Transferring molecular structure data

The attention of software developers and users is drawn to current problems in redirecting all data input to be read from files and in allowing alternative entry points which avoid repeated initialisation. They are urged to make more use of the Standard Molecular Data (SMD) format for transfer of structure data. 

Eq. (3.8) assumes harmonic vibrational motion, a satisfactory approximation for the range of momentum transfers covered by the neutron data. NVR adjusted the OD distance, its rms-variation, and the rms-variation in the intramolecular DD distance by least-squares. The DD distance itself was computed from the OD distance and an assumed DOD angle of 104.5°, because its value, 1.58 A, is too close to the hydrogen-bonded D2O...D distance expected near 1.8 A. The molecular structure function 5m(s) calculated from these parameters is compared with the total structure function BN(s) in Fig. 7d. 

Ohmic error is not obvious in data on the Ni(II)/Ni(I) couple for this molecule (Table 23.3B), since a systematic decrease in the determined values of ks/D1/2 is not found. With a ks value of 0.025 cm/s, this couple has AEp values that are much larger than those of the Ni(III)/Ni(II) couple, and errors of, for example, 10 mV are small when compared to the inherent AEp arising from sluggish electron transfer kinetics. In this system, the slow electron transfer kinetics probably arise from molecular structure changes concomitant with the Ni(II)/Ni(I) electron transfer. A good discussion of the influence of ohmic errors on determination of kj values in various nonaqueous media is available [13]. 

The force constants and intrinsic parameters are assumed to be transferable, at least within families of related compounds and can therefore be optimized in terms of large volumes of experimental data. As the data banks grow, force fields become ever more precise and eventually should enable the optimization of any approximate structure to the desired degree of accuracy. From a theoretical perspective there is an understandable desire to explain molecular structure in terms of basic theory, rather than empirical modelling. It is therefore important to remember that the parameters of a valence force field are not arbitrary mathematical functions, but are defined in terms of... 

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