Conformation bond length

An enormous number of different 1,3-dioxane structures have been reported since 1996 in Figure 3, mono-, bicyclic and spiro variants are presented, while Figure 4 contains examples of tricyclic structures with the 1,3-dioxane moiety. The conformations, bond lengths, bond and dihedral angles of the 1,3-dioxane rings are determined by the ring fusion, the attached substituents, and the presence of exocyclic double bonds. Thus, published structures are classified as either monocyclic (mono), spiro-substituted (spiro), bicyclic (bi), or tricyclic (tri). The well-known Meldrum s acid derivatives (M) have been most intensively studied. 

Calculated conformations, bond lengths, and bond angles which reproduce correctly the experimental values have shown that compound 7 is planar while molecules 8 and 9 show different degrees of nonplanarity (Table 1) <1997JST(413)1>. 

MM2 Structural Data for BBL Lowest Energy Conformers (bond lengths are in A and distortion parameters are in °I ... 

Considerable progress has been made in the development of theories that can predict the complete ROA spectrum, provided that a good normal coordinate analysis is available, and this leads us to the hope that it might be possible eventually to deduce the total stereochemistry (absolute configuration, conformation, bond lengths and angles) of a chiral molecule in a chemically relevant environment from the measured ROA spectrum (or indeed from the infrared CD spectrum). 

In order to consider the 3D structure but make the chirality code independent of a specific conformer, r- is taken as the sum of the bond lengths between atoms i and j on the path with a minimum number of bond counts. 

Each combination of four atoms (A, B. C. and D) is characterized by two parameters, e and e.. As for the CICC, is a parameter that depends on atomic properties and on distances, and is calculated by Eq. (27), with r, again being the sum of bond lengths between atoms on the path with the minimum number of bond counts. However c is now a geometric parameter (dependent on the conformation)... 

Monte Carlo searching becomes more difficult for large molecules. This is because a small change in the middle of the molecule can result in a large displacement of the atoms at the ends of the molecule. One solution to this problem is to hold bond lengths and angles fixed, thus changing conformations only, and to use a small maximum displacement. 

The amount of computation necessary to try many conformers can be greatly reduced if a portion of the structure is known. One way to determine a portion of the structure experimentally is to obtain some of the internuclear distances from two-dimensional NMR experiments, as predicted by the nuclear Over-hauser effect (NOE). Once a set of distances are determined, they can be used as constraints within a conformation search. This has been particularly effective for predicting protein structure since it is very difficult to obtain crystallographic structures of proteins. It is also possible to define distance constraints based on the average bond lengths and angles, if we assume these are fairly rigid while all conformations are accessible. 

Try changing the geometry. First, slightly shorten a bond length. Then, slightly extend a bond length and next shift the conformation a bit. Consider trying a different basis set. 

Annelation can introduce large conformational barriers, to the extent of making possible the resolution into enantiomers of a tribenzoxepine (71CB2923). Chapters 5.16, 5.17, 5.18 and 5.19 contain much more information on inversion barriers, bond lengths and bond angles. 

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