Bonds geometric parameters

The geometrical parameters and hydrogen-bonding geometrical parameters [11-14] of these peptides and polypeptides are shown in Table 6.5.2. Some... 

Sample Geometrical parameters Hydrogen-bonding geometrical parameters Ref. 

Crystalline amino acids form readily hydrates, salts and various molecular complexes and co-crystals. The molecular conformations, the hydrogen bond geometric parameters and patterns, dipole moments and the charge distributions can be tuned finely in these systems, and many structure-forming units and structural patterns... 

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)... 

The relationship between two bond vectors can be represmted using a distance, two angles and a torsion indicated (top). To derive the data for the database all possible pairs ofexocyclic vectors are considered and ur geometric parameters calculated. 

G Nemethy, KD Gibson, KA Palmer, CN Yoon, G Paterlini, A Zagari, S Rumsey, FIA Scher-aga. Energy parameters in peptides. Improved geometrical parameters and non-bonded interactions for use in the ECEPP/3 algorithm, with application to prolme-contammg peptides. J Phys Chem 96 6472-6484, 1992. 

Of the various geometric parameters associated with molecular shape, the one most nearly constant from molecule to molecule and most nearly independent of substituent effects is bond length. Bond lengths to carbon depend strongly on the hybridization of the carbon involved but are little influenced by other factors. Table 1.2 lists the interatomic distances for some of the most common bonds in organic molecules. The near constancy of bond lengths from molecule to molecule reflects the fact that the properties of individual bonds are, to a good approximation, independent of the remainder of the molecule. 

The computation of furoxans (l,2,5-oxadiazole-2-oxides) is very demanding. Very strong electron correlation effects hamper a proper treatment of this class of molecules. With respect to the geometric parameters, it is the endocyclic N—O bond that can be treated reliably either at the B3-LYP or at the MP4(SDQ) level [99MI1 ]. Table II demonstrates the problems associated with the exact determination of this bond length. 

Table 4-2. Ground-slalc and lowcsl-cxcilcd slate AM l/CI-oplimized C-C bond lengths (in A) in a cofacial dimer formed by two stilbenc molecules separated by 3.5, 4.0, and 4.5 A, respectively. The geometrical parameters for single molecules arc reported in the right-hand-side column.

Table 4 Geometrical parameters of two bond lengths data from ref [17]) conformational isomers of gaseous trisulfane (r ...

The trisulfane molecule exists as two conformers which have been termed as cis- and trans-HzSi. While the trans-form is a helical molecule of C2 symmetry with the motif ++ (or — for the enantiomer), the cfs-form is of Q symmetry with the motif +- (identical to -+). Both forms have been detected by rotational spectroscopy [17, 45, 46]. The motif gives the order of the signs of the torsion angles at the SS bonds. The geometrical parameters [17] are presented in Table 4. The trans-isomer is by only 1 kj mol more stable than the cfs-form but the barrier to internal rotation from tmns to cis is 35 kJ mor [46]. The dipole moments were calculated by ab initio MO theory at the QCISD/TZ+P level as 0.68 D (trans) and 2.02 D (cis) [46]. For geometrical parameters of cis- and trans-trisulfane calculated at the MP2/6-311++G> > level, see [34]. 

Scheme 21 Inverted angle calculated from the X-ray geometrical parameters and bond lengths of the bridgehead bond...

Table 1 Geometric parameters for halogen bonded complexes with nitrogen and oxygen electron donors... 

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