Single-molecule force spectroscopy measurements of bond elongation during a bimolecular reaction

It is experimentally challenging to directly obtain structural information of the transition state (TS), the high-energy bottleneck en route from reactants to products, for solution-phase reactions. Here, we use single-molecule experiments as well as high-level quantum chemical calculations to probe the TS of disulfide bond reduction, a bimolecular nucleophilic substitution (S N2) reaction. We use an atomic force microscope in force-clamp mode to apply mechanical forces to a protein disulfide bond and obtain force-dependent rate constants of the disulfide bond reduction initiated by a variety of nucleophiles. We measure distances to the TS or bond elongation (Delta x), along a 1-D reaction coordinate imposed by mechanical force, of 0.31 +/- 0.05 and 0.44 +/- 0.03 A for thiol-initiated and phosphine-initiated disulfide bond reductions, respectively. These results are in agreement with quantum chemical calculations, which show that the disulfide bond at the TS is longer in phosphine-initiated reduction than in thiol-initiated reduction. We also investigate the effect of solvent environment on the TS geometry by incorporating glycerol into the aqueous solution. In this case, the Delta x value for the phosphine-initiated reduction is decreased to 0.28 +/- 0.04 A whereas it remains unchanged for thiol-initiated reduction, providing a direct test of theoretical calculations of the role of solvent molecules in the reduction TS of an S N2 reaction. These results demonstrate that single-molecule force spectroscopy represents a novel experimental tool to study mechanochemistry and directly probe the sub-?ngstr?m changes in TS structure of solution-phase reactions. Furthermore, this single-molecule method opens new doors to gain molecular level understanding of chemical reactivity when combined with quantum chemical calculations.     

Single-molecule force spectroscopy for studying kinetics of enzymatic dextran elongations

Catalytic elongation of dextran by a single molecule of dextransucrase (DSase) was directly monitored by observing the movements of the positions of a rupture peak, which represented the adhesive force between an isomaltoheptaose (dextran 7-mer)-immobilized probe and a DSase-immobilized mica surface. This was initiated with the addition of sucrose monomers. From the histograms of the rupture peaks after elongation reactions on each individual enzyme and the continuous peak shift of certain single enzymes, the catalytic elongation rate constant (k(cat)) was ascertained to be 1.2-2.7 s(-1).     

Single-molecule force spectroscopy of selenium-containing amphiphilic block copolymer: toward disassembling the polymer micelles

Selenium-containing polymers are a new type of responsive polymer material. Here, a selenium-containing amphiphilic block copolymer (PEG-PUSe-PEG) has been investigated using atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS). The deviation between force-extension curves of PEG-PUSe-PEG in water and in DMSO is found to be related to the disassembly of the micellar structures in water. SMFS experiments on PEG-PUSeox-PEG suggest that the change from selenide to oxidized selenone contributes significantly to the change in amphiphilicity, without obviously influencing the single-chain elasticity.     

Alkyl exchange reactions of organocobalt porphyrins. A bimolecular homolytic substitution reaction

Reaction of organocobalt(III) porphyrins with a cobalt(II) complex of a distinguishable porphyrin or tetrapyrrole resulted in the reversible exchange of the organic axial ligand. The exchange reaction was facile in such solvents as benzene, toluene, dichloromethane, chloroform, and pyridine; was unaffected by total exclusion of light; was faster than would be expected for a homolytic process given known Co-C bond dissociation energies; and was of broad scope with respect to the organic ligand. Methyl, benzyl, primary alkyl, secondary alkyl, and acyl groups exchanged, but phenyl groups did not. The position of the exchange equilibrium was independent of the direction of approach and was nonstatistical. The relaxation to equilibrium appeared to be consistent with that of a second-order process. The rate of the reaction varied with the identity of the R group in the order Bzl > or = Me > Et approximately n-Pr > i-Pr > i-Bu > acetyl approximately neopentyl approximately 2-adamantyl. However, the total variation in reaction rates was remarkably small. Attempts to find evidence of free-radical intermediates by trapping with TEMPO or CO or by alkyl group interchange with an excess of an alkyl halide of a distinct alkyl group were unsuccessful over a time scale comparable to multiple half-lives of the exchange reaction. In addition, no rearrangement products were detected in exchange reactions of the 5-hexenyl group. Use of cobalt porphyrin reactants that were sterically encumbered on both faces with groups large enough to prevent formation of a bridged, Co-C-Co structure resulted in a 5 or more order of magnitude decrease in the rate of methyl exchange, if not its outright cessation, when run with total exclusion of light. The decrease in the rate of the thermal exchange process revealed the existence a slow photochemical exchange process that was driven by room lights. All evidence was consistent with a bimolecular S(H)2 mechanism for the thermal exchange mechanism.     

Promoting effect of ionic liquids on ligand substitution reactions

Ionic liquid solvents N-hexylpyridinium bistrifylimide ([C₆pyr][Tf₂N]] and 1-butyl-3-methylimidazolium hexafluorophosphate ([C₄mim][PF₆]) promoted the displacement of anionic ligands by pyridine derivatives in trans-(Ph₃P)₂Rh(CO)NO₃ to a much greater extent than did dichloromethane. Thus, addition of a slight excess of 2-fluoropyridine to trans-(Ph₃P)₂Rh(CO)NO₃ in [C₄mim][PF₆] gave a 29:71 product mixture of trans-(Ph₃P)₂Rh(CO)NO₃:[trans-(Ph₃P)₂Rh(CO)(2-fluoropyridine)][NO₃], while the ratio was 91:9 in dichloromethane.     

Single-molecule force spectroscopy measurements of "hydrophobic bond" between tethered hexadecane molecules

The hydrophobic effect is important for many biological and technological processes. Despite progress in theory, experimental data clarifying water structure and the interaction between hydrophobic solutes at the nanometer scale are scarce due to the very low solubility of hydrophobic species. This article describes an AFM single molecule force spectroscopy method to probe the interaction between molecules with low solubility and reports measurements of the strength and the length scale of the "hydrophobic bond" between hexadecane molecules. Hexadecane molecules are tethered by flexible poly(ethylene glycol) linkers to AFM probes and substrates, removing the aggregation state uncertainty of solution-based approaches as well as spurious surface effects. A shorter hydrophilic polymer layer is added to increase the accessibility of hydrophobic molecules for the force spectroscopy measurements. Statistical analysis of the rupture forces yields a barrier width of 0.24 nm, and a dissociation rate of 1.1 s(-1). The results of single molecule measurements are related to the theoretical predictions of the free energy of cavitation in water and to the empirical model of micellization of nonionic surfactants. It is estimated that approximately one-quarter of each molecule's surface is hydrated during forced dissociation, consistent with an extended (nonglobular) conformation of the hexadecane molecules in the dimer.     

Rapid ligand substitution reactions in ionic liquids studied by stopped-flow technique

Detailed kinetic studies on ligand substitution reactions of [M(II)(terpy)Cl](+) complexes (M = Pt, Pd; terpy = 2,2':6',2'-terpyridine) with thiourea as entering nucleophile were for the first time performed in the imidazolium based ionic liquid [emim][NTf(2)] using stopped-flow techniques, opening the route to study fast reactions of transition metal complexes in ionic liquids.     

Recent advances in crossed-beam studies of bimolecular reactions

A critical overview of the recent progress in crossed-beam reactive scattering is presented. This review is not intended to be an exhaustive nor a comprehensive one, but rather a critical assessment of what we have been learning about bimolecular reaction dynamics using crossed molecular beams since year 2000. Particular emphasis is placed on the information content encoded in the product angular distribution-the trait of a typical molecular beam scattering experiment-and how the information can help in answering fundamental questions about chemical reactivity. We will start with simple reactions by highlighting a few benchmark three-atom reactions, and then move on progressively to the more complex chemical systems and with more sophisticated types of measurements. Understanding what cause the experimental observations is more than computationally simulating the results. The give and take between experiment and theory in unraveling the physical picture of the underlying dynamics is illustrated throughout this review.     

Screening of a phosphite-phosphoramidite ligand library for palladium-catalysed asymmetric allylic substitution reactions: the origin of enantioselectivity

We have designed a new library of readily available, highly modular phosphite-phosphoramidite ligands for asymmetric allylic substitution reactions. They are easily prepared in one step from commercially available chiral 1,2-amino alcohols. The introduction of a phosphoramidite moiety into the ligand design is highly advantageous for the product outcome. This ligand library affords high reaction rates (TOFs of up to 800 mol (mol h)(-1)) and enantioselectivities (ees of up to 99%) and, at the same time, contains a broad range of disubstituted hindered and unhindered substrate types. NMR study of the Pd-pi-allyl intermediates provide a deeper understanding of the effect of the ligand parameters on the origin of enantioselectivity.     

Interrelationship between reactivity and bulk activation effects in radical substitution reactions

Conclusions Similar to other reactions of this type, the reaction for cleaving H atom from saturated hydrocarbons by Cl atom obeys a linear equation with a small slope coefficient, which relates the logarithms of the rate constants and V. This is explained by a difference in the structures of the transition state.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 2, pp. 478–480, February, 1977.     

Rate-determining cooperative effects of bimolecular reactions in solution

An expression for the rate constant of condensed-phase bimolecular reactions is derived. The key feature of the proposed model is the formulation of the energy-dependent rate constant in terms of the diffusion rate and the ratio of the volume in phase space that leads to product over the total volume. The dependence of the bimolecular rate constant by the reduced barrier x = E thermod/kT is given in explicit form in terms of the incomplete and the complete gamma functions of Euler. The performance of the proposed model is tested against the experimental rate constants for the Menschutkin reaction by fitting the parameters of the expression for the rate constant to experimental data at various temperatures. The potential energy barrier obtained from the regression (16.75 kcal mol-1) is close to the independently computed value at the CPCM B3LYP/CRENBL.6-311(+)G(d) level of theory (16.84 kcal mol-1). The corresponding fitting to the transition state theory expression affords the lower value of 14.65 kcal mol-1.     

Many-particle effects in kinetics of bimolecular diffusion-controlled reactions

Starting from the generalized theory of bimolecular diffusion-controlled reactions between reagents in solids and liquids, we have performed calculations of the A + B → AB (Frenkel defect annihilation) and A + A → B (exciton annihilation) reaction kinetics over a wide time interval and for high initial concentrations. The predicted lowering at long times of the reaction rate in the course of the A + B → AB reaction and acceleration at short times of the A + A → B reaction due to dynamical aggregation of similar non-interacting reagents are demonstrated. The possibility of experimental checks of these effects is discussed.     

Anomalous features of the kinetics of subdiffusion-assisted bimolecular reactions

Some specific features of the kinetics of subdiffusion-assisted bimolecular reactions are analyzed in detail with the use of the non-Markovian stochastic Liouville equation (SLE) recently derived within the continuous time random walk approach. The SLE allows for describing important peculiarities of the reactions: Slow long time behavior of the kinetics, nonanalytical dependence of the reaction rate on the reactivity of particles, the onset of quasistatic regime independently of particle mobility in the case long-range reactivity, strong manifestation of fluctuation kinetics showing itself in very slow reaction kinetics at long times, etc.     

Mechanism of the bimolecular reactions of ethylene and propylene

Rate constants for the bimolecular reactions of ethylene and propylene to form radicals and to form cyclobutane or its derivatives have been calculated using thermodynamic and kinetic data. Comparison of these rates with the kinetics of the thermal reactions of ethylene and propylene show that cyclobutane and its derivatives are probably not important intermediates in the processes forming radicals.     

Gas-phase ligand loss and ligand substitution reactions of platinum(II) complexes of tridentate nitrogen donor ligands

The source of protons associated with the ligand loss channel of HX((n - 1)+) from [Pt(II)(dien)X](n+) (X = Cl, Br and I for n = 1 and X = NC(5)H(5) for n = 2) in the gas phase was investigated by deuterium-labelling studies. The results of these studies indicate that these protons originate from both the amino groups and the carbon backbone of the dien ligand. In some instances (e.g. X = Br and I), the protons lost from the carbon backbone can be even more abundant than the protons lost from the amino groups. The gas-phase substitution reactions of coordinatively saturated [Pt(II)(L(3))L(a)](2+) complexes (L(3) = tpy or dien) were also examined using ion-molecule reactions. The outcome of the ion-molecule reactions depends on both the ancillary ligand (L(3)) as well as the leaving group (L(a)). [Pt(II)(tpy)L(a)](2+) complexes undergo substitution reactions, with a faster rate when L(a) is a good leaving group, while the [Pt(II)(dien)L(a)](2+) complex undergoes a proton transfer reaction.