C-C length.


Acid and Bases: Reduction Oxidation Reactions:

Lewis Acid, Bronsted Acid, Lewis Base, Bronsted Base,

Buffer, K, pK, Strong vs Weak Acids, Titration, Hydrolysis,

Electrolytic Cell, Anode Cathode, Galvanic vs Electrolytic Cell, Reduction Potential.


Arrhenius Acids yield H+.

If a substance accepts a pair of electrons to form a covalent bond it is condsidered a Lewis Acid.

Reducing Agents: Reductor: Reducer: looses electrons: LiAlH4, H2.

Metals act as electron donors giving off ions in solution.Then it is said that the metal has been oxidized. Fe(s)-> Fe++ + 2e-. Substances that are oxidized act as REDUCING AGENTS.

Reducing Agents are oxidized. Oxidizing Agents are Reduced.

Oxidant = Oxidizing Agent = Oxidizer

Reductant = Reducing Agent = Reducer. Reducers gain Electrons given by the Reducing Agent that has been Oxidized (donating electrons).

LiAlH4 + 4 H2O → LiOH + Al(OH)3 + 4 H2

CARDIO Base: Charge-Atomis size-Resonance-Dipole Induction-Orbital: more negatively charged species are more basic, larger atoms with negative charges are more stable weaker bases, more resonance more stability, sp3 more basic than sp2...

NADP+ + 2H2O -> 2NADPH + 2H+ +CO2

NADP+ accepts electrons from water. This is a reduction. NADPH is the reducing agent.


Acidity and Melting Point are not related.

Larger atoms are more acid because can form more stable anions.



Oxidation: Gain of O, Loss of e-, Loss of H+



Arrhenius Definition


Arrenius Acids : Donate H+

Arrhenius Base: Accepts H+

Compounds ionize in solution (water only).


Lewis Definition


Lewis Acid accepts e- pair: Electrophile: Trigonal Planar BR3 with empty p orbital. H+ is a LA.

H+ + NH3 → NH4+ . Carbonium is electrophilic thereby a strong LA.

Strong Lewis acids are electron deficient. Strong Lewis Bases are electron rich.

Lewis Acid Base Pair

Lewis Base donates NONBONDING e- pair: H-, F-; are NUCLEOPHILES

Basic Amino Acids: Lys, Arg, His.

Conjugates of Strong Acid/Base have no effect on pH:


Bronsted Lowry Acids increase H3O+, Bases Increase -OH  
Conjugate Acid/Base Pairs

To find the conjugate base of an acid, take off a H+

HCl is a strong acid. Cl-, its conjugate base has no effect on pH. Acids dissociate completely. The more stable is the anion the more acid is the molecule.

NH4Cl: NH4+ is the conjugate acid of weak base NH3

Weak base NH3, conjugate acid NH4+ strong acid.

acid + base = conjugate acid + conjugate base

Strong Acids: HNO3, H2SO4, HCl, HClO4, HBr, HI

SuperStrongAcids: HFSO3-SbF5

other scales beside pH are used to measure SSA.

Corrosiveness NOT EQUAL to Strength = HF

Ka vs pKa

COOH has a pKa of 4 - 5

The lower the pKa the higher the Ka. Low pKa are acidic. High pKa are basic.

When pKa and Ka are equal the compound is in equilibrium and the slope of titration curve is linear.





From Nerst to Current Trends



Electrostatic Energy

Lattice Energy

kQq/r vs F =k(q1q2)/r^2

ΔU = ΔH - p ΔV

Gauss Law: I = EAcos(-)

F = qvB sin(-)

F = qE

Coulomb's law k = 9E9 Nm^2/C^2

Electric field lines move out of the positive charge and into negative charges.


A dipole aligns so that the positive lines are "into the negative and out of the positive". The positive end of the dipole will be aligned with the electric field lines.

Charge moving in a circle: F = qvB = mv^2/r ; if qvB> mv^2/r the charge is spiralling in. if qvB<mv^2/r the charge is curving.

Current Carrying wires:

F = qvB sinθ = (it)vB sinθ = (it)(L/t)B sinθ = iLB sinθ

A negative Force means that charges are attracting.


CURRENT TRENDS: Conventional Current Flow is Opposite to Electron Current Flow. Arbitrarily the current flows out of the short battery symbol into the circuit.

The Current in a Parallel Circuit is Split at Ramifications like water flow.

The current in a Series Circuit is Steady. What drops is the voltage (like water pressure), as a loss to Impedance.


Resistors in series have the SAME current.

Electrolytic Cell

E(cell) > 0, the reaction is spontaneous and happens in a galvanic cell.

Faraday's law

E(cell) = E(oxidation) + E(reduction)

Galvanic = Voltaic Cell

Two pure metals connected by a salt bridge.

Oxidized species + e- = Reduced Species

Metal cations induce reduction of metals in other cell. So the more positive Oxidation Potential Metal gives off electrons from the Anode to the other metal Cathode . Zn + Cu2+ → Zn2+ + Cu . In a galvanic cell of Zn and Cu electrodes. The Zinc electrodes looses mass as electrons go to Cu2+ and Zn++ goes into solution.

Ionization Energy increases to the left and down a column. +
Difference b/w Electrolytic and Galvanic Cell    
Capacitor U = (1/2)CV^2  
Laws Ideal Gas, Boyle, Charles, Avogadros: Henry, Raoult, Arrhenius, Hess, Zeroth, First Law, Second Law, Rate Law, Le Chatelier, Faraday, Newton's First, Newton's Second Law, Dalton's Law  

Kinetic Theory of Gases

k = R/Na

Partial Pressure, Mole Fraction

STP: 0C, 1atm

Boyles law: PV = k: inverse proportionality P1V1 = P2V2

Charles law: V/T = k: direct proportionality: V1/T1 = V2/T2

Avogradro's Law: V1/N1 = V2/N2

Dalton's Law: p = xP also vi = V * pi/P

Henry's law pi = k ci: pi is the partial pressure of the solute.

"At a constant temperature, the amount of a given gas that dissolves in a given type and volume of liquid is directly proportional to the partial pressure of that gas in equilibrium with that liquid."

Raoult's law: p = p* x; p* is the vapor pressure of pure component.

Raoult vs Henry: Henry is more related to solute, Raoult to solvent: When the solvent is in a great quantity the constant of proportionaliy is the partial pressure of the solvent.

Real Gas Law, Van der Waaaals \left(p + \frac{a'}{v^2}\right)\left(v-b'\right) = kT  

Molarity: kg / L

Molality: mol / L

Normality: meq / L

Molar Volume at 0C and 1atm = 22.4L/mol

f = Av


Mass Effects Return Home Surface Tension  

Colligative Equations


Solubility vs T, P.

Osmotic Pressure: Solvent moves across a semipermeable barrier from high concentration to low concentration. The pressure difference across the chambers is the osmotic pressure.

Chaotropic agents: increases solubility of non polar. (Alcohol, Urea, Lithium acetate). Denature proteins by increasing hydrophobic solubility.

Kosmotripic increase water-water interactions. Stabilizes intermolecular protein interactions thereby preventing aggregation. (Mg2+, Li+1, Zn2+), mostly small positive ions). Ammonium sulfate.


Surface Tension

Mechanical Properties of Liquids



All 1A metal salts are water soluble

All NH4+ salts are water soluble

All NO3--, ChH3O2-, ClO4- , are water soluble. KNO3

SO4 -2 sulfate

PO4 --- phophate

Complex Ion formation, solubility

Common Ion effect

Silver salts are insoluble in water with the exception of silver nitrate, silver acetate and silver sulfate.

Chlorides Bromides Iodides, are soluble with the exception of AgCl2, PBCl2, HgCl2

Base Solubility: Ca(OH)2 is soluble.

Group 1 and NH4+ salts are soluble

Group 2 MgO, metal oxides Insoluble.

Sparingly soluble salts derived from weak acids tend to be more soluble in an acidic solution.

Which of the following insoluble salts—AgCl, Ag2CO3, Ag3PO4, and/or AgBr—will be substantially more soluble in 1.0 M HNO3 than in pure water?

Answer: Ag2CO3 and Ag3PO4

Good Reference:

Buffers Tritration Curve effect  

Ksp describes saturated solutions.

BaC O 3(s) ---- Ba 2+(aq )+C O 2 3(aq )

Ksp= [Ba2+][CO32-] = 5.1 x 10-9


Heat Effects

Conduction, Convection Radiation, Work, Rankine Scale, Absolute Scale, Conservation, Decay, Half Life

Return Home



Bond Dissociation


Endo, Exo, Enthalpy, Heat Capacity, Specific Heat, Entropy, Gibbs Free Energy, Spontaneity, Heat of Fusion, Heat of Vaporization

Zeroth Law, First Law, Second Law.

Heat of Hydration

Thermodinamically favorable. Solvation releases heat.

First heat is required (ENDOTHERMIC) to break up an ionic crystal lattice. The hydration step is exothermic.

Think of Dissolving Salts, is it Exo/Endo Thermic?
Heat of Combustion

Energy released when a compound is completely combusted with O2 under 1atm, 298K.

Ring Strain and Transanular effects result in increasd Heat of Combustion.

Ciclohexane has lowest heat of Combustion per CH2 group. o

Heat of Formation

Standard States 1atm of gas, or elemental solid. at constant T 298K, P 1atm.

Sum of all the bonds broken and all bonds formed from elemental atoms or molecules in their std state.

Le Chatelier In an equilibrium reaction mass of a species, temperature, or pressure can shift the equilibrium concentrations to favor an increae of products or reactants. Reference:

ΔG is negative. Standard Reduction Potential is positive E0.

DeltaG = -RTln(K); DeltaG = -nFE

Kinetic Effects    
Catalysis, Enzymes,

Reaction Order,

Reaction Rate

Rate Determining Step



enzyme-catalysed reactions display saturation kinetics.

increasing substrate concentration means an increasing rate at which the enzyme and substrate molecules encounter one another.

Enzymes lower Activation Energy. Enzymes do not change the Thermodynamics of a Reaction.


Alpha particles: He nucleus: 2 protons, 2 neutrons

Beta particles: +/-

Beta Decay: neutron decomposes. Beta decay is usually B(-)

B(+): Nucleus converts a proton into a neutron and a positron.The positron is liberated. Atomic number decreases. Occurs when the isotope has too few neutrons.

B(-): electron is liberated. Atomic number is increased. Neutron is decomposed into electron and proton. Electron is referred to as B particle.

Electron Capture EC: electron meets proton and is converted into a neutron. Mass number stays the same but proton number is reduced. Element change.

Gamma Radiation: Eenergy emmitted as electromagnetic radiation.

Alpha particles are very destructive. 4/2. They are quickly absorbed by skin.

c = 3(10)^8 m/s


Wave Duality, Wave Properties, Amplitude, Intensity, Superposition, Resonance, Diffraction, Refraction, Harmonic Motion, Pendulum, Differential Movement

Materials Sciences

Solids, Density, Thermal Expansion, Viscosity, Magnetism, Force Direction, Coulomb, Ampere, Field Line, Charge Distribution, Insulation,



L= Iw moment of inertia times angular velocity around axis of rotation

tangential velocity = rl: product of radius and angular velocity


Centripetal force F = -mv^2/r

Momentum p = mv; m = Δ P / Δ t

Impulse I = Ft

Hook's law F = -kx

Momentum is always conserved: in elastic and inelastic reactions momentum is conserved.

In Inelastic collisions KE is NOT conserved. KE is lost.

Sound Waves

Transverse Wave: Displacement of medium is perpendicular to direction. A transverse wave can only occur in the surface of a liquid, not in its body. TW can occur in solids.

Longitudinal Wave: Displacement of medium is along direction of motion.

Sound can be represented as a Longitudinal wave.

Light can be represented as a Transverse Wave.

Spreading Equation Δθ = λ / d
Half Life N= No(1/2)^(t/t(1/2))  

Current, Voltage, Resistance, Ohms, Resistivity, Capacitance

Circuits, Capacitor, Dielectric, Power, Circuits in Series, Circuits in Parallel

V = IR

I = Δ Q / Δ t

P = VI = RI^2



B = [Ns/Cm] = Force/ ChargexVelocity

Ohms Law is used to calculate Voltage Drop across a resistor.
How do you know the Magnetic Field is Perpendicular to the Electric Field?    
Applied Effects —°µ    
Hydrostatic Pressure, Surface Tension, Bernoulli's Equation, Flow Profiles    
Normal Force, Vectors


Perfectly Inelastic p = (m1 + m2) v


Theta = arc length/ radius


2pi/360 =

Refer to spreading equation of light and sound. The spreading is proportional to the wavelength of the emitted wave over the distance of the orifice of emission.
Power Units: Watts: [W] P = VI = V^2 R  
Energy Work Units: Joules: [J]  
Potential Energy



PEg= -GmM/r

ΔPE=qDeltaPHI: electric lines point in the direction of the lower electric field..


Force Fspring = -kx  
Waves Light, Polatization, Refraction, Diffraction, Doppler Effect  

Interference, Young's double slit, laser, Color and Energy

Angle of Incidence = Angle of Reflectio n with respect to the NORMAL. The angle is often referred with respect to the surface. Index of Refraction n = c / v. n1 sin( 1) = n2 sin(2). Internal reflection occurs when light travels from a medium of lesser light speed to greater light speed (greater n to less n)

Because the index of refraction of red and blue light is different the eye cannot focus on red and blue light in the same place.


Visualize Water.
Magnetism Direction and force of charge in magnetic field.  
Resistance Resistance is added in series.  



Parallel Voltages are equal. Voltage is a Potential Difference

V = I R

Galvanic and Voltaic cells are the same.

Electrolytic cells drive nonspontaneous reactions.



Current, Voltage, Resistance, Resistivity p = RA/L, Capacitance

RMS Voltage, RMS current.




Capacitors in series are 'parallel added'



(1/f) = (1/i) + (1/o); Magnification: M= -i/o; Focal length (f) is 1/2 radius of curvature: f = r/2;

Lens Power: [Diopters] = 1/f

Snells law: n sin () = n sin ()

Concave Mirror: Real (always Inverted) image small, same, larger to underfined, Virtual larger image

Convex Mirror: Virtual Erect smaller image. The

Cocave Lenses are Diverging.focal length is (-) for a diverging lens. Diverging Lenses form only Virtual Images. Virtual Images are upright so their magnification value is (+)

Mirror 1) beyond C 2) at C 3) between C and f 4) at f 5) in front of f

Inverted, Reduced,

gradually increasing in size as you move farther

Inverted, Equal Inverted, Larger no image

Upright,Larger, gradually reducing size as you move closer




Gradually INCREASING in size as you move CLOSER

Diverging. Convex mirrors and Concave lenses NEVER form Real Images.

Real images can be cast on a Screen?

f is positive for a concave mirror and negative for a convex mirror.

All real images are inverted and all virtual images are upright.

How does the image of a Concave Mirror change as you move closer?

Optics: Eye Correction

Myope: Nearsighted: cannot see far away. Light focuses in front of retina. Divergent lenses are needed.

Hypermetropy: Farsighted: cannot see close. Light focuses behind retina. Convergent lens needed.

We loose Acccomodation as we age. Accomodation is the ability to

Converging Lens  
Nomenclature of Alkanes

1. Take longer chain

2. Number the carbons of the parent chain from the end that gives the substituents the lowest numbers. When compairing a series of numbers, the series that is the "lowest" is the one which contains the lowest number at the occasion of the first difference. If two or more side chains are in equivalent positions, assign the lowest number to the one which will come first in the name.

3. If chains of equal length are competing for selection as the parent chain, then the choice goes in series to:
a) the chain which has the greatest number of side chains.
b) the chain whose substituents have the lowest- numbers.
c) the chain having the greatest number of carbon atoms in the smaller side chain.
d)the chain having the least branched side chains.




sp is 50% s character which is less energetic than p. This results in increased acidity.

SP2 Hibridization: Trigonal planar geometry. Free p electron. Nitrogen in a cycle. Nitrogen in a cycle has the free pair projected outside the plane in trigonal planar geometry, sp2 hibridization.

SP Hibridization examples: triple bonds.

Exceptions: BH3 is sp2 hybridized.

CO2: sp with 180'

Formal Charge


FC = V- (N + B/2); e.g. NH4+:

Nitrogen has a +1 formal charge (5- (0 + 8/2) = +1)

Oxygen in NO2- : 6 - (4 + 4/2) = 0

Formal Charge of Phosphoric Acid.P=0, hibridized sp3

FC = Valence - (alone bond pairs - half of bonding electrons)

5-(0+10/2) = 0

Degrees of Saturation

(C2n+2 - H) / 2; example BuckyBall C60: (122 - 0) / 2 = 61

Nitrogens count as 0.5C

Oxygen does not count.

Halogens count as Hydrogens.


Additional Equations exist that give the same result for degrees of unsaturation.

Shortcut: Double bond = 1deg of unsat.

1 triple bond = 2 deg of unsat

1 cyclic molecule = 1 degre of unsat

Functional Groups

BP: Alkoxide>Carboxilic acid> Alcohol>Ether>Alkane

BP Amines: Amonium Salt>1ry>3ry

Amines basicity is increased with electron donating groups. Secondary amines are stronger bases than primary amines. Imine R=N-H

Chirality Geometric Isomers: cis-trans  
Stereoisomer: 2^n: same chemical formula. R, S  
Enantiomer R to S, RR to SS, SR to RS  
Diastereomer RS to SS, SR to RR  
Optical Activity: +/- indicate physical bend of light. R/S only indicate imaginary rotation. Diastereomers and Racemic Mixtures are NOT optically active.

Constitutional Isomers: Ortho ./ Para : same molecular formula with different connectivity.

Configurational (R), (S): differe in bond configuration.

Rotamers: Conformational Isomer.

Regioisomer: Different starting material configuration give different structuraly isomeric products.



Acidity S-S-C-P-A-alpha-SP-SP1-SP2-SP3: "Recall Misscissipah"

Contributing structures with delocalized electrons in free p orbitals.

The contributing stuctures are not equal. The structure that locates the charge in the more electronegative atom is more stable.

Resonance contributes to increasing acidity by stabilizing the negative charge of conjugate bases.
Hydrogen Hydrogen Proton H+, Hydride ion H: -1  
Heterolytic Hydrogen Cleavage The electron pair of the bond goes to same atom.  
Homolytic Hydrogen Cleavage each electron of the bond goes to a different atom. Radicals are stabilized by electron donating groups. Peroxides give antiMarkovnikov products with alkenes.  
Radical Reactions





Radical Stability: Alllylic and Benzyllic Radical are comparable. Vinyllic Radical has higher bond energy because the double bond in more electronegative.

Stereochemical Considerations

Br2 vs Cl2: Selectivity; ratio of products

Good Reference:


Increases going down the periodic table F- < Cl- < Br-< I-;

Increases to the left across a period CH3-> NH2- > OH-

Nu: are Lewis Bases. Donate protons.








Solvent: Polar Aprotic DMSO, DMF, MeCN, Dimethyl Ketone, Acetone: Polar Aprotic Solvents stabilize Carbocation. Polar Aprotic solvents cannot bond with Nu:

[Adjust], most stable carbocations. Racemization Likely so result is either a racemic mixture or diastereomer.

3ry>2ry: Carbocation is formed. Reaction Rate = k [electrophile]

Weak Nucleophiles Favor Sn1


Alcohols and Alkyl Halides undergo substitution reactions.

Solvent: Polar Aprotic DMSO,DMF, MeCN, Acetone,

Polar Protic Solvents favor E2 over SN2.

Polar APROTIC Solvents Favor SN2 over E2.

Sn2: Reaction is favored by 1 > 2 > 3 substitution because of crowding in the transition state. All other reactions are 3 > 2 > 1. Transition state is crowded so less substituted molecules undergo reaction faster. The reaction rate = k [nucleophile][electrophile]. Hydrogen bonding solvents prevent the nucleophile from initiating the reaction.


Pointer: Rule Out Possibilities: if you see a protic solvent rule out Sn2...



Solvent: Hydrogen Bonding Solvents

Reaction Rate = k [Haloalkane]



Polar Protic Solvents favor E2 over SN2.

STRONG Base Favors E2 because: base can deprotonate to free a pair of electrons.

Reaction Rate = k [Haloalkane] [Base]

Antiperiplanar proton


Reminder: "Protic = Pi = double bonds use a Pi bond"



Reaction Rate


Stability of Intermediate

Strength of Nucleophile



Markovnikov more stable carbocation is formed. H and CH3- migration  
antiMarkovnikov less substituted alkyl bromide bond is formed. HBr/hv with Peroxides
Hoffman Rule    
Zaitzeff Rule priority  
Molecular Geometry    
Trigonal Bipyramidal upon loosing a pair of electrons becomes a seesaw.  

Organic Acids


Henderson Hasselbach

pH = pKa + log [A-]/[HA]

low pKa = High Ka = Strong Acid. If pH < pKa: Protonated.

If pH > pKa: BASIC, Unprotonated

A proton becomes acid when the bond breaks heterolytically.

Homolytic Bond Breaking: Homolysis: the bond breaking kcal/mol is higher = requires more energy. Electron pairing in heterolysis stabilizes.

Alkene Reactions    
Alkene HaloAlkane Addition Markovnikov, Not Enantioselective.  
Alkene HaloAlkane Addition with Peroxide

Gives Halogenated less substituted haloalkane.


Alkene Hydration Acid Catalyzed

Gives Alcohol

Pi bond is protonated initially, forming a carbocation.

Alkene Oxymercuration/Demercuration

Gives Alcohol. Markovnikov.

Pi bond is protonated initially, forming a carbocation.

Alkene Hydroboration

Give Alcohol


Alkene DiHaloxen X-X Attack

Sn2: Trans Product

Reaction proceed by instant (-) polarization of pibond by X-X

Reaction can yield Halogenated and -OH groups. -OH is Markovnikov.

Alkene Epoxide Formation

Gives Epoxide and Carboxylic acid..

Followed by acid or base hydrolysis to give Diol.

Alkene Oxidation with KMnO4

Gives cis-Diol

trans diol with peroxy acid.

Alkene Hydration (Reduction) (cis or trans)

Gives Alkane.

H2 with Ni, Pd, Pt. cis addition. Lindlar Catalyst with dopant stops reaction at alkene.

trans addition is with Na, NH3

Recall Reduction.
Alkene Ozonolysis

Gives Ketones.

Reactant O3 + Zn in H20

Aromatic Compounds

Aromaticity: Huckel Number: 4n + 2; Cyclic, free p orbital with a Huckel number, flat and planar.

Can be accomplished via Cyclic Delocalization , Resonance, Conjugation

If an electron like Oxygen is in the bond we only use one pair of electrons for aromaticity

Examples: Purine, Pyridiine, Thymine

Good Reference:
Aromatic Electrophilic Substitution

The Benzene ring is succeptible to electrophilic attack. Heat is required because the ring is pi stabilized.

Ortho/Para: have lone pair of electrons on the atom bonding the ring. with the exception of alkyl R.

-NO2 is a META deactivator


Activators have free electrons in the atom bonded to the benzene ring: -NH2, -OC6H5, -OR, -O(-)

OrthoPara Deactivators: Cl, Br, I are deactivators

Deactivators increase anion stability upon protonation: acidity is increased.
Aromatic Diels Alder

Concerted Formation of Ciclic Compounds from conjugated diene.

Dienophyle = alkene or alkyne



Ketone Reactions

Keto/Enol Tautomerism

Acid Alpha proton

Ketones do not undergo substitution reactions.

Beta keto Acid. Beta keto ester.

Ketone Formation from 2ry Alcohols with Chromate Oxidation.
Ketones: Acetal

Cyclic Contains 2 'ketones'

Biologicaly Important.

Ketones: Hemiacetal

Cyclic Contains 1 ketone

Biologicaly Important

Ketones: Imines   Convert the Carbonyl to an Imine
Ketones: Aldol Condensation

"one ketone stays the same and bonds with a double bond through the alpha carbon, after dehydration, so the carbonyl oxygen of the ketone that does not have alpha hydrogen is lost.

study mechanism


Acyl Group Carboxylic Acids> Acyl Halide, Acid Anhydride, Ester, Amide

Acyl derivatives interconvert to lower reactivity.

Acid Halide > Acid Anhydride > Ester > Amide

less hindered carbonyl is more reactive.

Carboxylic Acids

Acetate CH3 COOR

Acidity Order: HC l> Carboxylic Acid > Substituted Phenol > diketone > ketone

Bases Deprotonate to give COO- Salts

Carboxylic Acids:

Nucleophilic Addition Elimination

electronegative groups allow attack at the Carbonyl and serve as good leaving groups.  
Carboxylic Acids Transesterification: Alcohol + Carboxylic Acid gives Ester.  
Ester are neutral in solution.  
Ester Hydrolysis

Nucleophilic Acyl substitution : Addition Elimination : Saponification

Acid and Basis Catalyzed

Inorganic Esters Central Carbon P, S. Contain more than one double bond. See reaction of PBr3 with 3ROH -> H3PO3 + 3RBr

Reductive Amination: Amines Attack of Ketones to yield 1,2,3ry substituted Imines that are Reduced with H2/Pd to Amines.

Amines to Alkenes via HoffMann Elimination: Less substituted alkenes.


Acid Base Reactions with Carboxylic Acids

Basic Leaving groups decrease reactitvity of Acid Chlorides with respect to Anhydrides> Esters>Amides

Hoffman Rearrangement: Amides are converted to Amines

Imines   Schiff Base R1R2C=NR3

Sugars, Proteins, Fats, Metabolism, pKa, Anomeric Carbon

See SSSFFF Biology

Good References:


Fructose, Glucose, Ribose

LOOK at chirality FARTHEST from C1 to determine L/R.

Sucrose: Glc + Fru: Alpha-1,2

Lactose: Gal + Glc: Beta-1,4

Maltose: Glc + Glc: Alpha-1,4

Cellobiose: Glc + Glc: Beta-1,4

Glycogen: α 1-4

EPIMERS are NEVER Enantiomers. Epimers differ only in one stereogenic center that IS NOT the last chiral carbon. Alpha/Beta epimers: Alpha = Axial, Beta = Equatorial

HAWORTH Projection: Beta is UP!!!



D, L

Aldohexose vs ketopentose, vs aldotriose (threeOHgroups)

ketohexoses (6OH and 1 C=O)

Anomeric Carbon: cyclic: opposite the CH2OH outside the rinh

C1 orientation

Hexoses Glucose  



Sulfur Containing Molecules Mesylate, Triflate, Tosylante  

All natural AA are L, amphoteric

Carboxylic pKa aprox 2. Amino Group pKa aprox 10


Form salt to become water soluble: Carboxilic acids are extracted with weak bases.

NaHCO3 is better than NaOH because it destabilized aromatic structures.


10 Enzymes Everyone should know

Glycogen Phosphorylase


Glucose 6-Phosphatase


Hexokinase/ Hexose / Dehydrogenase / Oxidase




Cytochrome Oxidase


Reactant List HNO3 EAS Activator of
Br2 + FeBr3 (heat) EAS Bromination
H2SO4 (heat) EAS Sulfonation
Friedel-Craft RCOCl + AlCl3 (heat) EAS Aryl Ketone
Friedel-Craft RCl + AlCl3 (heat) EAS Alkylation
Hg(OAc) in Water then NaBH4 Alkene Oxidation to Markovnikov Alcohol
BH3 in THF then H2O2 Alkene Anti Markovnikov Alcohol
KMnO4 cis Diol
OsO4 cis Diol
PCC Anhydrous Oxidant: 1ry Alcohol to Aldehydes
CrO3/ H2CrO4/Cr2O7-2/CrO3 Aqueous Oxidants: 2ry Alcohol to Ketones

NaBH4 in EtOH

Reductor of Carbonyl
LiAlH4 in Ether (aprotic) Reductor of Carbonyl
NaH, KH Hydride bases
Grignard RMgBr in Acid Reductor of Carbonyl + R
RLi Reductor of Carbonyl + R
Wittig Phosphonium Ylide Reductor of Carbonyl to Alkene
  NaOH/H2O Acid

Aldol Condensation. Base attacks Alpha proton.

Beta Hydroxyl Carbonyl or Alpha/Beta unsaturated Carbonyl

  NaOH / KOH Saponification
  SOCl2 Inorganic Ester reactions.
  NaHCO3 Extraction of Carboxilic Acids
  10% HCl Extraction of Amines
  Tosyl Chloride Stabilizez anion charge in COO-, H leaves
  Wolf-Kishner Reduction  
Molecules to know Furan, Pyran, Toluene, Naphtalene, Phenanthrene  
Polymer Chemistry    
Elastic Properties Elastic Limit  
Thermal Expansion Coefficient    
Short Path Distillation    
Detection Techniques Detection IR  



3600-3200 -OH

3300 Amines (OH broadest, NH sharper)

3000 C-H

2300 - 2100 C---C or C---N

1700 C=0 (Carbonyl, Carboxylic Acids)

1650 C=C

Chromatography Separation of derivatized diastereomers. Enantiomers can be reacted with a known stereochemistry comp.  








Wet Column


Also referred to as Gravity Column Chromatography




TLC R factor: Polar molecules are retained by Silica, so have smaller R f.  
Size Exclusion Chromatography SEC Large Elute First.

Size Exclusion, gel permeation chromatography or gel filtration chromatography. separates particles on the basis of molecular size (actually by a particle's Stokes radius). It is generally a low resolution chromatography and thus it is often reserved for the final, "polishing" step of the purification. It is also useful for determining the tertiary structure and quaternary structure of purified proteins. SEC is used primarily for the analysis of large molecules such as proteins or polymers. SEC works by trapping these smaller molecules in the pores of a particle. The larger molecules simply pass by the pores as they are too large to enter the pores.



Electrophoretic mobility. Native proteins, or denatured. Structured or unstructured, .

SDS is anionic detergent to linearize proteins and give negatice charge. Even proportionation of charge to mass, so particles are sorted by size. Membrane hydrophobic proteins are difficult to treat with sds. Silver Staining.

Scintillation counting

Iodomelatonin in the presence of selective antagonist for the receptor

We have pharmacologically characterized recombinant human mt1 and MT2 receptors, stably expressed in Chinese hamster ovary cells (CHO-mt1 and CHO-MT2), by measurement of [3H]-melatonin binding and forskolin-stimulated cyclic AMP (cAMP) production.

[3H]-melatonin bound to mt1 and MT2 receptors with pKD values of 9.89 and 9.56 and Bmax values of 1.20 and 0.82pmolmg−1 protein, respectively. Whilst most

Whilst most melatonin receptor agonists had similar affinities for mt1 and MT2 receptors, a number of putative antagonists had substantially higher affinities for MT2 receptors, inclu ding luzindole (11 fold), GR128107 (23 fold) and 4-P-PDOT (61 fold).

In both CHO-mt1 and CHO-MT2 cells, melatonin inhibited forskolin-stimulated accumulation of cyclic AMP in a concentration-dependent manner (pIC50 9.53 and 9.74, respectively) causing 83 and 64% inhibition of cyclic AMP production at 100nM, respectively. The potencies of a range of melatonin receptor agonists were determined. At MT2 receptors, melatonin, 2-iodomelatonin and 6-chloromelatonin were essentially equipotent, whilst at the mt1 receptor these agonists gave the rank order of potency of 2-iodomelatonin>melatonin>6-chloromelatonin.

In both CHO-mt1 and CHO-MT2 cells, melatonin-induced inhibition of forskolin-stimulated cyclic AMP production was antagonized in a concentration-dependent manner by the melatonin receptor antagonist luzindole, with pA2 values of 5.75 and 7.64, respectively. Melatonin-mediated responses were abolished by pre-treatment of cells with pertussis toxin, consistent with activation of Gi/Go G-proteins.

Mass Spectroscopy

Base Peak is the largest peak. It is fragmented.

Parent peak is the ion of the molecule without fragmentation.

Uncharged molecules are not detected.

More fragmentation produces smaller peaks.

Quantitative and Qualitative: The m/z ratio

Nuclear Magnetic Resonance


Electron donating are shielding, Electron Withdrawing are deshielding.

Left axis has larger number. So deshielded protons appear to the left=downfield (-RCOOH). Shielded protons appear to the right (H-C-CH3x3)

1-propyne vs 1 propene: s haracter is less shielding.

ORDER: Aldehyde and Carboxylic- Aromatic- Vinillyc--- Halogen, ether, allyl, alkyne, benzyllic .


Allylic proton is very deshielded.

Memorize the 6-8ppm region is Aromatic.

Geminal Methyl Groups are identical.

Good Reference:

C NMR Height of Peak proportional to number of H attached to C.  

Enzyme Linked Immuno Sorbent Assay

Antibody binds antigen-Wash-Enzume Linked antibody-Wash-Color Change


Vulcanic Chemistry


Tectonic Plates

Nazca Plates


Hotspots, Magma, 700C to 1600C, SiO2, Fe, Mg, 2200-2800kg/m3, IDDP magma geothermal energy generator

Phreatic vs Phreatomagmatic vs Magmatic Eruption

Magmatic Eruption: Decompression of Gas

Phreatic Eruption: Superheated Water Expansion

Phreatomagmatic Eruption: Compression of Gas within Magma


Mount Pele in St Pierre, Martinique exploded in 1903 killing 30k.

Tools for Earthquake Prediction:

Thermal tools: Heat

Chemical: Vulcanic Chemistry, Water Quality and Gas Composition

Nuclear: Particle Counters through volcanic Mass

Mechanical: Earthquakes and Sound waves.

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H                             He
Li Be                 B C N O F Ne
Na Mg                 Al Si P S Cl Ar
K Ca                 Ga Ge As Se Br Kr
Rb Sr                 In Sn Sb Te I Ke
Cs Ba                 Tl Pb Bi Po At Rn
Fr Ra                            

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  One Arcminute is equal to 1/60 of one degree. One Arcsecond is equal to 1/60 Arcminute. So One Arcsecond is equal to 1/3600 of a degree.  
  One degree is 1/360 of a circle. One Arcminute is (1/60)(1/360)=(1/21600) of a Circle. 1deg=3600arcseconds;  
  To complete a circle of 360deg, with a frequency of 500arcsec/century will take (360)(3600)/500 centuries.  

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