Experimental reference data bond distances

In Figure 15.7, we have plotted the normal distributions of the errors in the calculated bond angles. The main difference from the plots for bond distances in Figure 15.4 is that, for bond angles, the CCSD(T) distributions are less sharply peaked and similar to those of the MP2 model, reflecting the poorer quality of the experimental reference data for bond angles than for bond distances. 

Fig. 8.4 Dependence of the computed average distance between the C -atoms as a function of Fq for the polypeptide model black circles), cystine (red circles), and DEDS (green circles) and obtained from force field equilibrium (at zero force) and force clamp MD (for Fq > OnN) simulations. Computational reference data for DEDS obtained from QM/MM simulations are shown by GEOMETRY FILE/created by CPMD brown triangles and the experimental reference based on the strained macrocycle [43] is marked by a violet square. The horizontal blue, pink and orange dotted lines are the average C -C distances of disulfide bonds in TDi, DO and interchain Ig proteins, respectively, whereas the cyan dotted line corresponds to intrachain Ig proteins. Reprinted from Ref. [42]...

In order to test the point-charge method experimentally measured dissociation energy and interatomic distance are required for each chemical bond. Dissociation energies for most homonuclear diatomic molecules have been measured spectroscopically and/or thermochemically. Interatomic distances for a large number of these are also known. However, for a large number of, especially metallic diatomic molecules, equilibrium interatomic distances have not been measured spectroscopically. In order to include these elements in the sample it is noted that for those metals with measured re, it is found to be related, on average, to 5, the distance of closest approach in the metal, by re = 0.78(5. On this assumption reference values of interatomic distance (d) become available for virtually all elements, as shown in the data appendix. In some special cases well-characterized dimetal bond lengths have also been taken into account for final assessment of interatomic distance. 

Filled dots indicate the experimental data, the continuous line gives the best fit. Open dots represent the laserpulse. edge separation (Re) of the chromophores is also indicated in Fig.2. The latter is defined as the shortest atom-to-atom distance between the donor- and acceptor -systems, whereas the former refers to the distance between the centre of the naphthalene unit and the midpoint of the exocyclic C=C bond of the acceptor. X-Ray structure data of 1(6) and of precursors of 1(8) and 1(10) were used to evaluate these distances (Craig and Paddon-Row, 1987). 

Fig. 14. Proximity relationships in H8 and TM7 relative to 65 in TM1. Examples of interspin distances measured in solution. In each distance measurement, only two R1 side chains were in the protein, one on the reference site 65 and the other at a site in the sequence 306-319. The R1 side chains were modeled based on crystal structure data with minimization subject to the experimentally determined distance constraints (indicated in A). In each case, the measured distance in solution was in good agreement with that expected from the rhodopsin crystal structure. Substituted cysteine residues 315, 316, and 319 most rapidly formed disulfide cross-links with a cysteine at 65 in TM1. The potential disulfide bonds are indicated as gray dashed lines.

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