Reaction Mechanisms & Pathway

Reaction mechanism, or reaction pathway, describes the successive steps at the molecular level that take place in a chemical reaction. In each step, molecular bonds are either created or broken. Reaction mechanisms are postulated, and then either supported or disproved but the overarching conditions for defining a reaction mechanism/reaction pathway is that all of the discrete steps together make sense with regard to the overall reaction equation, and that the rate law for the slowest step complies with the empirically measured overall rate.

The individual steps that make up most reaction mechanisms are described as unimolecular or bimolecular. A unimolecular mechanism occurs when a molecule either dissociates to form two species or undergoes internal rearrangement. The rate equation for a unimolecular reaction is described as first order since it only depends on the concentration of one reactant and is written as d[A]/dt= - k[A], where k is the rate constant. A bimolecular reaction occurs when two molecules combine and the rate equation is d[A]/dt = - k[A][B] (second order) or second order in one of the molecular species, d[A]/dt = - k[A]²

There are a number of mechanisms frequently used to explain a reaction. For example, in nucleophilic substitution reactions, the nucleophile brings an electron pair to the substrate molecule and the leaving group departs with an electron pair. In the S_n2 mechanism, the bimolecular substitution is a single step process in which no intermediate forms. The nucleophile attacks and the leaving group departs simultaneously. In the unimolecular substitution S_n1 mechanism, there is a slow ionization of the substrate, forming a transition state carbonium ion that is quickly attacked by the nucleophile. In this reaction, the rate determining step is the formation of the transition state carbonium ion.

Another example of a common reaction mechanism is electrophilic substitution. As in the S_n2 reaction, in SE2 mechanism, the new bond forms at the same time that the old bond breaks. In the S_n2 mechanism, the incoming group attacks at a position that is 180 degrees from the leaving group, due to repelling electron clouds so the location of the ligands on the molecule is different. In the SE2 mechanism, the incoming group can approach from the same side, leading to retention of configuration. 

Chemical reactions can be complex and competing reactions are commonplace, further complicating outcomes. With this much complexity and diversity, the chemist must understand the fundamentals of why molecules react, thus enabling logic and predictability in comprehending how a reaction is likely to proceed. By correctly understanding the mechanisms occurring in the elementary reaction steps, one can begin to understand how to affect the overall result.

For example, some elementary steps may result in important transient species or intermediates that are transition states to the final product or side products. Understanding the mechanisms in the sequential elementary steps of a reaction provides insight into how modifying reaction conditions can affect the overall reaction outcome, purity, and reaction rates.

Reaction mechanisms are postulated and then either supported or disproved. The requisite experimental data typically arises from measuring the kinetics of the key reaction species, which allows the calculation of rate laws for the individual steps comprising and consistent with the proposed reaction mechanism.

The analytical methodology for making these kinetic measurements are broadly classified as online and offline. Online techniques are widely used because of the significant volume of data that is collected as a function of time. With online methods, rather than running a large number of reactions to understand rate dependencies, just a few experiments can provide the necessary information to determine the driving forces that support a reaction mechanism. Moreover, transient reaction species, which often have an important role in reaction mechanism, are preserved by in-situ methods. Other online methods include UV/Vis, Nuclear Magnetic Resonance (NMR), and Mass Spectrometry (MS). The choice of technology used depends on the type of reaction being studied and the specific information required.

For certain reactions, such as those where low concentration species need to be tracked or where complex reaction mixtures require physical separation of compounds, removing a sample of reaction mixture at timed intervals, combined with offline analysis, is the best approach to obtain kinetic information. This process is tedious and problematic for chemistries that are:

• Slurries
• Operating at Elevated Pressure
• Low Temperature and/or For Reactions With Transient Intermediates
• Highly Exothermic

EasySampler allows unattended, automated sampling of reactions, and eliminates many of the aforementioned difficulties. When EasySampler is used in conjunction with chemical reactors, which enable reactions to be run with controlled parameters, accurate kinetic information is obtained on these complex reaction mixtures.

FTIR spectroscopy equipment is often used in conjunction with offline analytical techniques for a complete understanding of reaction kinetics and mechanism. Also, the use of EasySampler with HPLC offline measurements provides the data necessary to calibrate online spectroscopic methods, permitting the latter methods to report data as concentration vs. time, rather than absorbance vs. time.

ReactIR is an in-situ, real-time technique that provides second-by-second mid-IR vibrational spectra of a chemical reaction, under actual reaction conditions. By tracking individual reactions species as they change as a function of time and variables, detailed information is obtained about the individual elementary steps that contribute to a hypothesized reaction mechanism. Also, since reactions are measured without the need to remove a sample, transient intermediates, which are critical clues to reaction mechanisms, are preserved and identified.

• Study chemical reactions under actual reaction conditions
• Identify, track, and measure key reaction species including by-products formed
• Observe intermediate compounds that are critical clues to reaction mechanism
• Determine reaction kinetics of elementary steps to support postulated mechanism
• Test the effect of variables on reaction outcome and predicted reaction mechanism

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Manual sampling of chemical reactions for offline analysis by HPLC to determine reaction progress or impurity profiles is standard practice. Manual sampling is not always a precise operation and can be challenging or even hazardous with reactions at high or low temperatures, elevated pressures, with toxic reactants present, high exothermicity or reactions containing slurries. Manually sampled reaction mixtures must be then quenched and delays can lead to variable results and inaccuracies in the analytical information gained. EasySampler was designed to eliminate these challenges by providing an automated and robust inline method of taking representative samples from reactions, even at extreme conditions.

EasySampler provides automated, timed samples for offline analysis to measure:

• Product Quality and Yield
• Impurity Profiling
• By-Product Formation
• Reaction Trends and Progress
• Reaction Kinetics and Mechanism
• Reaction Species: in support of calibrating online spectroscopic analyses (ReactIR, ReactRaman)

ReactIR and ReactRaman are in-situ, real-time techniques that provide second-by-second spectra of a chemical reaction, under actual reaction conditions. By tracking individual reactions species as they change as a function of time and variables, detailed information is obtained about the individual elementary steps that contribute to a hypothesized reaction mechanism. Also, since reactions are measured without the need to remove a sample, transient intermediates, which are critical clues to reaction mechanisms, are preserved and identified.

• Study chemical reactions under actual reaction conditions
• Identify, track, and measure key reaction species including by-products formed
• Observe intermediate compounds that are critical clues to reaction mechanism
• Determine reaction kinetics of elementary steps to support postulated mechanism
• Test the effect of variables on reaction outcome and predicted reaction mechanism

Below is a selection of industry-related publications where inline techniques were used for mechanistic understanding:

• Hammarback, L.A., Robinson, A., Lynam, J., Fairlamb, I., “Mechanistic Insight into Catalytic Redox-Neutral C−H Bond Activation Involving Manganese(I) Carbonyls: Catalyst Activation, Turnover, and Deactivation Pathways Reveal an Intricate Network of Steps”, J. Am. Chem. Soc., 2019, 141 (6), pp 2316–2328.
• McMillan,A., Steven, A., Ashworth, I., Mullen, A., Chan, L., Espinosa, M., Pilling, M., Raw S., Jones, M., “Stereoretentive Etherification of an α-aryl-β-amino-alcohol using a Selective Aziridinium Ring-Opening for the Synthesis of AZD7594”, J. Org. Chem, Excellence in Industrial Organic Synthesis 2019, 6/19/2018
• Nicholls, R., McManus, J., Rayner, C., Morales-Serna, J., White, A., Nguyen B., “Guanidine-Catalyzed Reductive Amination of Carbon Dioxide with Silanes: Switching between Pathways and Suppressing Catalyst Deactivation“, ACS Catal. 2018, 8, 3678−3687
• Kutsumura, N., Koyama, Y., Suzuki, Y., Tominaga, K., Yamamoto, N., Saitoh, T., Nagumo, Y., Nagase, H., “Favorskii-Type Rearrangement of the 4,5-Epoxymorphinan Skeleton”, Org. Lett. 2018, 20, 1559−1562.
• Hua, A., Mai, D., Martinez, R., Baxter, R., “Radical C−H Fluorination Using Unprotected Amino Acids as Radical Precursors”, Org. Lett., 2017, 19 (11), pp 2949–2952
• Wen, G., Zhang, W-X., Wu, S., “A Novel Synthesis of 4-Acetoxyl 5(4H)-Oxazolones by Direct α-Oxidation of N-Benzoyl Amino-Acid Using Hypervalent Iodine”, Molecules, 2017, 22, 1102.
• Griffiths, J., Hofman, E., Keister, J., Diver, S., “Kinetics and Mechanism of Isocyanide-Promoted Carbene Insertion into the Aryl Substituent of an N‑Heterocyclic Carbene Ligand in Ruthenium-Based Metathesis Catalysts”, Organometallics 2017, 36, 3043−3052.
• Duan, S., Place, D., Perfect, H.H., Ide, N.D., Maloney, M., Sutherland, K., Price Wiglesworth, K.E.; Wang, K., Olivier, M., Kong, F., Leeman, K., Blunt, J., Draper, J., McAuliffe, M., O’Sullivan, M., Lynch, D. , "Palbociclib Commercial Manufacturing Process Development. Part I: Control of Regioselectivity in a Grignard-Mediated SNAr Coupling", Org. Process Res. Dev. 2016, 20, 1191−1202.

Duan, S., Place, D., Perfect, H.H., Ide, N.D., Maloney, M., Sutherland, K., Price Wiglesworth, K.E.; Wang, K., Olivier, M., Kong, F., Leeman, K., Blunt, J., Draper, J., McAuliffe, M., O’Sullivan, M., Lynch, D. , Palbociclib Commercial Manufacturing Process Development. Part I: Control of Regioselectivity in a Grignard-Mediated SNAr Coupling", Org. Process Res. Dev. 2016, 20, 1191−1202.

Palbococlib received accelerated approval from the FDA for the treatment of advanced breast cancer in postmenopausal women. In this study, the authors describe their process development program to further develop and optimize the process for the commercial manufacture of Palbociclib to improve scalability, efficiency and quality of the enabling process. There was a need to reduce the usage factor of an advanced intermediate, therefore mechanistic studies were necessary to understand why the second equivalent of the intermediate was necessary.

ReactIR monitored reaction progress and provided some insight into the reaction mechanism. Data confirmed the instantaneous deprotonation of the advanced intermediate upon addition of LiHMDS. Subsequent addition of pyrimidine resulted in the formation of a small amount of desired product and a larger amount of an intermediate that slowly converted to desired product.

EasySampler enabled the researchers to collect multiple reaction samples, and automatically quench at the time of sampling. The high-quality samples were used for structure elucidation to understand the reaction mechanism. 

Tsang, A., Kapat, A., Schoenebeck,F., “Factors That Control C−C Cleavage versus C−H Bond Hydroxylation in Copper-Catalyzed Oxidations of Ketones with O2”, J. Am. Chem. Soc. 2016, 138, 518−526.

In this project, the authors explore the mechanisms by which copper catalyzed oxidation of ketones with O2 can cleave the α-C−C bond and/or cause selective hydroxylation of tertiary α-C−H bonds without C−C cleavage. The project investigated the importance of various factors on the selectivity associated with the α-C−H bond hydroxylation versus C−C bond cleavage of ketones in the copper catalyzed reaction and explored different mechanistic pathways.

In-situFTIR measurements show the presence of IR bonds consistent with the formation both an α-hydroxy ketone and a C-C cleaved product from the ketone substrate. ReactIR data shows that the two products form simultaneously, suggesting that the formation of the cleaved C-C product does not arise from continued oxidation of the α-hydroxy ketone, but rather that the two products originate from a single hydroperoxide intermediate.