# Studying an Organic Reaction. How do we know if a reaction can occur? And if a reaction can occur what do we know about the reaction?

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1 Studying an Organic Reaction How do we know if a reaction can occur? And if a reaction can occur what do we know about the reaction? Information we want to know: How much heat is generated? How fast is the reaction? Will a catalyst speed up the reaction? (and if so what should the catalyst be?) Are any intermediates generated?

2 All of this information is included in an Energy Diagram Transition states Transition states Potential energy Intermediate Starting material Products Reaction Coordinate

3 Equilibrium Constants Equilibrium constants (K eq ) indicate thermodynamically whether the reaction is favored in the forward or reverse direction and the magnitude of this preference ΔG K eq = ([C][D]) / ([A][B]) = ([products]) /([starting material]) Reaction Coordinate

4 Gibb s Free Energy The K eq is used to determine the Gibb s free energy ΔG = (free energy of products) (free energy of starting materials) If we use standard free energy then ΔG (25 C and 1 atm) Keq = e (-ΔG /RT) or ΔG = -RT(ln K eq ) = RT(log 10 K eq ) A favored reaction thus has a negative value of ΔG (energy is released)

5 Contributions to Free Energy ΔG = ΔH -TΔS The free energy term has two contributions: enthalpy and entropy Enthalpy (ΔH ): heat of a reaction (due to bond strength) Exothermic reaction: heat is given off by the reaction (-ΔG ) Endothermic reaction: heat is consumed by the reaction (+ΔG ) Entropy (DS ): a measure of the freedom of motion - Reactions (and nature) always prefer more freedom of motion Organic reactions are usually controlled by the enthalpy

6 Bond Dissociation Energies The free energy of organic reactions is often controlled by the enthalpic term - The enthalpic term in organic reactions is often controlled by the energy of the bonds being formed minus the energy of the bonds being broken The energies of bonds is called the Bond Dissociation Energy Many types of bonds have been recorded (both experimentally and computationally) we can therefore predict the equilibrium of a reaction by knowing these BDE s

7 Kinetics A second important feature is the RATE of a reaction The rate is not determined by K eq, But instead by the energy of activation (E a ) E a Knowing the E a of a reaction tells us how fast a reaction will occur Reaction Coordinate

8 Rate Equation The rate of a reaction can be written in an equation that relates the rate to the concentration of various reactants Rate = k r [A] a [B] b The exponents are determined by the number of species involved for the reaction step - The exponents also indicate the order of the reaction with respect to A and B Overall order of the reaction is a summation of the order for each individual reactant

9 Relationship between Rate and Energy of Activation Referring back to our energy diagram the rate can be related to the energy of activation (E a ) k r = Ae (-Ea/RT) A is the Arrhenius preexponential factor E a is the minimum kinetic energy required to cause the reaction to proceed

10 Transition States vs. Intermediates A transition state is an unstable species (it has no measurable lifetime) Transition State An intermediate has a measureable lifetime (it can be isolated in theory) intermediate The energy of activation refers to the energy difference between the starting material and the transition state along the reaction coordinate Reaction Coordinate

11 Effect of Catalyst A catalyst only affects the energy of activation (starting material and product energies are unaffected, therefore K eq is the same) Potential energy Reaction Coordinate A catalyst therefore needs to stabilize the transition state structure -not starting material or products

12 Multistep Reactions In a multistep reaction, the overall reaction rate is determined by the highest energy barrier along the reaction coordinate E a (2) Potential energy E a (1) E a (1) > E a (2) Reaction Coordinate Referred to as the rate determining step

13 Let s Look at the Reactions of Alkanes Most alkanes are relatively inert Halogenation is one reaction type for alkanes As chemists we want to know the mechanism of this reaction (or how does the energy diagram appear) What we know: Reaction does not proceed in the dark or in the cold Reaction occurs with wavelengths corresponding to Cl 2 absorption Quantum yield is greater than 1 (therefore more moles of product are obtained than moles of photons of light used)

14 This data implies: 1) The chlorine molecule absorbs the light to initiate the reaction 2) The reaction proceeds in a chain mechanism To initiate: This chlorine radical is a reactive species it wants to fill its octet

15 The chlorine radical will react with methane The methyl radical (also a reactive species) will react further Cl H H Cl Cl H H H H Cl This step creates chloromethane and another reactive species in chlorine radical that will continue the radical chain process These steps are called propagation steps (the step creates the same number of reactive intermediates as it begins with)

16 A radical chain process will continue until a termination step (whenever two radicals combine to form less reactive species) For this reaction any step that destroys radicals will cause the reaction to terminate

17 How Does this Mechanism Look Like in an Energy Diagram? Cl H CH 3 H 3 C Cl Cl Potential energy HCl CH 3 Cl CH 4 Cl ClCH 3 Reaction Coordinate

18 Same Mechanism Can Occur with F 2, Br 2 and I 2 What is the difference compared to Cl 2? -BOND DISSOCIATION ENERGIES What is the E a for the rate-determining step? Starting material transition state Ea (Kcal/mol) F + CH 4 F H CH Cl + CH 4 Cl H CH 3 4 Br + CH 4 Br H CH 3 18 I + CH 4 I H CH 3 34 Therefore fluorine reacts the fastest and iodine the slowest

19 Stability of Reactive Intermediates Methyl radical (CH 3 ) is a reactive intermediate (its outer shell is not filled) Structure: sp 2 hybridized with single electron in remaining p orbital H H H This species is electron deficient (only 7 electrons in the outer shell)

20 How can we Stabilize CH 3? Since it is electron deficient we need to supply extra electron density to stabilize Ways to add extra electron density: 1) Inductive effect Have carbon-carbon bonds that can inductively supply electron density Therefore more substituted radical sites are more stable

21 Remember the nomenclature for alkyl sites -use same naming for radical sites Methyl radical H H H no alkyl substituents primary radical (1 ) H 3 C H H 1 alkyl substituent secondary radical (2 ) H 3 C 2 alkyl substituents CH 3 H tertiary radical (3 ) H 3 C CH 3 3 alkyl substituents CH 3

22 2) Hyperconjugation - Refers to neighboring C-H bond being able to donate electron density to electron deficient site Hyperconjugation stability also increases with increasing number of substituents (have more neighboring C-H bonds to potentially donate electron density)

23 3) Resonance Unsaturated sites in conjugation with radical sites will offer stabilization by allowing electron deficient site to be spread over more atoms Remember from previous discussions, resonance is primarily observed when there are p orbitals on adjacent sites due to π bonds or when there are atoms with lone pair of electrons adjacent to site Must have p orbitals in conjugation

24 Other Reactive Species Important to know the characteristics of these reactive species because many mechanisms have one somewhere along the reaction coordinate CARBOCATIONS Formal positive charge at a carbon site Carbocations are even more electron deficient than a radical site Therefore same stability factors as a radical

25 CARBANIONS (carbon anions) The carbon atom now has a filled outer shell of electrons Remember that lone pairs of electrons generally fill hybridized orbitals therefore the methyl carbanion is sp 3 hybridized (changes to sp 2 if resonance is available with lone pair) A carbanion is electron rich it has an excess of electron density therefore stability decreases with increasing number of substituents

26 Carbanions want to lower electron density -not add more Resonance, though, still stabilizes a carbanion -allows negative charge to delocalize over more atoms Similar to acid strengths observed earlier where delocalizing a negative charge will make the conjugate more acidic

27 What happens when an alkane is reacted in a halogenation reaction when various alkyl sites could react? For simplest example consider propane: Primary carbons H 3 C CH 2 CH 3 secondary carbon There are both primary and secondary carbon positions 2 site is favored over the 1 site

28 The energetic difference is greater than 60% / 40% Must also consider the possible sites for reaction In propane: There are 6 primary hydrogens and only 2 secondary hydrogens 40% / 6 = 6.66% per 1 hydrogen 60% / 2 = 30% per 2 hydrogen Therefore the selectivity for 2 hydrogen over 1 hydrogen is greater Selectivity = 30 / 6.66 = /1 for chlorination

29 What causes the selectivity? Consider only the rate determining step in the energy diagram: Potential energy propane 1 radical 2 radical 2 radical is more stable than 1 radical due to extra substitution E a Reaction Coordinate

30 What Occurs with Bromination? We already saw that bromination will be slower than chlorination (there is a higher E a for bromination than chlorination) This requires the reaction to be heated in order to get the reaction to proceed It is also found that brominations are much more selective Almost entirely form the product resulting from the more stable radical (usually for brominations only the most stable radical site is brominated!)

31 How Does the Energy Diagram Reflect this Selectivity? Potential energy 1 radical 2 radical 2 radical is still more stable than 1 radical due to extra substitution E a propane Greater difference in E a Reaction Coordinate As reaction becomes more endothermic there is a greater difference in E a - Causes a greater selectivity

32 Hammond Postulate In an ENDOTHERMIC reaction, the transition state is closer to the PRODUCTS in energy and structure. In an EXOTHERMIC reaction, the transition state is closer to the REACTANTS in energy and structure In the halogenation of propane the reactant is the same for both the 1 and 2 sites (same energy) The product is different in energy (which is actually the intermediate radical) due to the stability of the radical at a 2 site relative to a 1 site If the transition states are more reactant like the energy will be similar and thus the selectivity will be low If the transition states are more product like the energy difference will be greater and thus the selectivity will be higher

33 Reactivity vs. Selectivity Another way to use the Hammond postulate in organic reactions is to compare reactivity versus selectivity Reactivity: how fast is the reaction (how large is the E a in the energy diagram) Selectivity: if more than one site is available for reaction the ratio between each product obtained determines the selectivity (the difference in E a for each competing path in the energy diagram) This leads to an almost universal statement in organic chemistry: FOR A GIVEN REACTION THE MORE REACTIVE, THE LESS SELECTIVE

34 Relevance of Radical Chemistry Ozone Depletion Chemistry involved in stratosphere Ozone absorbs light in the nm range

35 Carbon Compounds can also React with Ozone It was discovered that chlorofluorocarbons (CFCs or freons) can react with ozone Therefore the concentration of ozone decreases with more CFCs in the stratosphere and the nm sunlight is not blocked as efficiently Same type of chemistry occurs with bromine radicals (called halons)

36 Biological entities can be destroyed with low wavelength (high energy) sunlight One estimate is that decreasing the ozone concentration by 1% causes a 1-3 % increase in skin cancer Solutions: replace chlorine (and bromine) containing carbon species Possibilities: CHClF 2 less chlorine CH 2 FCF 3 HFC (hydrofluorocarbons)

37 Radical Interactions in Drug Development As observed radicals are reactive species -when generated near biological targets, irreversible damage may occur An example: Calicheamicin γ 1

38 Calicheamicin binds specifically with the minor groove of DNA Yellow and magenta correspond to DNA backbone, Blue is Calicheamicin The binding of Calicheamicin brings reactive group (white in picture) near DNA backbone *R.A. Kumar, N. Ikemoto, D.J. Patel, J. Mol. Biol., 1997, 265, 187.

39 Reactive part (called enediyne) forms a diradical This DNA cleavage can kill cancer cells used in drug Mylotarg for acute leukemia

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