Hydrogen positions

Brunger, A. T., Karplus, M. Polar hydrogen positions in proteins Empirical energy placement and neutron diffraction comparison. Proteins Struct. Func. Genet. 4 (1988) 148-156. 

The algorithm that is usually employed to account for the hydrogen positions is SHAKE [15,16] (and its variant RATTLE [17]). Stated in a simplistic way, the SHAKE algorithm assumes that the length of the X — H bond can be considered constant. Because in a numerical simulation there are always flucmations, this means that the deviation of the current length dt(t) of the Mi bond from its ideal (constant) bond length d° must be smaller than some tolerance value e. 

A search for intermolecular bonds resulted in one possible hydrogen bond between hydroxyl 013 and lactone carbonyl Ol. The distance between 01 and 013 is 2.85 A, a value well within the range expected for OH-O hydrogen bonds (25). The hydrogen atom position for hydroxyl 013 was chosen to be along the 013-01 vector. The hydrogen position was not evident in the difference electron density map, presumably due to problems modeling the 013 position. 

The discussions of the structure and the electron density are based on the structure found by a full multipole refinement of the X-ray data with the hydrogen positions fixed at the neutron values and the hydrogen thermal parameters fixed at scaled neutron values (Figure 5).1 The interatomic distances and intramolecular bond angles are given in Table 2. 

The proposed mechanism of the exchange suggests that the intermolecu-lar exchange should not involve the center CH bond. On the other hand, if the exchange were random among the six hydrogen positions, one would expect about one out of three molecules to have a deuterium on the central carbon at equilibrium. Analysis by IR shows no evidence for a deuterium at this position even for the nearly equilibrated surface products. Thus, this result also conforms to expectations based on the proposed mechanism. 

Rundle, R. E. The Hydrogen Positions in Uranium Hydride by Neutron... 

Fig. 5. Contour plot of the adiabatic potential-energy surface of an H atom in the (110) plane for the neutral H—B pair from a local-density pseudopotential calculation. The boron atom is at the center. For every hydrogen position, the B and Si atoms are allowed to relax, but only unrelaxed positions are indicated in the figure (Reprinted with permission from the American Physical Society, Denteneer, P.J.H., Van de Walle, C.G., and Pantelides, S.T. (1989). Phys. Rev. B 39, 10809.)...

Just as in the preceding examples, early indications of tunneling in enzyme-catalyzed reactions depended on the failure of experiments to conform to the traditional expectations for kinetic isotope effects (Chart 3). Table 1 describes experimental determinations of -secondary isotope effects for redox reactions of the cofactors NADH and NAD. The two hydrogenic positions at C4 of NADH are stereochemically distinct and can be labeled individually by synthetic use of enzyme-catalyzed reactions. In reactions where the deuterium label is not transferred (see below), an... 

Other very interesting results show that even the splitting of hydrogen positions in bmcite Mg(OH)2 can be clearly revealed in the electron diffraction stmcture analysis. ... 

Fig. 11.3 Nitrogen configuration example Indoline/cytochrome C peroxidase complex (PDB laek). Alternative hydrogen positions indicated by dotted lines.

The last example (Figure 11.3) underlines the importance of the correct nitrogen configuration. In the indoline/cytochrome C peroxidase complex, only one of the three sketched hydrogen positions allows for an interaction with an active site aspartate. 

Scheme 4.2 Bond energy as a function of hydrogen position (black solid line), assuming identical pff, values for the donor and acceptor, relative to the lowest vibrational energy level of the hydrogen atom (highlighted by a dotted line), (a) A standard, symmetric hydrogen bond (b) the corresponding low-barrier hydrogen bond (LBHB). The red line represents the probability density function [27, 28].

Wenkert and Khatuya (51) examined the competition between direct insertion of a carbene into furan (via cyclopropanation) and ylide formation with reactive side-chain functionality such as esters, aldehydes, and acetals. They demonstrated the ease of formation of aldehyde derived carbonyl ylides (Scheme 4.30) as opposed to reaction with the electron-rich olefin of the furan. Treatment of 3-furfural (136) with ethyl diazoacetate (EDA) and rhodium acetate led to formation of ylide 137, followed by trapping with a second molecule of furfural to give the acetal 138 as an equal mixture of isomers at the acetal hydrogen position. 

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