Intramolecular distances and

Table III Intramolecular Distances and Bond Angles Involving...

A series of molecular mechanics and ab initio calculations of an isolated single molecule have been performed with the Gaussian software package (using MM+ and STO-3G, 3-21G, 6-3IG and 6-3IG basis sets, respectively) to explore the expected positions of the peaks corresponding to intramolecular distances and also to determine the optimal procedure to find them. 

After loosing its two hydrogen atoms, the pyrrolie cycle can bind a meal forming a metalloporphyrin. Figures 9.4 and 9.5 show respectively the intramolecular distances and the angles of the chemical bonds of the porphyrin (Webb and Fleischer, 1965). 

There is no consensus in the scientific community on the definition of the metric M that should be used to compare the two internal distances llfl,- —flyll and Wbi — bjW. When comparing two pairs of atoms between two structures, Taylor and Orengo defined a distance or similarity score in the form e/ D + f), where D is the difference between the two intramolecular distances and e and / are arbitrarily defined constant values. Holm and Sander defined a similarity score as e — [D/(D)])exp(—[(D)//] ), where (D) is the average of the two intramolecular distances. Rossmann and Argos and Russell and Bar-ton used a score defined as exp(—[D/e]2)exp(—[S/e]2), where S takes into account local neighbors for each pair of atoms. Currently, no clear evidence exists as to which score performs best. 

The solvent-accessible surface area depends on the 3D structure of the molecule, as do the intramolecular distances and interactions. For these reasons, the quantitative molecular lipophilicity potential varies with the 3D structure of a molecule. As discussed in the next section, the MLP is a modeling... 

The applicability of the above approach to the study of intramolecular distances and dynamics has first been demonstrated for a series of flexible oligopeptides (10,15,16). Based on the results obtained for model compounds, the experimental and theoretical methods were applied in a study of protein folding and dynamics. In the following we shall review experiments done towards the investigation of protein denatura-tion and folding by fluorescence labeling and energy transfer measurements. 

In the crystal of 1,4-dicinnamoylbenzene (1,4-DCB) (see Fig. 12), the distances between the intermolecular photoadductive carbons are 3.973 and 4.086 A for one cyclobutane ring, and 3.903 and 3.955 A for the other. The two topochemical pathways may occur competitively in a single crystal of 1,4-DCB at the initial stage of reaction. Then, both intramolecular photodimerization and intermolecular photopolymerization of the diolefinic mono-cyclobutane intermediate occur competitively to give tricyclic dimer 21,22,23,24-tetraphenyl-l,4,ll,14-tetraoxo-2(13),12(13-diethanol, [4.4] para-cyclophane or oligomers (Hasegawa et al., (1985). On photoirridation at room temperature the 1,4-DCB crystal gives >90% of the tricylic... 

The intramolecular distances measured at room temperature with the AEDANS FITC pair were similar in the Ca2Ei and E2V states [297]. Ca and lanthanides are expected to stabilize the Ej conformation of the Ca -ATPase, since they induce a similar crystal form of Ca -ATPase [119,157] and have similar effects on the tryptophan fluorescence [151] and on the trypsin sensitivity of Ca -ATPase [119,120]. It is also likely that the vanadate-stabilized E2V state is similar to the p2 P state stabilized by Pi [418]. Therefore the absence of significant difference in the resonance energy transfer distances between the two states implies that the structural differences between the two conformations at sites recorded by currently available probes, fall within the considerable error of resonance energy transfer measurements. Even if these distances would vary by as much as 5 A the difference between the two conformations could not be established reliably. 

The TCNQ molecule in [TR(bzim)]2-TCNQ is sandwiched between two units of [ J,-N, C -bzimAu]3 in a face-to-face manner so that it is best represented by the formula (7t-[ J,-N, C -bzimAu]3)( j,-TCNQ)(7t-[p-N, C -bzimAu]3). The cyanide groups clearly are not coordinated to the gold atoms. The distance between the centroid of TCNQ to the centroid of the AU3 unit is 3.964 A. The packing of [TR(bzim)]2-TCNQ shows a stacked linear-chain structure with a repeat pattern of-(Au3)(Au3)(p-TCNQ) (Au3)(Au3)(p-TCNQ)- an ABBABB repeat The complex [TR(bzim)]2-TCNQ contains two very short intermolecular Au Au distances of 3.152 A (identical for the two aurophilic bonds). The intermolecular Au Au distance is even shorter than the intramolecular distances in the starting compound, which are 3.475, 3.471, and 3.534 A. The adjacent AU3 units in [TR(bzim)]2-TCNQ form a chair-type structure rather than the face-to-face (nearly eclipsed) pattern reported in Balch s studies of the nitro-9-fluorenones adducts with the trinuclear Au(I) alkyl-substituted carbeniate complexes. 

The form and shape of a molecule (i.e. its steric and geometric features) derive directly from the molecular genotype , but they cannot be observed without a probe. Furthermore, they vary with the conformational, ionization and tautomeric state of the compound. Thus, the computed molecular volume can vary by around 10% as a function of conformation. The same is true of the molecular surface area, whereas the key (i.e. pharmacophoric) intramolecular distances can vary much more. 

The calculated intramolecular XY distances and the lengthening relative to the unperturbed monomers are given in Table 6. In all cases, the XY distances are elongated in the complex and these elongations range from about 0.01 A in F2 NH3 to about 0.07 A in BrF NH3. With the exception of F2- -NH3, all methods predict quite similar modifications of the XY distances... 

Tablell MP2/6-311++G(3df,2p) calculated intermolecular Y---N distances and intramolecular X-Y distances [A] of XY- -amine complexes3 ...

We will confine ourselves to those applications concerned with chemical analysis, although the Raman microprobe also enables the stress and strain imposed in a sample to be examined. Externally applied stress-induced changes in intramolecular distances of the lattice structures are reflected in changes in the Raman spectrum, so that the technique may be used, for example, to study the local stresses and strains in polymer fibre and ceramic fibre composite materials. 

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. 

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