Proton motion

The QM/MM and ab initio methodologies have just begun to be applied to challenging problems involving ion channels [73] and proton motion through them [74]. Reference [73] utilizes Hartree-Fock and DFT calculations on the KcsA channel to illustrate that classical force fields can fail to include polarization effects properly due to the interaction of ions with the protein, and protein residues with each other. Reference [74] employs a QM/MM technique developed in conjunction with Car-Parrinello ab initio simulations [75] to model proton and hydroxide ion motion in aquaporins. Due to the large system size, the time scale for these simulations was relatively short (lOps), but the influences of key residues and macrodipoles on the short time motions of the ions could be examined. 

We can expect to see future research directed at QM/MM and ab initio simulation methods to handle these electronic structure effects coupled with path integral or approximate quantum free energy methods to treat nuclear quantum effects. These topics are broadly reviewed in [32], Nuclear quantum effects for the proton in water have already received some attention [30, 76, 77]. Utilizing the various methods briefly described above (and other related approaches), free energy calculations have been performed for a wide range of problems involving proton motion [30, 67-69, 71, 72, 78-80]. 

The proton motion from Asp27 to 04 comprises a trajectory of approximately 0.6 A (Figure 6). There is a decrease in the free energy due to the surroundings, which corresponds to nearly 4.5 kcal/mol of stabilization by the protein. Further stabilization occurs as the 04-H04 bond rotates toward the N5 atom, which corresponds to a proton movement of about 1.4 A (Figure 6b)... 

P. Zielke and M. A. Suhm, Concerted proton motion in hydrogen bonded trimers A sponta neous Raman scattering perspective. Phys. Chem. Chem. Phys. 8, 2826 2830 (2006). 

Schuster, P., Jakubetz, W., Beier, G., Meyer, W., Rode, B. M. Potential curves for proton motion along hydrogen bonds. In (Bergmann, E. D. and Pullman, B., eds.), Chemical and biochemical reactivity. Jerusalem Academic Press, in press. 

Petersen et al., Petersen and Voth,i Spohr, Spohr et al., and Walbran and Kornyshev developed EVB-based models to study the effect of con-finemenf in nanometer-sized pores and fhe role of acid-functionalized polymer walls on solvation and transport of protons in PEMs. The calculations by the Voth group revealed an inhibiting effect of sulfonate ions on proton motions. The EVB model by Kornyshev, Spohr, and Walbran was specifically designed to sfudy effecfs on proton mobilify due to charge delocalization within SOg groups, side chain packing density, and fluctuations... 

The deviations from Gaussian behaviour were successfully interpreted as due to the existence of a distribution of finite jump lengths underlying the sublinear diffusion of the proton motion [9,149,154]. A most probable jump distance of A was found for PI main-chain hydrogens. With the model... 

Valuable information on the geometry of the proton motion is offered by the Q-dependence of the elastic incoherent intensity (EISF) (see Fig. 4.34). For two site jumps this intensity is described by ... 

For aminophenols, one-electron oxidation and the proton elimination can run together in one stage. This leads to a cation-radical containing O and +NH3 fragments within one and the same molecular carcass (Rhile et al. 2006). Such concerted reactions are classified as proton-coupled electron transfer (Mayer 2004). Proton-coupled electron transfer differs from conventional one-electron redox reaction in the sense that proton motion affects electron transfer. Because the transfers of a proton and an electron proceed in a single step, we can say about the hydrogen-atom transference, (H+ -I- e)=H. It is the fundamental feature of proton-coupled electron-transfer reactions that the proton and electron are transferred simultaneously, but from different places (see Tanko 2006). 

Similarly, Tuckerman (excerpt 12K) cites works that emphasize widespread interest in the research area, highlighting, for example, that crystal hydrates have attracted the attention of crystallographers and spectroscopists over several decades (46—28, 123-125). Specific benefits of crystal hydrates are touted, including their possible use as proton conductors (J26) and as important media for the study of proton motion. The latter is currently of interest in the field of low temperature spectroscopy (127-129). 

Potassium dihydrogen phosphate is a particularly good example, since reliable data concerning the distances of the atoms in the hydrogen bonds ace available [11]. From Bacon and Pease s data, the distance between the minima of potential energy of the proton motion (if a double minimum potential curve is assumed) is between 0 3 and 0-5 A. 

Efforts to understand the state of hydrogen in metals and metal hydrides have involved the use of NMR for many years. This study combines the conventional solid state NMR techniques with more recently developed high-resolution, solid state NMR techniques (5,6). Conventional NMR techniques furnish information on dipolar interactions and thus can furnish static geometrical information on hydrogen positions and information on proton motion within such solids. The newer multiple pulse techniques suppress proton-proton dipolar interaction and allow information on other, smaller interactions to be obtained. This chapter reports what the authors believe is the first observation of the powder pattern of the chemical shift tensor of a proton that is directly bonded to a heavy metal. 

Th4Hi5. Three kinds of information are obtained from the samples of Th4H15 information on rigid lattice structure from free induction decays, on proton motion from relaxation time measurements, and on internal fields from peak locations that were found using the multiple pulse techniques. Figure 1... 

To extract information on the proton motion from NMR measurements, one can use the following approximate equations appropriate for the various NMR relaxation times measured in this work (24, 25, 26). 

The observed T1 can have two contributions 1/T = 1/T e + l/Tij. T e results from relaxation effects caused by conduction electrons, and Tm results from dipolar relaxation effects caused by the motion of nuclear spins. At temperatures below 110°C, the conduction electron effect appears to dominate T1 since a plot of T vs. 1/T can be fit with a straight line passing through the origin. At higher temperatures, the relaxation caused by the proton motion becomes... 

Little difference was found between the NMR results on the LP and HP samples at either room temperature or as the temperature was raised, although the T1 for the HP sample was 10% shorter than that for the LP sample. After maintaining the samples at temperatures near 200°C for 1 hr., a major difference was noted upon cooling, with the HP sample exhibiting a marked time-temperature hysteresis of all of the measured NMR properties while the LP sample exhibited no time-temperature hysteresis in any of the NMR parameters measured. A more dramatic manifestation of this is that after the sample was cooled to room temperature, the proton motion took weeks to return to the original state... 

Figure 2. Estimated correlation times, r, for proton motion as a function of inverse temperature in Th4Hi5 ( ) r values estimated from T2 data (O) from T i data (A) from T iP with Hi = 20.6 g and ( ) from Tlp with Hi = 4.7 g below...

Recently, we reported observations of the femtosecond dynamics of tautomerization in model base pairs (7-azaindole dimers) containing two hydrogen bonds. Because of the femtosecond resolution of proton motions, we were able to examine the cooperativity of formation of the tautomer (in... 

Linear arrays of protonatable or hydrogen bonded sites may allow the directed long range transfer of protons, thus functioning as proton-conducting channel, i.e., as proton wire. Relevant systems would be linear polyamines or polyphenolic condensed aromatic units [8.218], self-assembled hydrogen bonded heterocyclic ribbons such as 116 (see Section 9.4.4) or polyelectrolyte membranes [8.219] in which collective proton motion may take place and lead to proton conductivity. 

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