Organic Chemistry 1

Heat of Combustion

When molecules are combusted, all of the bonds are broken and then reformed via a radical reaction. The less stable bond, the greater the heat of combustion. The more stable the bond, the lower the heat of combustion.

What is the percent "s" character of the hybrid oxygen orbital in water?

When orbital hybridize they do so in a weighted manner such that the character of the hybrid orbital is an average of its contributors. Therefore, an sp hybrid orbital has 50% s character and 50% p character. By this same logic, the oxygen in water—which is sp3 hybridized, exhibits 25% s character and 75% p character. Mathematically, 1s orbital and 3p orbital's equal 4 orbitals (1s + 3p = 4 orbitals). 1 out of 4, 1⁄4 , or 25% is from the s orbital.

Rank the bonds listed above according to increasing stability.

When you see the term "stability" on the MCAT they mean "thermodynamic stability"—which in essentially every case will be reflected by the strength of the bond. Remember that strong bonds are a "lower-energy" state and weaker bonds represent a "higher-energy" state. Therefore, TRIPLE BONDS are the MOST thermodynamically STABLE, meaning it will require the most energy to break them apart. In increasing order of stability they would be ranked: single < double < triple. (Be careful not to confuse stability with reactivity.)

The second bond or third bond to be formed between two elements...

are ALWAYS pi bonds and involves side to side overlap of two p-orbitals. Because pi bonds require side-to-side overlap, the atoms must be fairly close to one another.

Which is the weaker bond c=o or c=n?

c=n, because the radii are further apart. As the radius of either atom increases, the p orbitals are spread apart, resulting in less overlap and a weaker pi bond. Remember that atoms with smaller radius ( like Fluorine) will be able to hug other things more easily because of its small radius.

The first bond to form between two elements...

is ALWAYS a sigma bond (ex. a single bond, or the first bond or a double or triple bond) and involves head to head overlap of two atomic orbitals.

Aliphatic

non-aromatic compounds

Hybridization

sp= linear (180) sp2 = Trigonal planar or bent (120) sp3 = Tetrahedral, trigonal pyramidal, or bent (109.5) sp3d= Trigonal bipyramidal, seesaw, T-shaped, or linear (90, 120, or 180) sp3d2= Octahedral, square pyramidal, or square planar (90)

Rank the following according to decreasing bond length: a) triple bonds b)double bonds c)single bonds

Single > Double > Triple [bond length]

If a compound rotates light clockwise it is called ?

(+) or d (dextrorotary)

Rules when drawing resonance structures

1) Atoms can NEVER be moved 2) Single bonds can NEVER be moved 3) All structures must obey the octet rule 4) All structures must have the same number of valence e's (ex. the number of electrons in bonds plus the number of electrons in lone pairs). This is NOT to say that individual atoms will not change their valence. In one structure they may have a formal charge and in another they may not, but in all structures the total number of valence electrons for the structure as a whole must be constant. 5) Tail of an arrow showing electron flow during resonance can only start from a lone pair, a double, or a triple bond.

What are exceptions to the octet rule?

1) Hydrogen and Helium: stable with two electrons in their valence shells (ex. H2) 2) Boron and Be: stable with only six electrons in their valence shells (ex. BF3) 3) Atoms from the 3rd, 4th, 5th or higher periods can accept more than eight electrons (PCl5, SF6, PO4 3- and SO2 2-)

Enantiomers

Two molecules with the same formula and the same bond-to-bond connectivity that are non-identical, non-superimposable mirror images. They contain at least one chiral center.

Important Classifications of Resonance

1) Resonance is a "snapshot" of differing electron arrangements of electrons that contribute to the "actual structure". 2) The actual structure is a weighted average (ex. hybrid) of all the contributors and does NOT look exactly like any of the individual resonance structures. 3) Individual resonance structures contribute differently; The most stable structures contribute the most to the actual structure and the least stable structures contribute the least. 4) The actual structure DOES NOT resonate back and forth between forms, it is a PERMANENT weighted hybrid of the contributing structures.

Shape and bond angle are determined by?

1). Hybridization 2). Lone pairs of electrons

How do you find the maximum number of optically active sterioisomers?

2^n n= the number of chiral centers

Describe the forces responsible for the strength of a bond. What is the relationship between potential energy and bond length?

A chemical bond is a balance of electrostatic forces. We know that species with opposite charges (i.e., nuclei and electrons) will be attracted to each other with a force given by Coulomb's Law: F = Kqq/r2. However, remember that there are also repulsive forces between the two nuclei and between electrons. The bond is formed at a sort of "sweet spot" where potential energy is lowest. Increasing bond length or decreasing it would raise the energy of the bond and therefore weaken it.

Coordinate covalent bonds

A covalent bond in which both electrons shared in the bond are donated by one atom. Usually more than one of these "donor" molecules (ex. Lewis bases) surround and bind a single "recipient" molecule (ex. Lewis acid; usually a metal). For the MCAT, if a molecule does not have a lone pair of electrons it will NOT participate in a coordinate covalent bond. The complex formed by the metal and the molecules forming coordinate covalent bonds with that metals, is called a "coordination complex".

Mesyl/ Tosyl

Alcohols: there are times you need to get rid of them. Except there's one problem. They're terrible leaving groups. Remember that good leaving groups are weak bases? Hydroxide ions are strong bases, and therefore very poor leaving groups. However there's a way to turn the OH group into a good leaving group - if you can convert it into a weaker base. One practical way this is done is with the sulfonates p-toluenesulfonylchloride (TsCl) and methanesulfonylchloride (MsCl). Treatment of an alcohol with TsCl or MsCl, usually in the presence of a weak base such as pyridine, results in the sulfonate esters. Conversion to the sulfonate esters does one thing: the conjugate bases - toluenesulfonate and methanesulfonate are now extremely weak bases, since they're heavily stabilized by resonance. Weak bases, you say? That makes them great leaving groups. And you are right. The sulfonate esters participate easily in reactions such as substitution and elimination reactions.

How can you tell which is the most stable species between two that have resonance?

Among similar species that both experience resonance, the more stable species will be the one with the most possible resonance structures. (ex. CLO4- is more stable than CLO3- because perchlorate has four resonance forms and chlorate has only three).

Dipole Moment

Any time charge is not evenly distributed within a bond (ex. when the two atoms have non-identical electonegativities) that bond will have a dipole moment, μ. The dipole moment can be calculated using μ= δ × d; where δ represents charge and d represents distance between charges. (Note: observe that δ is also the symbol often used to denote partial positive and partial negative charges; ex. +δ — δ). You may recall seeing the dipole moment represented on paper as an arrow with a plus sign on its tail. When this convention is used, the arrow points in the direction to which electrons in the bond will be pulled by the more electronegative atom.

Aromaticity

Aromatic compounds are conjugated, unsaturated, ring systems that exhibit greater stability than one would expect based on either resonance or conjugation alone. For example, benzene shows far greater stability than other unsaturated compounds with three bonds and two resonance forms. Conjugated systems are always very stable, but benzene is far MORE stable than a conjugated straight-chain alkene.

What is the Octet Rule?

Atoms of low (<20) atomic number tend to gain or lose electrons to obtain exactly eight electrons in their valence shell. Highly stable "noble gas" configuration. This is why sodium forms the ion Na+ and not Na2+.

Hybridization definition

Atoms, when bonded, hybridize (mix) their higher and lower energy valence orbitals to form "hybrid" orbitals with intermediate energy. Carbon has 2 e's in s and p orbitals. However, Carbon will form 4 orbitals with sp3 energy.

What is an example of two atoms with different electronegativites having NO NET dipole?

CCl4 Molecules with two or more dipole moments can still have no NET dipole when their geometric orientation causes the dipole moments to cancel each other out. This concept explains why carbon tetrachloride is non-polar even though carbon and chlorine clearly have different electronegativities.

What does this tell us about the relative reactivity of the carbons in a C=O vs. a C=N bond?

Comparing electronegativity, we see that the partial positive charge on the carbon in a C=O bond is greater than the partial positive charge on the carbon in a C=N bond. This indicates that carbonyls are more reactive than comparable imines.

How do you determine Hybridization?

Count the number of sigma bonds and add the number of lone PAIRS (of unbonded electrons). This number will equal the sum of the superscripts on one of the following hybridizations: sp, sp2, sp3, sp3d, sp3d2 (Note: no superscript indicates a superscript of one).

Rotation of plane-polarized light in enantiomers

Enantiomers rotate plane-polarized light. R and S enantiomers rotate this light to the same degree but in opposite directions. R enantiomers can rotate this light in a clockwise or counterclockwise direction, as can S enantiomers.

Geminal/Visinal

Geminal- comes from latin meaning twins. Two atoms or groups identical on a carbon eg CH2CH2CHBr2, the bromines are geminal Vicinal- comes from latin meaning neighbors. Two atoms or groups being identical and are on neighboring carbons: eg CH2BrCH2Br, the bromines are vicinal.

What is VESPR?

Valence Shell Electron Pair Repulsion Theory. Predicts the shape molecules will take due to the repulsion of lone pairs of electrons. Hybridization state determines the possible shapes for the molecule.

Absolute Configuration (R and S)

How two enantiomers are distinguished. Assign priority to all four substituents based on molecular weight, with higher molecular weight atoms receiving higher priority. Rotate the LOWEST priority substituent to the back motion, the absolute configuration is R; if proceeding in order from one to three requires a counter-clockwise motion, the absolute configuration is S.

Ranking Resonance structures

If determining the relative contribution of various resonance structures to the actual structure, the individual structure that contributes the MOST to the actual structure is the one that: 1) Allows the most atoms to have a full octet (unless atom is a common exception for the octet rule). 2) Has the least formal charge (ex. no charge is better than some charge and one formal charge is better than multiple formal charges) 3) Places formal charge on atom most receptive to that charge (ex. it is preferable to have a negative formal charge on oxygen than on carbon because oxygen is more electronegative).

Polarity results in?

In partial positive and partial negative charges, which are clues when trying to identify the nucleophile and electrophile in a reaction. To be a base or nucleophile, a molecule must have a full or partial negative charge. To act as an electrophile, it must have a full or partial positive charge.

Rank the bonds listed above according to increasing reactivity.

In this case, reactivity is measured in terms of how readily a species will react in the presence of a nucleophile or electrophile. You should definitely know that alkanes are very unreactive, and that alkenes are far more reactive. However, it is perhaps surprising that alkenes are actually slightly MORE reactive than alkynes. Still, alkynes are far more reactive than alkanes. The higher reactivity of alkenes is accounted for by the fact that the pi electrons in an alkyne are slightly more stable than the pi electrons in an alkene. One potential explanation is that the sp hybridized carbons in the alkyne have more s character and pull more tightly on those pi electrons, making them more centralized and therefore lower energy than the pi electrons in an sp2 hybridized alkene. In increasing order of reactivity they would be ranked: single < triple < double.

What is the Hybridization of BeCl2?

Linear BeCl2 is going to have: Be has a sigma bond with each of the chlorines. Which gives it a linear Hybridization. Be --> 2 valence e- Cl --> 7 valence e- (2x) Total = 16 valence e- Each chlorine has 6 valence electrons (nonbonding) and 2 valence electrons (bonding with the Be). Formal Charge = (valence e-) - (nonbonding e-) - (bonding e- / 2) Each Cl and Be has a formal charge of 0, which lets me know that this is the correct structure.

IUPAC nomenclature

Met-, eth-, prop-, but-, pent-, hex-, hept-, oct-, non-, dec- (sec-butyl, isopropyl, isobutyl, tertbutyl)

Provide a conceptual definition for each of the following: observed rotation, specific rotation, polarimeter, plane-polarized lights, optically active vs. optically inactive, and racemic mixture.

Observed rotation is simply the degree to which a sample rotates plane polarized light. However, that rotation is not a universal constant for a particular molecule. Rather, it varies depending on concentration, length of the tube, etc. Specific Rotation takes these factors into account by dividing observed rotation by the length of the tube and the concentration. Specific rotation could therefore be described as "observed rotation per length, per concentration unit." A polarimeter is an apparatus that measured the rotation of plane-polarized light as it passes through a sample. Plane- polarized light is light that exist in only a single plane. Normally, light waves are oriented in an infinite number of planes from zero to 360°. A polarizer can sift out all of these leaving, for example, only vertically oriented waves. To be optically active means that a substance does rotate plane- polarized light. Optically inactive compounds do not rotate plane-polarized light. A racemic mixture is a 50/50 mix of the two absolute configurations of a compound (i.e., R and S).

Chirality

Often referred to as "handedness". Any atom attached to four DIFFERENT substituents must be chiral. Any atom with less than four substituents cannot be chiral (and therefore cannot be an enantiomer). Double or triple bonds count the same as if that atom were bonded to the other atom two or three different times. Sot it would have more weight, so higher priority.

Important Note on Pi Bonds

Pi bonds themselves are weaker associations than are sigma bonds. However, a double bond (one sigma bond plus one pi bond ) is stronger together than a single bond (one sigma bond only). Also, triple bonds are much shorter, stronger bonds than are single bonds, but are also more reactive. Reactivity has to do with the tendency of the third bond (a pi bond) to react. Bond strength is at measure of the energy needed to completely break the two atoms apart (ex. break all three bonds)

Energy is always ________ when a bond is formed and ________ when a bond is broken.

Released ; required. One example that often confuses students is ATP. They have the general concept that breaking the phosphate bond in ATP releases energy. That is wrong. Breaking the ATP bond does require energy, but the new bonds formed—in particular the new -OH bond resulting from hydrolysis, releases more energy than was required to break the phosphate bond of ATP.

Structural Isomers

Same formula, different bond-bond connectivity (For example: 2-methylpentane and 3-methylpentane are both C6H14)

Stereoisomers

Same formula, same bond-to-bond connectivity, but different in the 3-D arrangement of their substituents. There are two categories of stereoisomers: enantiomers and diastereomers.

Which is stronger, a sigma bond or a pi bond? Why?

Sigma bonds are significantly stronger than pi bonds. This is because sigma bonds allow for electron density to be concentrated to a much larger degree between the two nuclei. The lowest energy state for electrons—being electrostatically attracted to both nuclei simultaneously, is between those two nuclei and as close to each nuclei as possible. In a pi bond the p orbitals overlap above and below the atom, localizing the electrons above and below the plane of the bond—a higher energy state compared to the head-on overlap of a sigma bond. You can also conceptualize that pi bonds are weaker simply because we know those electrons are in a higher-energy state. It is universally true that when a bond is HIGHER in energy it will require LESS energy to break it.

Rank the bonds listed above according to increasing bond strength.

Single < Double < Triple

1) The H-O-H bond angle in water is measured experimentally to be 104.4°. The related angle H-N-H in ammonia is expected to be: A) larger due to the greater electron repulsion in ammonia B) larger due to the greater electron repulsion in water C) smaller due to the greater electron repulsion in water D) smaller due to the greater electron repulsion in ammonia

Solution: Both molecules are approximately tetrahedral in shape, but experience some distortion due to the repulsion of lone pairs of electrons. In water, two lone pairs push both hydrogen substituents away from the plane shared by the two lone pairs, decreasing the H-O-H bond angle. Ammonia has only one lone pair, so the same effect is observed, but to a lesser degree. Thus, the bond angle is larger in ammonia due to the greater repulsion in water than in ammonia, or answer B.

Provide multiple examples of coordinate covalent bonds. Include a human-body example.

Students will see two types of coordinate covalent bonds. The first one is illustrated any time a nucleophile with a lone pair abstracts a proton: NH3 + HCl <--> NH4 + Cl-. The amine binds a fourth hydrogen, but the electron belonging to that hydrogen stays with the Chlorine. Both electrons that were part of the amine lone pair now form the new covalent bond between nitrogen and the fourth hydrogen. Another example, and the one we've seen most on the MCAT, is easily recognizable. It involves a metal coordinated with one or more molecules that have lone pairs. When you see something like Fe(NH3)4 or Co(NH3)3, these structures should stand out because they look almost like ionic compounds, but obviously the amine does not have a charge (so they cannot be ionic). This thought would lead one to wonder how the amines are attached to those metals? The answer is via coordinate covalent bonds. A common and very applicable example of coordinate covalent bonds in the human body is the binding of iron in the heme unit of hemoglobin (see below).

How does rotational limitation of pi bonds relate to our previous study of proteins?

The amide functional group in a protein (created when the amino group of one amino acid attacks the carboxylic acid group of another amino acid) exhibits resonance and therefore both the C-O and C-N bonds have double-bond character. This prevents rotation—a key characteristic of peptide bonds.

Draw two energy coordinate diagrams demonstrating why the combustion of a less-stable molecule results in a heat of combustion than the combustion of a more-stable molecule.

The diagram below shows two RXN coordinate diagrams combined, one for combustion of Reactant1 and one for Reactant2. Both reactants are hydrocarbons and therefore the products of combustion are the same—carbon dioxide and water. That is the key to understanding why less stable molecules release more energy: the energy of the products is always going to be the same (i.e., the energy of CO2 + H2O). Therefore, the higher the energy of the reactants the greater will be the difference in energy between them. (Note: This diagram shows the energy of the transition state being the same for both reactions, but that is arbitrarily chosen. This is a path-independent process and so the only concern is the difference in energy between the reactants and the products).

Formal Charge

The difference between the # of electrons in an atom's valence shell when it is in its ground/elemental state and the number assigned (lone-pair electrons and 1/2 of the bonding electrons) to it in a molecule. Formal charge= valence - assigned or FC = (valence e-) - (nonbonding e-) - (bonding e- /2 )

Electronegativity

The greater the difference in the electronegativity of two atoms in a bond, the more polar the bond. This shows us that oxygen forms stronger hydrogen bonds than does nitrogen. It is worth knowing that carbon and hydrogen have similar, but not identical, electronegativities (carbon=2.5; hydrogen=2.2). Fluorine has the largest electronegativity (4.0) and Francium has the smallest (0.7). Beyond these general trends, if specific electronegativity figures are required they will always be given.

Which of the above models is the most accurate visual representation of an actual molecule?

The most conceptually-accurate representation in terms of what you would actually see if you could take an "Incredible Voyage" down to the molecular level would be the space-filling model. However, remember that those electron clouds would not be nicely color-coded for you. They are only math functions that predict where the electrons might be. If you were seeing a real methane molecule at that size and scale you would most likely see nothing. The first thing you could see would be the nucleus and you would need to have magnification many, many times that to see an electron.

Valence

The number of bonds an atom "normally" makes: carbon and its family are tetravalent; nitrogen and its family are trivalent; oxygen and its family are divalent and fluorine and its family are monovalent.

Draw all possible resonance structures for a) an amide (R-CONH2) and b) the phosphate ion (PO4 3-). In each case rank each structure in terms of its contribution to the actual structure.

The possible resonance structures are drawn below. For the amide, the most stable structure is the one to the far left because there is no separation of charge. Next in line is the middle structure because it places a positive formal charge on carbon, whereas the structure to the right places that charge on nitrogen. Among the phosphate structures, the least stable will be the structure with a positive formal charge on the phosphorous because this has more formal charges and is the only one with both negative and positive formal charges. The other four structures will be equal contributors.

Lone pairs of electrons

The presence or absence of unpaired electrons determines the exact shape from among those choices. For example, an sp2 hybridized atom can take on the trigonal planar shape (no lone pairs) or the bend shape (one lone pair). Sp hybridized atoms are always linear.

Conformational isomers

These are NOT true isomers!!! They are the same exact molecule. When a molecule twists or rotates around its bonds these are considered "conformers" NOT isomers.

Huckels Rule

To be aromatic, a ring system must have 4n + 2 pi electrons. The number of pi electrons is set equal to = 4n +2 and if n is 0, 1, 2, 3 the rule is met.

Isomers

Two molecules are isomers if they have the same molecular formula but are actually different compounds.

Relative Configuration

Two molecules have the same relative configuration if their spatial arrangement is identical, but they have one and only one non-identical substituent.