Hydrogen bonding fluctuations

In the presence of both order-disorder and displacive, as in the KDP family, the two dynamic concepts have somehow to be merged. It could well be that the damping constant Zs becomes somewhat critical too (at least in the over-damped regime of the soft mode), because of the bihnear coupling of r/ and p. It would, however, lead too far to discuss this here in more detail. The corresponding theory of NMR spin-lattice relaxation for the phase transitions in the KDP family has been worked out by Blinc et al. [19]. Calculation of the spectral density is here based on a collective coordinate representation of the hydrogen bond fluctuations connected with a soft lattice mode. Excellent and comprehensive reviews of the theoretical concepts, as well as of the experimental verifications can be found in [20,21]. 

A significant difference between chemically crosslinked networks and hydrogen bonding (fluctuation) networks, is the absence of the plateau region in the high temperature region. 

Notably, the outlined defect mechanism of proton transfer resembles the protocol of proton transfer in water, viz. transformation between localized and delocalized proton states (water H904 -0-11502TAM solid stable crystal configuration -o- metastable intermediate state), triggered by hydrogen-bond fluctuations and molecular rotations. Sequences of these transformations, hydrogen-bond rotations and proton transfers generate the net proton motion. 

At least three major scales must be distinguished in simulations of heterogeneous media (i) the atomistic scale, required to account for electronic structure effects in catalytic systems or for molecular and hydrogen bond fluctuations that govern the transport of protons and water (ii) the scale of the electrochemical double layer, ranging from several A to a few nm at this level, simulations should account for potential and ion distributions in the metal-electrolyte interfacial region and (iii) the scale of about 10 nm to 1 pm, to describe transport and reaction in heterogeneous media as a function of composition and porous structure. 

Assume that water retains its dynamic properties, that is, water molecule rotation and hydrogen bond fluctuations occur on similar timescales as in free bulk water. 

H3O+ ion transitions involve rapid hydrogen bond fluctuations, orientational fluctuations of SGs and translational H3O+ ion motion. Laborious metadynamics runs were performed to find appropriate CVs from the set of degrees of freedom and to fine-tune metadynamics parameters. As a conclusion from these benchmarking studies, the lateral H30 ion shift was chosen as a sole metadynamics CV, defined by dev = d 2 — d23 in Figure 2.34. Relocation distances of H3O+ ions during transitions are 3 A. 

Knight C, Singer SJ (2009) Site disorder in ice VII arising from hydrogen bond fluctuations. JPhys Chem A 113 12433-12438... 

Molecular dynamics simulations have also been used to interpret phase behavior of DNA as a function of temperature. From a series of simulations on a fully solvated DNA hex-amer duplex at temperatures ranging from 20 to 340 K, a glass transition was observed at 220-230 K in the dynamics of the DNA, as reflected in the RMS positional fluctuations of all the DNA atoms [88]. The effect was correlated with the number of hydrogen bonds between DNA and solvent, which had its maximum at the glass transition. Similar transitions have also been found in proteins. 

Ludwig s (2001) review discusses water clusters and water cluster models. One of the water clusters discussed by Ludwig is the icosahedral cluster developed by Chaplin (1999). A fluctuating network of water molecules, with local icosahedral symmetry, was proposed by Chaplin (1999) it contains, when complete, 280 fully hydrogen-bonded water molecules. This structure allows explanation of a number of the anomalous properties of water, including its temperature-density and pressure-viscosity behaviors, the radial distribution pattern, the change in water properties on supercooling, and the solvation properties of ions, hydrophobic molecules, carbohydrates, and macromolecules (Chaplin, 1999, 2001, 2004). 

It is instructive to illustrate the use of Equations 5.19 and 5.29 using a simplistic 3-atom model calculation for water. Even though it is well established that the condensed phase structure of water is complicated and involves the coordinated motions of many molecules coupled through a constantly fluctuating hydrogen bond network, the fundamentals of the VPIE are represented reasonably well by the simplified model. 

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