Theoretical calculations of heavy-atom isotope effects

Unprecedently large 37Cl/35Cl equilibrium isotopic fractionation on nano-confinement of chloride anion

Confinement can result in unusual properties leading to new, exciting discoveries in the nano-realm. One such consequence of confinement at the nanoscale is extremally large isotopic fractionation, especially at sub-van der Waals distances. Herein, on the example of chlorine isotope effects, we show that at conditions of nanoencapsulation these effects may reach values by far larger than observed for the bulk environment, which in the case of nanotubes can lead to practical applications (e.g., in isotopic enrichment) and needs to be considered in analytical procedures that employ nanomaterials.

Heavy-Atom Kinetic Isotope Effects: Primary Interest or Zero Point?

Chemists have many options for elucidating reaction mechanisms. Global kinetic analysis and classic transition-state probes (e.g., LFERs, Eyring) inevitably form the cornerstone of any strategy, yet their application to increasingly sophisticated synthetic methodologies often leads to a wide range of indistinguishable mechanistic proposals. Computational chemistry provides powerful tools for narrowing the field in such cases, yet wholly simulated mechanisms must be interpreted with great caution. Heavy-atom kinetic isotope effects (KIEs) offer an exquisite but underutilized method for reconciling the two approaches, anchoring the theoretician in the world of calculable observables and providing the experimentalist with atomistic insights. This Perspective provides a personal outlook on this synergy. It surveys the computation of heavy-atom KIEs and their measurement by NMR spectroscopy, discusses recent case studies, highlights the intellectual reward that lies in alignment of experiment and theory, and reflects on the changes required in chemical education in the area.

Isotopic Consequences of Host-Guest Interactions; Noncovalent Chlorine Isotope Effects

Although weak intermolecular interactions are the essence of most processes of key importance in medicine, industry, environment, and life cycles, their characterization is still not sufficient. Enzymatic dehalogenations that involve chloride anion interaction within a host-guest framework is one of the many examples. Recently published experimental results on host-guest systems provided us with models suitable to assess isotopic consequences of these noncovalent interactions. Herein, we report the influence of environmental and structural variations on chlorine isotope effects. We show that these effects, although small, may obscure mechanistic interpretations, as well as analytical protocols of dehalogenation processes.

On the use of noncompetitive kinetic isotope effects to investigate flavoenzyme mechanism

This account describes the application of kinetic isotope effects (KIEs) to investigate the mechanistic properties of flavin dependent enzymes. Assays can be conducted during steady-state catalytic turnover of the flavoenzyme with its substrate or by using rapid-kinetic techniques to measure either the reductive or oxidative half-reactions of the enzyme. Great care should be taken to ensure that the observed effects are due to isotopic substitution and not other factors such as pH effects or changes in the solvent viscosity of the reaction mixture. Different types of KIEs are described along with a physical description of their origins and the unique information each can provide about the mechanism of an enzyme. Detailed experimental techniques are outlined with special emphasis on the proper controls and data analysis that must be carried out to avoid erroneous conclusions. Examples are provided for each type of KIE measurement from references in the literature. It is our hope that this article will clarify any confusion concerning the utility of KIEs in the study of flavoprotein mechanism and encourage their use by the community.

(12)C/(13)C fractionations in plant primary metabolism

Natural (13)C abundance is now an unavoidable tool to study ecosystem and plant carbon economies. A growing number of studies take advantage of isotopic fractionation between carbon pools or (13)C abundance in respiratory CO(2) to examine the carbon source of respiration, plant biomass production or organic matter sequestration in soils. (12)C/(13)C isotope effects associated with plant metabolism are thus essential to understand natural isotopic signals. However, isotope effects of enzymes do not influence metabolites separately, but combine to yield a (12)C/(13)C isotopologue redistribution orchestrated by metabolic flux patterns. In this review, we summarise key metabolic isotope effects and integrate them into the corpus of plant primary carbon metabolism.

A new scheme to calculate isotope effects

We present a new scheme to calculate isotope effects. Only selected frequencies at the target level of theory are calculated. The frequencies are selected by an analysis of the Hessian from a lower level of theory. We obtain accurate isotope effects without calculating the full Hessian at the target level of theory. The calculated frequencies are very accurate. The scheme converges to the correct isotope effect.

A New Insight into Using Chlorine Leaving Group and Nucleophile Carbon Kinetic Isotope Effects To Determine Substituent Effects on the Structure of SN2 Transition States

Chlorine leaving group k(35)/k(37), nucleophile carbon k(11)/k(14), and secondary alpha-deuterium [(kH/kD)alpha] kinetic isotope effects (KIEs) have been measured for the SN2 reactions between para-substituted benzyl chlorides and tetrabutylammonium cyanide in tetrahydrofuran at 20 degrees C to determine whether these isotope effects can be used to determine the substituent effect on the structure of the transition state. The secondary alpha-deuterium KIEs indicate that the transition states for these reactions are unsymmetric. The theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion; i.e., they suggest that the transition states for these reactions are unsymmetric with a long NC-C(alpha) and reasonably short C(alpha)-Cl bonds. The chlorine isotope effects suggest that these KIEs can be used to determine the substituent effects on transition state structure with the KIE decreasing when a more electron-withdrawing para-substituent is present. This conclusion is supported by theoretical calculations. The nucleophile carbon k(11)/k(14) KIEs for these reactions, however, do not change significantly with substituent and, therefore, do not appear to be useful for determining how the NC-C(alpha) transition-state bond changes with substituent. The theoretical calculations indicate that the NC-C(alpha) bond also shortens as a more electron-withdrawing substituent is placed on the benzene ring of the substrate but that the changes in the NC-C(alpha) transition-state bond with substituent are very small and may not be measurable. The results also show that using leaving group and nucleophile carbon KIEs to determine the substituent effect on transition-state structure is more complicated than previously thought. The implication of using both chlorine leaving group and nucleophile carbon KIEs to determine the substituent effect on transition-state structure is discussed.

Investigation of the mechanism of nicotine demethylation in Nicotiana through 2H and 15N heavy isotope effects: implication of cytochrome P450 oxidase and hydroxyl ion transfer

Heavy-atom isotope effects for the N-demethylation of nicotine have been determined in vivo in static-phase biosynthetically incompetent plant cell cultures of Nicotiana species. A (2)H kinetic isotope effect of 0.587 and a (15)N kinetic isotope effect of 1.0028 were obtained. An identical (15)N kinetic isotope effect of 1.0032 was obtained for the nicotine analogue, N-methyl-2-phenylpyrrolidine. The magnitude of the (15)N heavy-atom isotope effect indicates that the fission of the CN bond is not rate limiting for demethylation. The theoretical calculation of heavy-atom isotope effects for a model of the reaction pathway based on cytochrome P450 best fits the measured kinetic isotope effect to the addition of hydroxyl ion to iminium to form N-hydroxymethyl, for which the computed (2)H- and (15)N kinetic isotope effects are 0.689 and 1.0081, respectively. This large inverse (2)H kinetic isotope effect is not compatible with the initial abstraction of the H from the methyl group playing a significant kinetic role in the overall kinetic limitation of the reaction pathway, since computed values for this step (4.54 and 0.9995, respectively) are inconsistent with the experimental data.

Viewpoint: How large is the carbon isotope fractionation of the photorespiratory enzyme glycine decarboxylase?

Despite the intense effort developed over the past 10 years to determine the ¹²C / ¹³C isotope fractionation associated with photorespiration, much uncertainty remains about the amplitude, and even the sign, of the ¹²C / ¹³C isotope fractionation of glycine decarboxylase, the enzyme that produces CO₂ during the photorespiratory cycle. In fact, leaf gas-exchange data have repeatedly indicated that CO₂ evolved by photorespiration is depleted in ¹³C compared with the source material, while glycine decarboxylase has mostly favoured ¹³C in vitro. Here I give theoretical insights on the glycine decarboxylase reaction and show that (i), both photorespiration and glycine decarboxylation must favour the same carbon isotope - the in vitro measurements being probably adulterated by the high sensitivity of the enzyme to assay conditions and the possible reversibility of the reaction in these conditions, and (ii), simplified quantum chemistry considerations as well as comparisons with other pyridoxal 5'-phosphate-dependent decarboxylases indicate that the carbon isotope fractionation favour the ¹²C isotope by ~20‰, a value that is consistent with the value of the photorespiratory fractionation (f) obtained by gas-exchange experiments.

Viewpoint: Isotopic fractionation by plant nitrate reductase, twenty years later

Plant nitrate reductase, the enzyme that reduces nitrate (NO₃^-) to nitrite (NO₂^-), is known to fractionate N isotopes, depleting nitrite in ¹⁵N compared with substrate nitrate. Nearly 20 years ago, the nitrogen isotope effect associated with this reaction was found to be around 1.015. However, the relationships between the isotope effect and the mechanism of the reaction have not yet been examined in the light of recent advances regarding the catalytic cycle and enzyme structure. We thus give here the mathematical bases of the ¹⁴N / ¹⁵N and also the ¹⁶O / ¹⁸O isotope effects as a function of reaction rates. Enzymatic nitrate reduction involves steps other than NO₃^- reduction itself, in which the oxidation number of N changes from +V (nitrate) to +III (nitrite). Using some approximations, we give numerical estimates of the intrinsic N and O isotope effects and this leads us to challenge the assumptions of nitrate reduction itself as being a rate-limiting step within the nitrate reductase reaction, and of the formation of a bridging oxygen as a reaction intermediate.

Viewpoint: Carbon isotope effect predictions for enzymes involved in the primary carbon metabolism of plant leaves

Carbon isotope effects of enzymes involved in primary carbon metabolism are key parameters in our understanding of plant metabolism. Nevertheless, some of them are poorly known because of the lack of in vitro experimental data on purified enzymes. Some studies have focused on theoretical predictions of isotope effects. Here we show how quantum chemical calculations can be adapted for calculation of isotope effects for the Rubisco-catalysed carboxylation and oxygenation reactions and the citrate synthase reaction. The intrinsic isotope effect of the carboxylation by Rubisco appears to be much smaller than previously thought, being close to the overall isotope effect of the reaction that is, between 25 and 30 per mil. The same applies to the enzyme citrate synthase, that catalyses the first step of the Krebs cycle, with an isotope effect of around 23 per mil. Combined with the isotope effects of equilibrium reactions calculated with β-factors, the Krebs cycle then has an overall isotope effect that depletes organic acids in ¹³C.

Chlorine kinetic isotope effects on enzymatic dehalogenations

Enzymatic dehalogenation reactions are important for the bioremediation of the environment because of the increasing anthropogenic pollution with halogen-containing organic compounds. Chlorine kinetic isotope effects have been measured for four hydrolytic dehalogenases. On the basis of these isotope effects, several details of the mechanisms of the enzymatic dehalogenation reactions have been revealed.

Computational study of the influence of solvent on (16)O/(18)O equilibrium isotope effects in phosphate deprotonation reactions

Results from theoretical calculations of (16)O/(18)O equilibrium isotope effects (EIEs) on deprotonation of phosphate and methyl phosphate monoanions as well as their deuterated counterparts are reported. The EIEs are calculated from the Bigeleisen equation using harmonic vibrational frequencies from several quantum mechanical methods (HF, DFT, MP2, and AM1). All methods correctly predict the qualitative trends in the EIEs related to the different isotope substitutions. However, the calculated gas-phase values are found to be systematically higher than those experimentally observed in aqueous solution. On the other hand, the addition of explicit solvent molecules (up to 24 waters) in the first solvation shells of the phosphate ion substantially improves the calculated EIE, which approaches the experimental value with increasing size of the water cluster. The large effects of surrounding water molecules on the phosphate deprotonation EIE can be explained by the strong solute-solvent interactions, which result in solvent coupled vibrational modes of the phosphate ions.

Thermolysis of alkyl sulfoxides and derivatives: a comparison of experiment and theory

Gas-phase activation data were obtained for model sulfoxide elimination reactions. The activation enthalpy for methyl 3-phenylpropyl sulfoxide is 32.9 +/- 0.9 kcal/mol. Elimination by methyl vinyl sulfoxide to form acetylene has an enthalpic barrier of 41.6 +/- 0.8 kcal/mol and that of 3-phenylpropyl methanesulfinate to form hydrocinnamaldehyde is 34.6 +/- 0.6 kcal/mol. Calculations at the MP2/6-311+G(3df,2p)//MP2/6-31G(d,p) level for simplified models of these reactions provide barriers of 32.3, 40.3, and 32.7 kcal/mol, respectively. A series of other compounds are examined computationally, and it is shown that the substituent effects on the sulfoxide elimination reaction are much more straightforward to interpret if DeltaH data are available in addition to the usually determined DeltaH++. The activation enthalpy of the reverse addition reaction is also subject to structural variation and can usually be rationalized on the basis of nucleophilicity of the sulfur or polarity matching between the sulfenic acid and olefin derivative.

13C and (15)N Kinetic Isotope Effects on the Decarboxylation of 3-Carboxybenzisoxazole. Theory vs Experiment

Nitrogen and carbon kinetic isotope effects were measured on the decarboxylation of 3-carboxybenzisoxazole at room temperature. The nitrogen isotope effect in acetone is 1.0312 +/- 0.0006. The carbon isotope effect shows no dependence on the solvent polarity: 1.0448 +/- 0.0007 in 1,4-dioxane, 1.0445 +/- 0.0001 in acetonitrile, 1.0472 +/- 0.0013 in DMF, and 1.0418 +/- 0.0027 in water. These isotope effects were modeled theoretically at the semiempirical (AM1, PM3, SAM1) and ab initio (up to B3LYP/6-31++G) levels. The comparison of the theoretical and experimental results leads to the conclusion that none of the theory levels employed is capable of quantitatively predicting these isotope effects.