Solvation dynamics in liquid water: III: energy fluxes and structural changes

In previous installments it has been shown how a detailed analysis of energy fluxes induced by electronic excitation of a solute can provide a quantitative understanding of the dominant molecular energy flow channels characterizing solvation—and in particular, hydration— relaxation dynamics. Here this work and power approach is complemented with a detailed characterization of the changes induced by such energy fluxes. We first examine the water solvent’s spatial and orientational distributions and the assorted energy fluxes in the various hydration shells of the solute to provide a molecular picture of the relaxation. The latter analysis is also used to address the issue of a possible “inverse snowball” effect, an ansatz concerning the time scales of the different hydration shells to reach equilibrium. We then establish a link between the instantaneous torque, exerted on the water solvent neighbors’ principal rotational axes immediately after excitation and the final energy transferred into those librational motions, which are the dominant short-time energy receptor.Postprint (author's final draft

Translational versus rotational energy flow in water solvation dynamics

Early molecular dynamics simulations discovered an important asymmetry in the speed of water solvation dynamics for charge extinction and charge creation for an immersed solute, a feature representing a first demonstration of the breakdown of linear response theory. The molecular level mechanism of this asymmetry is examined here via a novel energy flux theoretical approach coupled to geometric probes. The results identify the effect as arising from the translational motions of the solute-hydrating water molecules rather than their rotational/librational motions, even though the latter are more rapid and dominate the energy flow.Postprint (author's final draft

Tracking energy transfer from excited to accepting modes : application to water bend vibrational relaxation

We extend, via a reformulation in terms of Poisson brackets, the method developed previously (Rey et al., J. Phys. Chem. A, 2009, 113, 8949) allowing analysis of the pathways of an excited molecule's ultrafast vibrational relaxation in terms of intramolecular and intermolecular contributions. In particular we show how to ascertain, through the computation of power and work, which portion of an initial excess molecular energy (e.g. vibrational) is transferred to various degrees of freedom (e.g. rotational, translational) of the excited molecule itself and its neighbors. The particular case of bend excess energy relaxation in pure water is treated in detail, completing the picture reported in the work cited above. It is shown explicitly, within a classical description, that almost all of the initial water bend excitation energy is transferred—either indirectly, via Fermi resonance centrifugal coupling to the bend-excited water's rotation, or directly via intermolecular coupling— to local water librations, only involving molecules in the first two hydration shells of the vibrationally excited water molecule. Finally, it is pointed out that the Poisson bracket formulation can also be applied to elucidate the microscopic character of solvation and rotational dynamics, and should prove useful in developing a quantum treatment for energy flow in condensed phases.Postprint (published version

Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step

AbstractWe offer some thoughts on the much debated issue of dynamical effects in enzyme catalysis, and more specifically on their potential role in the acceleration of the chemical step. Since the term ‘dynamics’ has been used with different meanings, we find it useful to first return to the Transition State Theory rate constant, its assumptions and the choices it involves, and detail the various sources of deviations from it due to dynamics (or not). We suggest that much can be learned about the key current questions for enzyme catalysis from prior extensive studies of dynamical and other effects in the case of reactions in solution. We analyze dynamical effects both in the neighborhood of the transition state and far from it, together with the situation when quantum nuclear motion is central to the reaction, and we illustrate our discussion with various examples of enzymatic reactions

Non-adiabatic dynamics close to conical intersections and the surface hopping perspective

Conical intersections play a major role in the current understanding of electronic de-excitation in polyatomic molecules, and thus in the description of photochemistry and photophysics of molecular systems. This article reviews aspects of the basic theory underlying the description of non-adiabatic transitions at conical intersections, with particular emphasis on the important case when the dynamics of the nuclei are treated classically. Within this classical nuclear motion framework, the main aspects of the surface hopping methodology in the conical intersection context are presented. The emerging picture from this treatment is that of electronic transitions around conical intersections dominated by the interplay of the nuclear velocity and the derivative non-adiabatic coupling vector field

On the coupling between molecular diffusion and solvation shell exchange

The connection between diffusion and solvent exchanges between first and second solvation shells is studied by means of molecular dynamics simulations and analytic calculations, with detailed illustrations for water exchange for the Li+ and Na+ ions, and for liquid argon. First, two methods are proposed which allow, by means of simulation, to extract the quantitative speed-up in diffusion induced by the exchange events. Second, it is shown by simple kinematic considerations that the instantaneous velocity of the solute conditions to a considerable extent the character of the exchanges. Analytic formulas are derived which quantitatively estimate this effect, and which are of general applicability to molecular diffusion in any thermal fluid. Despite the simplicity of the kinematic considerations, they are shown to well describe many aspects of solvent exchange/diffusion coupling features for nontrivial systems

Modeling Spatial Correlation of DNA Deformation: DNA Allostery in Protein Binding

We report a study of DNA deformations using a coarse-grained mechanical model and quantitatively interpret the allosteric effects in protein–DNA binding affinity. A recent single-molecule study (Kim et al. Science 2013, 339, 816) showed that when a DNA molecule is deformed by specific binding of a protein, the binding affinity of a second protein separated from the first protein is altered. Experimental observations together with molecular dynamics simulations suggested that the origin of the DNA allostery is related to the observed deformation of DNA’s structure, in particular, the major groove width. To unveil and quantify the underlying mechanism for the observed major groove deformation behavior related to the DNA allostery, here we provide a simple but effective analytical model where DNA deformations upon protein binding are analyzed and spatial correlations of local deformations along the DNA are examined. The deformation of the DNA base orientations, which directly affect the major groove width, is found in both an analytical derivation and coarse-grained Monte Carlo simulations. This deformation oscillates with a period of 10 base pairs with an amplitude decaying exponentially from the binding site with a decay length $l_D \approx10$ base pairs as a result of the balance between two competing terms in DNA base-stacking energy. This length scale is in agreement with that reported from the single-molecule experiment. Our model can be reduced to the worm-like chain form at length scales larger than $l_P$ but is able to explain DNA’s mechanical properties on shorter length scales, in particular, the DNA allostery of protein–DNA interactions.Chemistry and Chemical Biolog