Single-molecule reactions

I. Tinoco, Jr. and C. Bustamante, The effect of force on thermodynamics and kinetics of single molecule reactions. Biophys. Chem. 102, 513—533 (2002). 

Part V focuses on single molecule chemistry at metal surfaces. Herein the chapter by S. W. Hla and K. Braun describes how the STM can be used to induce single molecule reactions, starting from bond breaking all the way to bond formation. The chapter by N. Lorente deals with atomic scale vibrational spectroscopy studies and how they allow to obtain chemical information on individual molecules. 

Kim, Y., Komeda, T. and Kawai, M. (2002) Single-molecule reaction and characterization by vibrational excitation. Phys. Rev. Lett., 89, 126104-126104-4. 

Hsin, T.M. and Yeung, E.S. (2007) Single-molecule reactions in liposomes. Angeweldte Chemie International Edition, 46 (42), 8032-8035. 

The tertiary alcohol is prone to generate carbocation under acidic condition. Therefore, the mechanism of tert- esterification is different from that of the primary and secondary alcohol, it follows the single-molecule reaction process(shown in Figure 4) The tertiary alcohol combines with protons to generate protonated alcohol(l) The protonated alcohol is got rid of a molecule water to produce tert-carbocation(2), which is very stable Then the electrophilic attacking is taken place between the tert-carbocation and oxygen atom of carboxylate, the protonated ester(3) is yielded The loss of a proton from the protonated ester gives the product(4) (Bart et al., 1994). 

Chemical reactions can be studied at the single-molecule level by measuring the fluorescence lifetime of an excited state that can undergo reaction in competition with fluorescence. Reactions involving electron transfer (section C3.2) are among the most accessible via such teclmiques, and are particularly attractive candidates for study as a means of testing relationships between charge-transfer optical spectra and electron-transfer rates. If the physical parameters that detennine the reaction probability, such as overlap between the donor and acceptor orbitals. 

Sauer M, Drexhage K H, Lieberwirth U, Muller R, Nerd S and Zander C 1998 Dynamics of the electron transfer reaction between an oxazine dye and DNA oligonucleotides motored on the single-molecule level Chem. Phys. Lett. 284 153-63... 

Tokunaga M, Kitamura K, Saito K, Iwane A H and Yanagida T 1997 Single molecule imaging of fluorophores and enzymatic reactions achieved by objective-type total internal reflection fluorescence microscopy Biochem. Biophys. Res. Commun. 235 47-53... 

Craig D B, Arriaga E A, Wong J C Y, Lu H and Dovichi N J 1996 Studies on single alkaline phosphatase molecules reaction rate and activation energy of a reaction catalyzed by a single molecule and the effect of thermal denaturation—the death of an enzyme J. Am. Chem. See. 118 5245-53... 

In the mid 1970s, Ugi and co-workers developed a scheme based on treating reactions by means of matrices - reaction (R-) matrices [16, 17]. The representation of chemical structures by bond and electron (BE-) matrices was presented in Section 2.4. BE-matrices can be constructed not only for single molecules but also for ensembles of them, such as the starting materials of a reaction, e.g., formaldehyde (methanal) and hydrocyanic add as shown with the B E-matrix, B, in Figure 3-12. Figure 3-12 also shows the BE-matrix, E, of the reaction product, the cyanohydrin of formaldehyde. 

Caution For ion ic reaction s in solution, solven t effects can play a sign ificari I roic. fhesc, of course, arc neglected in calculation s on a single molecule. You can obtain an indication of solvent effects from sem i-eni pirical calculations by carefully adding water molecules to th e solute m olectile. 

In comparing the reactivity at different positions in a heterocycle, a poly-substituted derivative is sometimes used with the idea that selective reaction of the same leaving group at different positions in a single molecule gives the most clear-cut answer. However, in a polychloroazine, the mutual activation of the chlorines by one another is not identical (unless the molecule is symmetrical, in which case the... 

At its best, the study of solvent kies by the formalism given can be used to learn about proton content and activation in the transition state. For this reason it is known as the proton inventory technique. The kinetics of decay of the lowest-energy electronic excited state of 7-azaindole illustrates the technique.25 Laser flash photolysis techniques (Section 11.6) were used to evaluate the rate constant for this very fast reaction. From the results it was suggested that, in alcohol, a double-proton tautomerism was mediated by a single molecule of solvent such that only two protons are involved in the transition state. In water, on the other hand, the excited state tautomerism is frustrated such that two water molecules may play separate roles. Diagrams for possible transition states that can be suggested from the data are shown, where of course any of the H s might be D s. 

The above results pertain to reactions in solution. In the gas phase reactions can take a different course, as illustrated by the reaction of carboxylic esters with MeO, which in the gas phase was shown to take place only by the Bal2 mech-anism, ° even with aryl esters, ° where this means that an Sn2 mechanism takes place at an aryl substrate. However, when the gas-phase reaction of aryl esters was carried out with MeO ions, each of which was solvated with a single molecule of MeOH or H2O, the Bac2 mechanism was observed. 

In APCI, droplets are generated by a combination of heat and a nebulizing gas. While the analytes are embedded in a droplet, and thus protected to some extent from the heat, many thermally labile materials are decomposed. In addition, ionization occurs mainly by ion-molecule reactions and yields predominantly singly charged ions. If, therefore, compounds do not undergo thermal degradation, a mass spectrometer with extended mass range would be required to detect any ions formed. 

These propagation reactions are circular. They consume a methane radical but also generate one. There is no net consumption of free radicals, so a single initiation reaction can cause an indefinite number of propagation reactions, each one of which does consume an acetaldehyde molecule. Ignoring any accumulation of methane radicals, the overall stoichiometry is given by the net sum of the propagation steps ... 

In contrast to chain transfer, termination reactions destroy free radicals. Two mechanisms are considered. Termination by combination produces a single molecule of dead polymer ... 

As an example, consider the industrial synthesis of ammonia (NH3). Ammonia is made by the Haber process, a single chemical reaction between molecules of hydrogen (H2) and nitrogen (N2) Although it is simple, this synthesis has immense industrial importance. The United States produces more than 16 billion kilograms of ammonia annually. 

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