EK Ch2 Org Chem Flashcards
formal charge
number of valence e- number of bonds- number of nonbonding electrons
sigma bonds
- stronger than pie bonds, forms when e are localized to the space directly btw the two bonding atoms - e are as close as possible to the two sources of positive charge, two nuclei -sigma bonds are the strongest, lowest energy and most stable type of covalent bond - a sigma bond is always the first type of covalent bond to be formed between two atoms so a single bond must be a sigma bond. - double and triple bonds contain one sigma bond each!
pie bonds
-created by overlapping p orbitals - double and triple bonds are made by adding pie bonds to a sigma bond! -so sigma bond leaves no room for other e orbitals directly btw atoms, so the first pie bond forms above and below the sigma bonding e, forming a double bond between the two atoms - weaker than sigma bond, less energy required to break it - always added to sigma existing bonds so strengthen the overall bond between the atoms, so overall bond energy is greater as pie bonds are added!
double bonds
-always consists of one pie bond adn one sigma bond - if another pie bond is formed the new orbital is formed on either side of the sigma bond forming a triple bond btw two atoms
triple bonds
- are always made of 2 pie bond and one sigma bond
adding a pie bond…
- shortens the bond length, since bond strength is inversely proportional to bond length
bond length
inversely proportional to bond strength - double bond is shorter than a single bond -single bonds are longest and easiest to break - db are shorter and harder to break -tp are shortest and hardest to break
bonds and hybrid orbitals
sigma bond formed where the hybrid orbitals of two atoms overlap, pie bonds are formed by the overlap of pure p orbitals
sp2 character
- formed from one s and two p orbitals, therefore has 33.3% s character and 66.7% p character - more s **character a bond has the shorter, stronger and more stable it is**
sp3 character
25% s and 75% p
sp character
- formed from one s and one p orbital, so 50% each character, 50% s character and 50 % p character
sp molecular shape
-linear, 180 bond angles ex c2h2 ethyne
sp2 molecular shape
- 120 trigonal planar* ex formaldehyde CH2O
sp3 molecular shape
109.5 degrees, tetrahedral, trigonal pyrmidal, or bent ex. methane CH4, ammonia NH3, water for shape ignore lone pairs, like ammonia has 1 lone pair, its shape is trigonal pyramidal the lone pair of electrons is treated as if it where invisible
conjugate base and resonance structures
- if the conjugate base of an acid exhibits resonance structures it is more stable and therefore a weaker base** - a more stable conjugate base corresponds to a stronger acid - Phenol, whose conjugate base is resonance stablized, is a stronger acid than ethanol
delocalized electrons
- result from pie bonds and lone pairs sometimes bonding electrons spread out over three or more atoms, these are defined as delocalized electrons
nucelophilic
hungry for positive charge
electrophilic
hungry for negative charge
nuc functional group
-partial neg charge and seek positively charged nuclei - donate es and usually attack functional groups with partial positive charges. -amines are an important class of nucleophilic functional groups -they “attack” with the lone pair of es on the nitrogen. -Because they donate electrons, nucleophilies are also called Lewis bases
electrophile functional group
-partial positive charge and seek electrons -provide a center of positive charge, they usually get attacked by electrons from other functional groups -carbonyl carbons are an impotant class of electrophilic functional groups, their reactivity increases as the partial positive charge on the carbonyl carbon increases - since these are electron acceptors, electrophilies are also lewis acids
alcohol
R-OH
ether
R-O-R’
amine
H2- N-R R, R’-N- H R, R’, R”-N
aldehyde
ketone
carboxylic acid
ester
amide
structural isomers
same molecular formula but different bond to bond connectivity, i.e. different connections between atoms
ex. isobutane (C4H10) and n-butane (C4H10)
isomers
same molecular formula but different compounds
conformational isomers
not true isomers, confomers are different sptial orientations of the same molecule
- at room temperature atoms rotate around their sigma bonds, resulting in a mix of conformational isomers at any given moment ( think newman projections)
newman projection
- staggered is lower energy than eclipsed confomers exist at higher energy
- difference in energy levels is due in large part to steric strain
- simplest way to distinguish btw confomers
steroisomers
two unique molecules with the same molecular fomrula and same bond to bond connectivity
ex. enantiomers and diastereomers
enantiomers
= nonsuperimposable mirror images of one another, they have the same molecular formula and connectivity, but are not the same moelcule becuase they differ in configuration
ex mirror images of each other, must have hte opposite absolute configurations at each and every chiral carbon
- they have opposite absolute configurations at all of their chiral centers, if a molecule has more than one!
chiral
any carbon is chiral when it is bonded to 4 different substituents!
S configuration
COUNTER CLOCKWISE
R configuration
CLOCKWISE
optically inactive
- compounds may be compoudns without a chiral cetner or molecules with internal mirror planes
- for comoounds without an enantiomer, or for an equal mxiture of enatiomers, there are so many millions of molecules colliding with photons that on average, photons leve the compound with the same electric field orientation with which they went in
- since no single molecular orientation is favored, the net result is no rotation of the plane of the electromagnetic field
enantiomers have the same chemicla and physical characteristics EXCPET:
- interactions with other chiral compounds
- interactions with polarized light
diastereomers
- same molecular formula, bond to bodn connectivity but NOT mirror images of each other
- not the same compound
- differ in their boiling points, melting points, solubilities, rotation of plane polarized light
- so these pairs have different physical properties (above) and in their chemcal properties
max number of optically active stereisomers formula
- max number is 2n
- n= the number of chiral centers
- so this formula is what the max number ofopticlaly active stereoisomers ( so dia. and enati.) that a single compound have is related to teh numebr of its chiral centers followed by this formula
meso compounds
multiple chiral centers, optically inactive
plane of symmetry through their center which divides hte moelcule into two halves that are mirror images of each other
- because of their symmetry the chiral centers offset each other and theoverall compound does not rotate plane-polarized light
ACHIRAL*
epimers
BIOCHEM
diasteromers that differ in configuration at only one chiral carbon
anomers
cyclic diasteremers that are formed whne a ring closure occurs at an epimeric carbon, chiral carbon of the anomer is called the anomeric carbon
carbohydrates classified according to their configuration at the anoemric carbon!
cis/trans isomers
differnt physical proeprties!
- cis have dipole moment, trans do not
- because they have dipole moment, cis molecules have stronger intermolecular forces than trans molecules, leading to higher boiling points–> it takes more energy to make them boil since they’re “stuck” together by stronger intermolecular forces
- sicne substituents concentrated on the same side cis molecules do not form crstyals as readily, and therefore have lower melting points than their respective trans isomers*
Sn1
- rate determing step is formation of carbocation, is the SLOW STEP
- so rate dependent on only one of the reactants
- this step has nothing to do with nuc, so rate is indepdent of hte concentration of the nucelophile and is directly proportional to teh concentration of the substrate, substrate is the electrophile or the molecule being attacked by nuc
- LG simply breaks away on its own leaving a carbocation behind
- second step happens very quickly, nuc attacks carbocation
- ONLY IF starts chiral c, both enantiomers are produced
- intrermediate carbocation is planar and the nucleophile is able to attack it from either side
Sn2
- rate is dependent on concentration of nuc and the substrate
- attack from behind
- rate dec from primary to secondary, third whould stericlaly hinder
- do not occur with tertiary carbons/substrates!
- if nuc a strong base and the substrate is too hindered an elimination E2 reaction may occur, in which case nuc acts as a base taking a proton and halogen leaves the susbtrate froming a cc double bond
- bulky nucleophiles also hinder sn2
nucelophilicity
- unimportant sn1, important sn2
- if nuc beahves as a base, elimination will occur so use a less bulky nuc, a neative cahrge and polarizaibility add to nucelophilicity!
- electronegativity reduces nuc
- nuc decreases going up and to the right on the periodic table!
- base is always a strong nucelophile than its conjguate acid, but nuclepholicity and basicity are not the same thing!
polar protic solvent
- stabilize nuc and any carbocation that may form
- that can hydrogen bond!
- stable nuc slows sn2 reactions, while stable carbocation inc the rate of sn1 reactions, so polar protic solvents inc the rate of sn1 and dec he rate fo sn2
polar aprotic solvent
- cannot form a hydrogen bond
- do not form strong bonds with ions and thus increase the rate of SN2 reactions while inhibiting sn1 reactions
- in sn1 solvent is often heated to reflux. boil, in order to provide energy for the formation of carbocation
- solvolysis hte solvent acts as the nuc
chirality and plane polarized light and amino acids
A chiral molecule is one that is asymmetrical in a way that makes it non-superimposable on its own mirror image. Often, this asymmetry results from a carbon atom, or chiral carbon, that is attached to four different substituents.
Chiral molecules promote the rotation of plane-polarized light. In contrast, achiral molecules are superimposable and do not rotate plane-polarized light.
In the specific context of amino acids, a chiral amino acid must have four different substituents bound to its α-carbon. This means that the α-carbon is a chiral center, or stereocenter. (A chiral amino acid might also have other stereocenters – in fact, threonine and isoleucine both do – but the α-carbon is the likely focus of an MCAT question.) Of the 20 standard amino acids, 19 are chiral.
***Only one is achiral: glycine, which contains two identical hydrogen atoms attached to its α-carbon. This means that glycine is unique in that it does not rotate plane-polarized light. Additionally, glycine is the only standard amino acid that cannot exist in two enantiomeric forms. (Enantiomers are mirror-image stereoisomers that rotate plane-polarized light in exact opposite directions.)
chirality and amino acids 2
Of the 20 standard amino acids, 19 are chiral. Only one is achiral: glycine, which contains two identical hydrogen atoms attached to its α-carbon. This means that glycine is unique in that it does not rotate plane-polarized light. Additionally, glycine is the only standard amino acid that cannot exist in two enantiomeric forms. (Enantiomers are mirror-image stereoisomers that rotate plane-polarized light in exact opposite directions.)
In chiral amino acids, the configuration of substituents around the α-carbon can be described in multiple ways. Under the R/S system, which is typically most familiar, all chiral amino acids are S except cysteine, which is R. Alternatively, amino acids (as well as sugars) can be classified using the D/L system, which classifies molecules based on their resemblance to glyceraldehyde. The MCAT is unlikely to ask you to determine whether an amino acid is D or L based on its drawn structure alone. However, it is important to know that only L amino acids are used by eukaryotic cells. (You can remember “L” for “living” eukaryotic cells.) However, prokaryotic – or bacterial – cells do use select D amino acids for incorporation into their cell walls.
Functional groups amines and sulfur
Amines (R–NH2, R–NHR’, or R-NR’R”), imines (R=NH or R=NR’), and enamines (C=C–NH2, C=C–NHR, or C=C–NRR’) are nitrogen-containing compounds with medium melting/boiling points that can act as weak bases. Sulfur-containing functional groups contain the root “thio” and generally act similarly to the corresponding oxygen-containing groups.
mercaptan
CH3SH
CH3SO3CH3
sulfonate ester
