How to obtain reaction free energies from free-energy profiles.

For chemical reactions that occur via the rearrangement of atoms from a configuration about one minimum (reactant, R) of the potential energy surface (PES) to a configuration about another minimum (product, P), an exact relation between the Helmholtz reaction free energy (ΔFRP) and the free-energy profile (FEP) can be derived. Since the FEP assumes a form similar to that of the PES along the minimum energy path between R and P, there is an unfortunate tendency to regard the FEP as the "free-energy" analog of the minimum energy path and consequently to equate ΔFRP to the difference between the values of the FEP at the minima corresponding to R and P. Analytic treatments of one- and two-dimensional models are presented that show how this mistaken idea leads to errors. In effect, treating the FEP by analogy with the minimum energy path neglects the role of entropy. The FEP is a function of a collective variable (CV), which must be chosen to describe the course of the rearrangement consistently with the exact relation between ΔFRP and the FEP. For large systems of common interest, the PES is often so complex that a straightforward way of choosing a CV is lacking. Consequently, one is forced to make an educated guess. A criterion for judging the quality of the guess is proposed and applied to a two-dimensional model.

From free-energy profiles to activation free energies.

Given a chemical reaction going from reactant (R) to the product (P) on a potential energy surface (PES) and a collective variable (CV) discriminating between R and P, we define the free-energy profile (FEP) as the logarithm of the marginal Boltzmann distribution of the CV. This FEP is not a true free energy. Nevertheless, it is common to treat the FEP as the "free-energy" analog of the minimum potential energy path and to take the activation free energy, ΔFRP ‡, as the difference between the maximum at the transition state and the minimum at R. We show that this approximation can result in large errors. The FEP depends on the CV and is, therefore, not unique. For the same reaction, different discriminating CVs can yield different ΔFRP ‡. We derive an exact expression for the activation free energy that avoids this ambiguity. We find ΔFRP ‡ to be a combination of the probability of the system being in the reactant state, the probability density on the dividing surface, and the thermal de Broglie wavelength associated with the transition. We apply our formalism to simple analytic models and realistic chemical systems and show that the FEP-based approximation applies only at low temperatures for CVs with a small effective mass. Most chemical reactions occur on complex, high-dimensional PES that cannot be treated analytically and pose the added challenge of choosing a good CV. We study the influence of that choice and find that, while the reaction free energy is largely unaffected, ΔFRP ‡ is quite sensitive.

Charge Migration in Eyring, Walter and Kimball's 1944 Model of the Electronically Excited Hydrogen-Molecule Ion.

In an elementary variational treatment of the electronic structure of H2+, Eyring, Walter, and Kimball (EWK) serendipitously discovered charge migration (CM) in 1944. Using an analytic expression for the electronic probability density (EPD), they found that if the electron is initially localized on one of the protons (by taking the initial state to be a superposition of the ground and first excited electronic energy eigenstates), then it oscillates adiabatically between fixed protons with a period T inversely proportional to the energy gap between the eigenstates. At the equilibrium internuclear separation, T = 550.9 as. As shown here, the EWK model also yields an analytic formula for the electronic flux density (EFD). While the EPD indicates where the electron is at any instant, the EFD reveals the pathways the electron follows during its migration. Thus, the EFD complements the EPD, providing valuable new insight into the mechanism of CM. The formula for the EFD is a simple product of a time factor and a spatial factor. This factoring exposes a plethora of spatial-temporal symmetry relations which imply novel and surprising properties. An especially significant finding is that, in contrast to multielectron systems, where electron correlation may play a role in CM, in the EWK model of H2+, CM is due strictly to quantum interference between the ground and first excited electronic states.

Quantum theory of concerted electronic and nuclear fluxes associated with adiabatic intramolecular processes.

An elementary molecular process can be characterized by the flow of particles (i.e., electrons and nuclei) that compose the system. The flow, in turn, is quantitatively described by the flux (i.e., the time-sequence of maps of the rate of flow of particles though specified surfaces of observation) or, in more detail, by the flux density. The quantum theory of concerted electronic and nuclear fluxes (CENFs) associated with electronically adiabatic intramolecular processes is presented. In particular, it is emphasized how the electronic continuity equation can be employed to circumvent the failure of the Born-Oppenheimer approximation, which always predicts a vanishing electronic flux density (EFD). It is also shown that all CENFs accompanying coherent tunnelling between equivalent "reactant" and "product" configurations of isolated molecules are synchronous. The theory is applied to three systems of increasing complexity. The first application is to vibrating, aligned H2(+)((2)Σg(+)), or vibrating and dissociating H2(+)((2)Σg(+), J = 0, M = 0). The EFD maps manifest a rich and surprising structure in this simplest of systems; for example, they show that the EFD is not necessarily synchronous with the nuclear flux density and can alternate in direction several times over the length of the molecule. The second application is to coherent tunnelling isomerization in the model inorganic system B4, in which all CENFs are synchronous. The contributions of core and valence electrons to the EFD are separately computed and it is found that core electrons flow with the nuclei, whereas the valence electrons flow obliquely to the core electrons in distinctive patterns. The third application is to the Cope rearrangement of semibullvalene, which also involves coherent tunnelling. An especially interesting discovery is that the so-called "pericyclic" electrons do not behave in the manner typically portrayed by the traditional Lewis structures with appended arrows. Indeed, it is found that only about 3 pericyclic electrons flow, in contrast to the 6 predicted by the Lewis picture. It is remarkable that the time scales of these three processes vary by 18 orders of magnitude: femtoseconds (H2(+)((2)Σg(+))); picoseconds (B4); kilosceconds (semibullvalene). It is emphasized that results presented herein are appearing in the literature for the first time.

Entropy and Energy Profiles of Chemical Reactions.

The description of chemical processes at the molecular level is often facilitated by the use of reaction coordinates or collective variables (CVs). The CV measures the progress of the reaction and allows the construction of profiles that track how specific properties evolve as the reaction progresses. Whereas CVs are routinely used, especially alongside enhanced sampling techniques, the links among reaction profiles, thermodynamic state functions, and reaction rate constants are not rigorously exploited. Here, we report a unified treatment of such reaction profiles. Tractable expressions are derived for the free-energy, internal-energy, and entropy profiles as functions of only the CV. We demonstrate the ability of this treatment to extract quantitative insight from the entropy and internal-energy profiles of various real-world physicochemical processes, including intramolecular organic reactions, ionic transport in superionic electrolytes, and molecular transport in nanoporous materials.

Chemically Realistic Tetrahedral Lattice Models for Polymer Chains: Application to Polyethylene Oxide.

To speed up the generation of an ensemble of poly(ethylene oxide) (PEO) polymer chains in solution, a tetrahedral lattice model possessing the appropriate bond angles is used. The distance between noncovalently bonded atoms is maintained at realistic values by generating chains with an enhanced degree of self-avoidance by a very efficient Monte Carlo (MC) algorithm. Potential energy parameters characterizing this lattice model are adjusted so as to mimic realistic PEO polymer chains in water simulated by molecular dynamics (MD), which serves as a benchmark. The MD data show that PEO chains have a fractal dimension of about two, in contrast to self-avoiding walk lattice models, which exhibit the fractal dimension of 1.7. The potential energy accounts for a mild hydrophobic effect (HYEF) of PEO and for a proper setting of the distribution between trans and gauche conformers. The potential energy parameters are determined by matching the Flory radius, the radius of gyration, and the fraction of trans torsion angles in the chain. A gratifying result is the excellent agreement of the pair distribution function and the angular correlation for the lattice model with the benchmark distribution. The lattice model allows for the precise computation of the torsional entropy of the chain. The generation of polymer conformations of the adjusted lattice model is at least 2 orders of magnitude more efficient than MD simulations of the PEO chain in explicit water. This method of generating chain conformations on a tetrahedral lattice can also be applied to other types of polymers with appropriate adjustment of the potential energy function. The efficient MC algorithm for generating chain conformations on a tetrahedral lattice is available for download at https://github.com/Roulattice/Roulattice .

Influence of spacer-receptor interactions on the stability of bivalent ligand-receptor complexes.

Experiments show that a ligand-receptor complex formed by binding a bivalent ligand (D) in which the two ligating units are joined covalently by a flexible polymeric spacer (S) can be orders of magnitude more stable than the corresponding complex formed with monomeric ligands. Although molecular models rationalizing this "enhancement effect" have been proffered, they ignore spacer-receptor (S-R) interactions, which can substantially influence the relative stability of complexes. Here, the results of a computational study designed to assess the impact of S-R interactions in the prototypic bivalent complex are presented and compared to results of experiments. The S-R interactions mimicking general features of biological systems are modeled by contoured R surfaces with hills (or depressions) at the binding sites. In the fictitious limit of vanishing S-R interactions, the enhancement is pronounced, as observed in experiments. For strictly repulsive S-R interactions (hard R surface), the enhancement vanishes, or even reverses. This is particularly the case if the R surface is convex (i.e., rising between the binding sites), while the enhancement is only moderately reduced if the R surface is concave. Alternatively, a weak S-R attraction close to the R surface can increase the enhancement. It is concluded that large enhancement should be observed only if both features are present: a concave R surface plus a weak S-R attraction. The latter occurs for spacer material such as polyethylene glycol (PEG), which is weakly hydrophobic and thus attracted by protein surfaces. It is shown that the enhancement of bivalent binding can be characterized by a single key parameter, which may also provide guidelines for the design of multivalent complexes with large enhancement effect.