CHAPT R 8 Experiments Related to Thermodynamics and Kinetics Intent and Purpose The intent of this chapter is to teach several of the experimental tools routinely applied by’ physical organic chemists in the study of reaction mechanisms. The majority of these meth- s build upon an analysis of kinetics and thermodynamics, providing a natural progres sion from the previous chapter. Both the theory behind the methodsand their application are covered, and many methods are illustrated by example. ‘The first topic isisotope effects. We consider the origin of isotope effects, what informa- tion they provide, and how they are analyzed. This includes solvent isotope effects, which are very relevant tothe analysis of enzymatic reactions. After isotope effects, we delve into linear free energy relationships (LFERS), and show how structural changes can be used in a systematic way to gain insight into the nature of reactive intermediates. Electronic substi tuent effects (Hammett plots) are discussed in detail, but we also examine how structural changes in the solvent, nucleophile, and nucleofuge (a synonym for leaving group) can be used to probea reaction mechanism. Itis particularly instructive within the context of linear free energy relationships to examine trends in reactivity. Hence, in this chapter we also dis- cuss the general effects of electron withdrawing and donating groups, changes in the ioniz~ ing power of the solvent, steric effects, and changes in nucleophilicty and leaving group ability (nucleofugality). The notionsare not specifi to individual reaction types, so they are discussed here instead of being examined only in the context of specific mechanisms in the next chapters. Finally, a variety of experiments that do not fit under any single heading are examined, such a5 cross-over experiments, scrambling experiments, clocks, etc. These ex- periments can be extremely important. We delineate the general approach used in each ex- perimental type, but teach the methods mostly by example, Inall the sections ofthis chapter, examples are drawn from the literature. In do show that the tools of physical organic chemistry are used in most chemical subdisciplines Ourexamples come from enzymology, bioorganic chemistry, organometallic chemistry, and. traditional small molecule organic chemistry. Our intention is for the student to learn how general the experiments discussed herein are, so that he or she will immediately incorporate them into his or her repertoire for studying chemical reactivity 8.1 Isotope Effects Inour analysis of kinetics in the last chapter, we emphasized that the information gained is limited, and that most studies of mechanisms involve other techniques. One piece of infor- mation that cannot be gained froma kinetic study is what bonds have been broken, formed, orrehybridized during the rate-determining step. Isotope effects can provice just this kind of information, Substituting one isotope for another at or near an atom at which bonds are breaking or rehybridizing typically leads to a change in the rate of the reaction. When the bonds being broken or formed involve those to hydrogen, the effect of replacing H with D often isrelatively largeand can be measured routinely. Isotope effects with other atoms have 421422 also been studied, but the effects are typically small and sometimes difficult to quantify. ‘Therefore, our discussion of isotope effects will focus on hydrogen, although we givea brief introduction to heavy atom isotope effects later. 8.11 The Experiment Anisotope effect is measured to determine if the bond at which the isotopic substitu isbeing made changes in some manner during the rate-determining step. We express an iso- tope effect as a ratio of rate constants, where the numerator isthe rate constant for the reac- tion with the natural abundance isotope, and the denominator is the rate constant for the re- action with the altered isotope. For example, when measuring isotope effects for reactions involving a substitution of hydrogen with deuterium, the isotope effect would be expressed. a ky:/ko- Measuring an isotope effect, therefore, typically requires us to run two kinetic analyses or to design a clever competition experiment. For a hydrogen isotope effect, typically a first order (or pseudo-first order) rate constant for the reaction of interest is determined with the bond that is being analyzed (X-H) having a natural abundance distribution of isotopes. This is because the natural abundance of deu- terium and tritium (0.015% and 1 X 10~%, respectively) is so low that their contribution to the rate is negligible. Next, the rate constant for the same reaction is determined with a ver- sion of the molecule in which synthesis (or solvent exchange; see Section 8.1.6) has intro- duced nearly 1007 deuterium in place of the hydrogen. ‘The magnitude of the isotope effect (the variation of k,/ky from unity) gives us i mation about the reaction mechanism. If y/ky is 1, one conclusion would be that the bond. where the substitution occurred is not changing during the rate-determining step. However, itmay just be that the isotope effect is too small to be measured accurately. Ifthe ratio of ky / {iyi different from one, more solid conclusions can be drawn, When ky/p is greater than ‘one, we cal the isotope effect normal. When ky,/fo is less than one, we call the isotope effect inverse. When the isotope effect can be attributed to a bond breaking event at the X-H/X-D bond, itis referred toas a primary isotope effect. When the effect isattributed to. rehybrid- ization or arises from isotopic substitution remote from the bonds undergoing reaction, itis referred toasa secondary isotope effect. The situation we have discussed thus far, in which the isotope substitution changes the rate of the reaction, is called a kinetic isotope effect (KIE). When the interchange of isotopes alters the position of an equilibrium, we call it an equilibrium isotope effect. 841.2. The Origin of Primary Kinetic Isotope Effects The origin of all isotope effects is the difference in frequencies of various vibrational mocles of a molecule that arise when one isotope is substituted with another. Let’ first ana- lyzea bond thatisbreaking during the rate-determining step ofa reaction (a primary kinetic isotope effec). Toa good approximation, the potential energy of the system does not change with substitution of one isotope for another. In other words, the relative energies ofthe min- ima and maxima on the energy surface do not change with isotopic substitution. However, we noted in Chapter thatthe shapes of the potential wells on an energy surface are compos- ites ofthe various vibrational states of the molecule. When considering a reaction, itis suff cient to consider the shapes of these wells as being dominated by the vibrational modes that are undergoing the most change during, the reaction. Recall from our discussion of IR spectroscopy (Section 2.1.4) that vibrational states are quantized, and that each potential energy well has several rungs that represent different en- cergies for that vibrational mode (Figure 2.2) The formula for the quantized energies (¢,) of the vibrational modesis given in Eq. 8.1, where vis the frequency of the vibrational mode be- ing considered. These energies are measured from the lowest point in the potential energy well. Atambient temperature, the vibrational modes for bond stretches are dominated by n= 0, with eg = iv. Thisenergy is referred to as the zero-point energy (ZPE) ty (neg 3) n=0,12,~ (Eq.8.1)