Resonance and M.. View of Butadiene The different resonance forms of butadiene suggest p bonding character between the two central carbon atoms. 2 2 2 2 carbanion 2 2 carbocation The M.. view of butadiene also shows p bonding between the two central carbon atoms. 2 2 radical Bond rder butadiene butane y4-3 y3-1 restricted rotation free rotation y2 1 Butadiene is conjugated, which means that the two p systems can interact. y1 3 Super-onjugated or Aromatic p e - Systems onjugation = at least two p bonds adjacent to each other. Allows for transfer of e- density or charge across all doubly-bonded atoms. onjugated? benzene p * p p * cyclobutadiene p Benzene is unusually stable, even relative to hexatriene. This arises from being both conjugated AD cyclic AD it has (4n2) p electrons = ARMATI! ow about?? as e - s in its non-bonding orbitals; it is T aromatic 2 1
Electronegativity and Bond Dipoles Electronegativity = e - attraction Atomic Scale: F>>l>>Br>S>I>>>P Group Scale: 2 >>F 3 > 6 5 >l 3 >.. 3 Enables an atom to polarize the electron density of a bond.. Dipole-dipole interactions unfavorable 2 F d d- favorable The F bond has a dipole moment, which means that it has a negatively and positively charged end Molecular Structure and Dipoles Electronegativity >> 3 bond dipoles.. lone pair Molecular Dipole Ammonia is a neutral molecule. It has a molecular dipole and, thus, it is a neutral polar molecule. Electronegativity >> 4 bond dipoles The bond dipoles cancel and, thus, there is no molecular dipole The ammonium ion is charged but it does not have a dipole. Dipole harge b-l-glucose The net molecular dipole for glucose is very small even though it has many bond dipoles. Regardless, it is a very polar molecule and proteins can easily discriminate it from other sugars. 2
Manifestations of Aromaticity pyrrole The p e- system for benzene is circular, above and below the ring plane. This annular system is stable and not easily disrupted. pyrrolidine onsider: 2 -l 2 2 - Pyrrolidine is 10 6 -fold more basic than pyrrole, why? via 2 sp 2 carbon The lone pair electrons of pyrrolidine are part of a p system- protonation would disrupt the p system. rder of reactivity: Q. Why is A so much more reactive than B? >> > 3 2 -l 2 -l 2 -l 3 2 3 2 3 A B Inductive vs Resonance vs Field Effects Through s bonds Through p bonds Through space rder of reactivity: Resonance explains the reactivity of A >> > 3 2 -l 2 -l 2 -l 3 2 3 2 3 A B Q. What about? Why is it not reactive? 2 A. The 3 - group is an e - withdrawing group and this will destabilize the () charge on 2. 3 annot draw resonance forms that put charge on oxygen 2 Difficult to separate field and inductive effects- here is one example: 3 mostly an inductive effect l l l 2 l 2 BUT, first, let s talk acids bases. 3
Acids and Bases Definitions: Bronsted acid = a proton donor Bronsted base = a proton acceptor Lewis acid = an electron pair acceptor Lewis base = an electron pair donor Lewis acids are often the acid of choice in enzyme catalyzed reactions. These include magnesium, zinc, etc These are equivalent but the Lewis definition is more general: 3 2 ( 2 3 3 2 - ( 2 3 Acid Base 3 2 - ( 2 3 3 2 - ( 2 3 But how about this reaction: - 3 2 Fel 3 3 2 -Fel 2 l - Lewis Acidity Scales: Difficult to measure since most good Lewis acids will react with water (a weak base). Most obvious trends are related to charge and size: Fe 3 > Fe 2 (charge and size) Li > a (size) Many are extremely reactive but proteins have evolved active sites to protect the acids from solution. Really should be thought of as: 3 e - pair donor the base - Fe l 2 l 3 e - pair acceptor the base Fe l 2 l - Bronsted Acidity Scales Defined relative to water, [ ][ - ] = 10-14 M 2 eutral p = 7.00 = -log[ ], blood ~ 7.4 Example (acetic acid, Ac): 3 2 = 3 2 -, K a = 1.74 x 10-5 M Define pka = -logka = 4.76 *At p 4.76 1/2 the molecule is protonated and 1/2 is not. At more acidic p (more, lower p), more of the acid is protonated. At a more basic p (less, higher p), less of the acid is protonated. Q. Is acetic acid mostly ionized, partly ionized, or not ionized at physiological p = 7.4? A. Example (Tris): 3 ( 2 = 3 ( 2 pka = 8.3 Q. Which form of Tris, protonated vs neutral, is the major species at p 7.4? A. Example (Tris Ac): Q. Does the equilibrium lie to the left or to the right? 3 2 3 ( 2 = 3-2 3 ( 2 A. 4
Molecular Structure and Acidity In general, have A = A - Remember, lower pka = stronger acid! eed to stabilize A - to have a good acid!! In order to stabilize A-, need to delocalize (spread out) charge Inductive effects Resonance effects Field Effects Example: pka - 2 2 4.8 l- 2 2 2.7 l 3-2 0.7 But, l 3 2 2 pka = 4.2 Inductive effects are mediated by s bonds, which are not easily polarized. The effect drops off rapidly with increasing number of bonds.difficult to separate from field effects but probably less important. ote- inductive effects are not sensitive to geometry but field effects are. Example: A l l 2 pka = 6.07 pka = 5.67 B l l 2 The number of bonds between chloro groups and the acid are the same in A & B and, thus, acid B is stabilized when the chloro groups are pointed away from the acid- Why? Resonance Effects on Acidity pka ~ 19 3 3 3 pka = 4.8 3 3 3 more accurate Resonance involves p bonds that can transmit an entire charge. The effects are often very large. For example, here resonance increases acidity by a factor of ~10 14!! Another example: In biology, you need to make carbon-carbon bonds. ow?? R 2 2 2 2 2 pka ~ 50-60 pka ~24 A biological system (p 7.4) doesn t stand a chance of de-protonating an acid with pka = 50-60. A pka of 24 might not seem much better but it is ~10 30 - fold more acidic This is a carbanion, which is extremely unstable because carbon is not electronegative. It is also partly stabilized by the inductive effect of the attached oxygen atom In this resonance structure the negative charge is now on an electronegative oxygen atom. If the oxygen atom is located near a metal ion in an enzyme active site, the additional stabilization (field affect) can bring the pka into the physiological regime. 5
ow to make molecules. Q. an you use carbocations to make - bonds? i.e. X X In order for this to happed need an -X substituent less electronegative than carbon so that it can donate negative charge and stabilize the cation. carbocation ow about Actually, there is one other possibility.. ot bad this is the major form and it is a protonated carbonyl, not really a carbocation but close enough- the only one seen commonly in nature. ften the is a metal ion. S i Silicon has electron density in d-orbitals and these can be used to form bonds that stabilize the carbocation. But, silicon is not usually used for biology (except for in an old Star Trek episode). But, if a life form that uses silicon did exist, it would likely use carbocations for chemistry. Still haven t made any - bonds. Let s All Get Together and Make a Bond We can start with a carbanion. and this protonated carbonyl. 2 2 2 This is a nucleophile- it has excess e - density and it is in search of an e - deficient species. And this is an electrophile- it is e - deficient and in search of an e - rich species. And it s a match! This is known as an aldol reaction 2 2 Q. Isn t that an e- pair donor (i.e. Lewis base)?? and an e- pair acceptor (i.e. Lewis acid)?? D YU MEA T SAY TAT. 6
Yes, there really aren t a whole bunch of different reactions- most of them are just plain ol Lewis acid-base reactions in disguise. onsider a classic nucleophilic substitution reaction. 3 2 3 e - pair donor acceptor B r 3 2 3 Br - The nucleophile is - and the electrophile is the bromoalkane This reaction can be concerted or, the Br - can leave first and then the - adds to the carbocation (S 2 vs S 1, respectively). It all depends on whether you have a good nucleophile (strong base) and a good electrophile (strong acid- stable carbocation). There s mostly only one other type of reaction and that s single electron transfer reactions (free radical or redox reactions). For example: 2 Fe 3 2 R-S 2 Fe 2 R-S-S-R 2 R S R S Fe 3 R S R S S R R S S R Fe 2 A free radical (it has an unpaired electron) Free radicals are generally very reactive and there are few carbon-centered radicals in biology- most are metal center based and highly regulated by spatial organization. 7