Reaction Landscapes

Hohng, S., Zhou, R., Nahas, M. K., Yu, J., Schulten, K., Lilley, D. M.J., andHa, T. (2007). Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction. Science 318, 279—283. 

Today, the application of hypervalent iodine reagents still dominates the reaction landscape of electrophilic N-atom transfer processes, a testament to the unique reactivity of such oxidants. Nevertheless, the past decade has witnessed a flurry of activity aimed at the invention of new reagents and protocols that enable amine and amine derivative synthesis through selective C-H bond modification. We have attempted to highlight many of these recent discoveries, with apologies in advance... 

We assume that the unbinding reaction takes place on a time scale long ( ompared to the relaxation times of all other degrees of freedom of the system, so that the friction coefficient can be considered independent of time. This condition is difficult to satisfy on the time scales achievable in MD simulations. It is, however, the most favorable case for the reconstruction of energy landscapes without the assumption of thermodynamic reversibility, which is central in the majority of established methods for calculating free energies from simulations (McCammon and Harvey, 1987 Elber, 1996) (for applications and discussion of free energy calculation methods see also the chapters by Helms and McCammon, Hermans et al., and Mark et al. in this volume). 

The process here symbolised is probably. . . the chemical reaction between metals and a chemical reagent and the subsequent restoration to a metallic condition... As the artist can see in the landscape graciousness, solemnity, terror, so Zosimos sees the rigour of death and pains of purgation in the turbid seething of the alchemical vessel. ... 

In qualitative terms, the reaction proceeds via an activated complex, the transition state, located at the top of the energy barrier between reactants and products. Reacting molecules are activated to the transition state by collisions with surrounding molecules. Crossing the barrier is only possible in the forward direction. The reaction event is described by a single parameter, called the reaction coordinate, which is usually a vibration. The reaction can thus be visualized as a journey over a potential energy surface (a mountain landscape) where the transition state lies at the saddle point (the col of a mountain pass). 

At the equilibriuni potential, some steps are uphill in free energy, meaning that the reaction on the surface is slow. A perfect catalyst in this analysis would be characterized by a flat potential energy landscape at the equilibrium potential, i.e., by all steps having the same height at zero potential. Whereas no such catalyst has yet been found, we can define the highest potential at which all steps are just downhill in free energy, C/qrr-Below we would say that the reaction starts to be transport-limited. At potentials... 

C.-B. Li, Y. Matsunaga, M. Toda, and T. Komatsuzaki, Phase-space reaction network on a multisaddle energy landscape HCN isomerization, J. Chem. Phys. 123, 184301 (2005). 

Figure 2.25. Energy landscape (BP/DNP) for the Cu ZSM-5 + 2NO- Cu—0 ZSM-5 + N20 reaction, showing all associated spin and conformation isomers calculated for the M5 site. The values are given in kcal x mol-1. The letters S, D and T indicate the singlet, doublet, and triplet states, respectively (after [75]).

The total energy change for the overall reaction of CuI M5+2N0->- Cu0 M5+N20 is equal to -47.3°kcal/mol. A more detailed reaction energetic landscape is shown in Figure 2.25, along with the proposed spectator species (drawn in gray), to provide a suitable integral chemical context. 

The low precipitation and freezing water stage during 10-11 months per annum have led to the development of arid polar and tundra landscapes. The characteristic features of these landscapes are the alkaline soil reaction (pH 7.5-8.0) and even the occurrence of modern carbonate formations. 

Onuchic J. N. and Wolynes P. G. Energy landscapes, glass transitions, and chemical-reaction dynamics in biomolecular or solvent environment. J. Chem. Phys. (1993) 98(3) 2218-2224. 

The temporally and spatially resolved transient structures elucidated by UED include structures in radiationless transitions, structures in non-concerted organic reactions, structures in non-concerted organometallic reactions, structures of carbene intermediates, dynamic pseudorotary structures, non-equilibrium structures and conformational structures on complex energy landscapes, transient structures of surfaces and bulk crystals, and solid-to-... 

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