Overlapping molecules

Example applies the orbital overlap molecule to the hydronium ion, and Example treats a molecule with two inner atoms. 

A similar type of emission is observed from some crystalline hydrocarbons. For example, pyrene crystals exhibit a broad structureless band in the visible region, very similar to that observed in concentrated solutions. The crystal lattice of pyrene consists of two overlapping molecules (Type B crystal lattice) (Figure 6.6). If the overlap is small as in anthracene... 

Scheme (3) affords an alternative (though less satisfactory) means whereby a B atom can make full use of its valence orbitals (and attain the octet configuration). The 2p orbitals of boron are (like those of Be) rather too diffuse for effective p -p overlap. Molecules X—B=Y (X = H, F, Cl etc. Y = 0, S) are known, but they are unstable with respect to polymerisation to give complex O- or S-bridged species. However, the situation depicted in scheme (3) may make a significant contribution to the bonding in molecules such as BF3, thus ... 

You can save each of the overlapped molecules separately (File -> Save -> Layer) as individuakpdb or save the superimposed molecules together (File->Save->Project) as overlap.pdb. 

The parameter used to characterize to what extent the "mimetism is achieved is the total exposed molecular area of this set of overlapping molecules. The aim of the calculations is to find what are the geometries of each of the n molecules which lead to a minimal value of S-p. 

If, in a better approach for overlapping molecules, one takes as zeroth-order wave function an antisymmetrized product of the monomer wave functions ... 

FIGURE 21>30 Two double Sirand DNA molecules imaged on mica, showing the ability of an AFM to resolve overlapping molecules. (Courtesy of W. B- Stine, University of California. San Diogo. With permission.)... 

Using the Warshel-Huler method (19) it was shown (44) that the free ("gas phase") excimer consists of a pair of completely overlapped molecules, and the Stokes shift is of the order of 7500 cm l. Starting from the configuration of a pair of molecules in the crystal, excimer formation involves marked displacements in the y and z directions. Applying the same method to the crystal gives results that are perhaps not unexpected. 

Some quasi-one dimensional materials have a curious low-temperature structure along the chains of highly overlapping molecules or atoms, both... 

In order to calculate 3D descriptors, the analyzed molecule is placed into a regular, virtual, three-dimensional network of points. The 3D descriptors are basically characteristics of some physical quantities, calculated in the points of the network. The value of the 3D descriptors depends on the position in space of the considered point and on the characteristics of the atoms in certain areas of the molecule. When a group of molecules is analyzed, the network of points includes the package of overlapped molecules. The methods used to overlap molecules are highly diverse. For example, molecules can be overlapped on the common skeleton if present. Other methods overlap the vectors of the dipole moments of the molecules in the package. The value of the 3D descriptors is influenced by the method used to overlap the molecules and by the distance between the network points. A different approach is to use the molecules in the package in their position within the effector-active site ensemble if such position can be determined. 

Covalent bond, electron cloud, overlap, molecule... 

In the absence of coupling between p and Pj, p would develop spatial modulation along the z axis at wavevector q2=lnll where I is of the order of a molecular length whereas P would develop modulations at wavevector =2nil where / is identified with the length of a pair of antiparallel partially overlapping molecules as discussed in the previous section. 

---