Chem Quickies

1. bimolecular
2. 2nd order
3. backside attack
4. concerted one step process, substitution and expulsion is simultaneous
5. Creates inversion of configuration at center of attack
6. Stereospecific: “inversion of configuration” from backside attack.
7. Steric Hinderance has a great effect on SN2 reactions
8. Fastest with halomethanes and is successively slower with 1º, 2º. 
9. Almost never takes place with 3º if it does it’s hella slow. 
10. Homolytic cleavage during transition state. Dipoles but no ions.

Good Leaving groups. 

http://www.organic-chemistry.org/namedreactions/nucleophilic-substitution-sn1-sn2.shtm

Within a molecule you have intramolecular and intermolecular interactions.

• Intra: Responsible for bonding between atoms. 
• Inter:  Responsible for forces between molecules. 

Right now I’m going to delve into what are know as Van Der Waals forces. All of these forces are intermolecular forces (between molecules).Here they are: dipole-dipole, dipole induced -dipole, and induced dipole-induced dipole

1. Dipole- Dipole

Essentially, a polar molecule which is bonded covalently (Ex: HCl). It has a dipole moment. The negative chlorine end aligns itself and is attracted to the positive hydrogen end of another HCl molecule. These forces in comparison to intramolecular interactions are incredibly weak, but they are the strongest type of intermolecular forces. Hydrogen bonding is a form of dipole-dipole intermolecular forces (and can have an effect on physical properties such as expected boiling points).

2. Dipole induced -Dipole:

In this scenario, we have one polarity covalent molecule and one very neutral molecule. An Example would be say, HCl and CH4 or Ar or any other molecule which does not have a dipole moment. Essentially what happens is the polar end (doesn’t matter which end) of the polar molecule exhibiting a dipole moment (in our example HCl) induces or causes the neutral molecule or atom to experience a temporary dipole moment.

3. Induced dipole- induced dipole

These are also known as London Dispersion forces. All systems of molecules contain them even if that system contains dipole-dipole forces (no one talks about them then because they are so weak in comparison!). I’m sure you can deduce what this type of interaction entails. Yes, two neutral molecules which temporarily induce a dipole moment between each other. To understand this you need to picture the system as dynamic. Electrons are always moving and even in “happy” neutral, stable molecules electrons sometimes find themselves lumped together for a small fraction of time before equalizing again. This can occur from interaction with light, changes in the thermodynamic properties of a system, intermolecular forces, electron movement, etc.When this happens a small negative charge will be at one end of the molecule and it will induce a neutral molecule next to it.

Most information from:

http://chemed.chem.purdue.edu/genchem/topicreview/bp/intermol/intermol.html

Lennard Jones Potential:

This is basically some math behind the qualitative explanation of attraction.

The below link is fairly concise. And here’s the equation in case seeing it rings any bells.

U(r) = 4 ε [(σ/r)¹² - (σ/r)⁶]

http://www2.physics.umd.edu/~alaporta/Lennard-Jones.html

In the early 1900s, a Canadian woman named Maud Leonora Menten went to Germany to work with Leonor Michaelis at the University of Berlin. By this time in scientific history, Michaelis and Menten knew that enzymes could perform chemical reactions. From the work of Victor Henri, they hypothesized that there would be a quantitative relationship between the amount of enzyme around compared to the concentration—but nobody had ever analyzed this properly before. Henri had the basic idea right, but had forgotten to take some key factors into account. In just that one year, Menten worked with Michaelis to set up experiments to test this and to properly control those other aspects that Henri didn’t, and collected the data to write the paper describing analyses and equations that transformed the way scientists thought about enzyme function and provided the foundation on which modern biochemistry is built.

All of this was done without even knowing how much enzyme they were working with, just diluting some kind of preparation of it in different proportions to substrate (which was sucrose) and without having modern molecular analysis tools available.

Source: http://scientopia.org/blogs/chemicalbilology

(#women in science: Maud Menten!)

So we left off with d[ES]/dt = 0 = k₁[E][S]-k_-1[ES]-k₂[ES]

But we want for the goal is to express the overall rate. The enzyme-substrate complex is an intermediate, and not in the overall rate formula, so [ES] needs to be expressed in terms of [E]. These two are connected by:

[ET] = [E] + [ES], where ET is the total concentration of enzyme in the system and it is equal to the amount of free enzyme plus the amount of the complexed enzyme. By solving for [E], we obtain the relation [E] = [ET] -[ES].

Now we substitute the [E] value in the equation for d[ES]/dt with the one just derived.

d[ES]/dt = 0 = k₁([ET]-[ES])[S]-k_-1[ES]-k₂[ES]

Distribute:

d[ES]/dt = 0 = k₁[ET][S]-k₁[ES][S]-k_-1[ES]-k₂[ES]

Solve for [ES]:

[ES] = (k₁[ET][S]/k₁[S]+ k_-1+ k₂)

The term (k_-1+ k₂/ k₁) is defined as the Michaelis constant, k_M. To get this constant in our equation, divide the numerator and the denominator by k₁ (essentially multiplying by one (k₁/ k₁)):

[ES] = ((k₁/k₁)[ET][S]/((k₁[S]+ k_-1+ k₂)/k₁))
which reduces to:

[ES] = ([ET][S])/ ([S]+ k_M)

The rate which the product is consumed is:

d[P]/dt = k₂[ES] which= (k₂[ET][S])/ ([S]+ k_M)

And this is how you derive the Michaelis-Menten equation.

My professor is doing biochemical research which means he’s going to be fond of putting some this stuff on the final. So this is a deeper look at catalysts, enzymatic catalysts in particular.  

Enzymes are proteins which selectively bind to small active sites on substrates. Enzymes are specific substrates and reactions which they catalyze. Most common way of naming enzymes is just to add the suffix -ase to the name of the substrate it binds to. 

Ex: Telomeres are the noncoding sequences at the end of DNA strands which protect genetic material from damage during DNA replication. Telomerase is the enzyme which allows for the production of telomeres. Active telomerase is present is early cells such as stem cells and cancer cells giving them a sort of “immortal” quality as they can indefinitely replicate. (Example: HeLa cells! We’re still using replications of her cells!)

Classes of Enzymes:

1. oxidoreductase- redox reactions (reaction is abbr. RXN)
2. transferase- functional group transfer RXNs
3. hydrolase- hydrolysis RXNs
4. lyase- addition to C=C double bonds
5. isomerase - isomerization RXNs
6. ligase - bond forming RXNs

Many enzymes require metal ions or small organic molecules, such as vitamins, which catalyze electron transfer RXNs. Enzymes find alternative pathways with lower activation energy and the kinetics of enzymes are calculated and studied by the steady-state approximation known as Michaelis-Menten kinetics.

Michealis-Menten Kinetics:

• E-Enzyme
• S-Substrate
• ES- Enzyme-Substrate intermediate
• P- Product
• K ₁ - forward rate constant 
• K _-1  - reverse rate constant 
• K 2 - rate constant for second reaction

Rate constant comes from rate law formula: Rate = k[A]ⁿ[B]^m

Two or more stable compounds which come together to form another stable compound are called coordination compounds. 

This is explained by Alfred Werner’s theory (1893): certain metals, especially transition metals, have two types of valence or bonding capacity. The primary valance is based on the number of electrons he atom loses in forming the metal ion. The secondary valence is what caused the bonding of other groups to the central atom. These groups are called ligands. 

A complex is any species involving coordination of ligands to a metal center, which can be an atom or an ion. The complex itself can be positive, negative or a neutral molecule. 

The coordination number is the number of points around the metal center where bonds to ligands can form (ranging typically from 2-12, with 6 as the most common). 

When two atoms become sufficiently close, getting trapped in potential energy well, their electron densities start to overlap and interact. It is established that electrons move both as a particle and as a wave (quantum theory!!), and when two or more electron densities overlap, they form new wave functions as their waves become superimposed. 

Shapes of atomic orbitals (AO’s) and molecular orbits (MO) are predictions based off Schrödinger’s equation for the hydrogen gas molecule ion, H₂⁺, which has an exact solution: the one electron wave function solution. 

Approximations for more complex molecular orbitals care calculated through the LCAO and VB method, the linear combination of atomic orbitals and valance bond method respectively. The difference is LCAO gives MO’s which are delocalized over the entire molecule and VB creates models where electrons are localized between a pair of atoms giving a quantum mechanical support of the VSPER and Lewis structures.


The Potential Energy diagram:

Photo: http://web.njit.edu/all_topics/Prog_Lang_Docs/html/autodock/AD3-12.gif

The formulas on the graph:

Ae^(-aR)* is the repulsion forces between the atoms. The smaller the distance between them becomes, the repulsion exponentially increases. A is simply a constant. 

*This is the form of my textbook, on this graph there are some constants (looks like epsilon…) which serve the same purpose. The distance term is also inside the exponential in my textbook version. 

(-C/r^6), is the called the Coulomb force or interaction. It’s basically a measurement of the potential energy between two atoms, charge over distance. C stands for one Coulomb which can be converted to any other charge unit you like, and r is the distance, SI unit is meters, but it’s usually more practical to use angstroms. The greater r gets, the more the potential energy decreases (dividing by a larger number!) and you end up with weaker and weaker attractive forces. 

In the well, or lowest point of the curve on the graph is the equilibrium between attractive and repulsive forces. The is described as the potential energy well. The energy required to destroy a bond is the distance from the bottom of the well to the x-axis. Usually any type of equilibrium or stability will be shown as the lowest point of a well. 

Halogens include group 17. They form diatomic molecules, (two of the same atoms bonded together.)

They have large electron affinities. Reactivity decreases down the column. Fluorine differs from other halogens in that it cannot expand its valence shell, and almost always forms one bond. It also has a tendency to form ionic bonds with metals. Fluorine stabilizes other elements in higher oxidation states.

Physical form at room temp:

1. F:pale yellow gas
2. Cl: yellow-green gas
3. Br: dark red liquid
4. I: violet black solid

Electronegativity:(you may find other values depending on the method used to derive the EN values and whether the standard is set at 4).

1. F: 4.0
2. Cl:3.0
3. Br: 2.8
4. I: 2.5

Hydrogenation: (ACIDS!)

When the halogens are hydrated they for hydrohalic acids which, with an exception of HF, form the strong acids. To prepare HF and HCl, a halide salt heated in the presence of a nonvolatile acid such as sulfuric acid will produce the HF or HCl acid in the gas phase.

Ex:

CaF₂ (s) + H₂SO₄ (con. aq) → 2 HF (g)  + CaSO_{4 (aq)}

Because sulfuric acid is an oxidizing agent, HBr and HI cannot be produced this way. In the presence of sulfuric acid they are reduced to Br2 gas and I2 gas. Instead, H3PO4 acid must be used which is nonvolatile and nonoxidizing.

All of these acids can be produced by directly mixing the elements needed together such as H and F, but this usually is very violently explosive.

Noble gases those elements in group 18 and are said to be inert because of their extremely high ionization energies they don’t react with other elements or compounds. The high ionization energy comes from the complete octet of elections in the outer valence shell of the noble gases giving them stable electronic configurations (for more insight refer to Coulomb energy potential in bonding) . However to say that the noble gases are completely inert is false.

Many of the noble gases can and do form compounds. The most prevalent of these are xenon, Xe, compounds. Radon, Rn, also forms compounds but due to its radioactivity, its chemistry is more complicated than xenon.

Xenon has four possible oxidation states:

+2, +4, +6, and +8.

Xenon compound are good oxidizing agents meaning that due to their instability they easily dissociate and xenon collects the electrons to return to neutral charge.

Because noble gases form compounds, it does not mean that it is especially easy by any means. Those which do most likely have higher atomic numbers (outer shells are farther from the nucleus and experience more electron shielding making it easier to remove them)and highly electronegative atoms, O^2- and F^-, must bond with them (actually noble gases pretty much exclusively bond with them).

Miscellaneous Info (wikipedia.org)
At 169 m/s, the speed of sound in xenon gas is slower than that in air due to the slower average speed of the heavy xenon atoms compared to nitrogen and oxygen molecules. Hence, xenon lowers the resonant frequencies of the vocal tract when inhaled. This produces a characteristic lowered voice timbre, an effect opposite to the high-timbred voice caused by inhalation of helium. Like helium, xenon does not satisfy the body’s need for oxygen. Xenon is both a simple asphyxiant and an anesthetic more powerful than nitrous oxide.

Royal water is 1 part nitric acid and 3 parts hydrochloric acid. Alone neither reagent dissolves gold, but together they can. Nitric acid is a strong oxidizing agent and dissolves trace amounts of gold which in the presence of the chlorine atoms from the HCl, complexes to form the complex ion: AuCl4 with a negative 1 charge.

When royal water is initially prepared the reaction which occurs is:

HNO₃(aq) + 3 HCl (aq) → NOCl (g) + Cl₂(g) + 2 H₂O (l)

This give the solution a deep yellow color and causes it to fume. The volatile gases produced during this reaction are important for the potency of royal water. 

History (wikipedia.org)

When Germany invaded Denmark in World War II, Hungarian chemist George de Hevesy dissolved the gold Nobel Prizes of German physicists Max von Laue (1914) and James Franck (1925) in aqua regia to prevent the Nazis from confiscating them. The German government had prohibited Germans from accepting or keeping any Nobel Prize after jailed peace activist Carl von Ossietzky had received the Nobel Peace Prize in 1935. De Hevesy placed the resulting solution on a shelf in his laboratory at the Niels Bohr Institute. It was subsequently ignored by the Nazis who thought the jar—one of perhaps hundreds on the shelving—contained common chemicals. After the war, de Hevesy returned to find the solution undisturbed and precipitated the gold out of the acid. The gold was returned to the Royal Swedish Academy of Sciences and the Nobel Foundation. They re-cast the medals and again presented them to Laue and Franck.

Transition Metals referred to elements which have an incomplete d-shell.
General Characteristics:

• High Melting Points
• Good Electrical Conductivity
• Usually hard solids
• Are Metals

Atomic Radii:

• Little variation except for Sc and Ti over 1st transition row
• Lanthanide Contraction: elements where the 4 f shell is filled to any degree and decrease in atomic radius is minimal. This happens from poor shielding of the f shell to other electrons from the nucleus.

Electronic Configuration and Oxidation:

• All have inner core e- w/ configuration of [Ar]
• 2 e- in 4s for 8 elements and 1 e- in the 4s for the remaining 2
• 3d e- ranging from 1-10

Ti: e- configuration: [Ar]3d2 4s2. Usually looses 4 e- for noble configuration. But sometimes looses 2 e-. Oxidation states  are +2 and +4.

This trend applies for V, Cr, and Mn. The max oxidation states being equal to the group number.