A-shaped molecules

New molecular design approach for non-centrosymmetric crystal structures - A-shaped molecules for frequency doubling. Appl Phys. Lett., 60, 935-7. [213]... 

It gives information on the geometry of the chromophore, the part of the molecule responsible for the NLO response (for an ideal donor/acceptor one-dimensional system DR = 5, for an octupolar molecule, DR = 1.5 whereas for a A-shape molecule, the amplitude of DR depends on the angle between the chromophore as well as on the D/A groups). On the other hand, the EFISHG measurements give information on the projection of the vector part of p on the dipole moment vector ... 

Haag W O, Lago R M and Weisz P B 1982 Transport and reactivity of hydrocarbon molecules in a shape-selective zeolite Faraday Disouss. Chem. Soo. 72 317-30... 

A simple example would be in a study of a diatomic molecule that in a Hartree-Fock calculation has a bonded cr orbital as the highest occupied MO (HOMO) and a a lowest unoccupied MO (LUMO). A CASSCF calculation would then use the two a electrons and set up four CSFs with single and double excitations from the HOMO into the a orbital. This allows the bond dissociation to be described correctly, with different amounts of the neutral atoms, ion pair, and bonded pair controlled by the Cl coefficients, with the optimal shapes of the orbitals also being found. For more complicated systems... 

Unlike the forces between ions which are electrostatic and without direction, covalent bonds are directed in space. For a simple molecule or covalently bonded ion made up of typical elements the shape is nearly always decided by the number of bonding electron pairs and the number of lone pairs (pairs of electrons not involved in bonding) around the central metal atom, which arrange themselves so as to be as far apart as possible because of electrostatic repulsion between the electron pairs. Table 2.8 shows the essential shape assumed by simple molecules or ions with one central atom X. Carbon is able to form a great many covalently bonded compounds in which there are chains of carbon atoms linked by single covalent bonds. In each case where the carbon atoms are joined to four other atoms the essential orientation around each carbon atom is tetrahedral. 

Phosphorus trifluoride is a colourless gas the molecule has a shape similar to that of phosphine. Although it would not be expected to be an electron donor at all (since the electronegative... 

Table 1 3 lists the dipole moments of various bond types For H—F H—Cl H—Br and H—I these bond dipoles are really molecular dipole moments A polar molecule has a dipole moment a nonpolar one does not Thus all of the hydrogen halides are polar molecules To be polar a molecule must have polar bonds but can t have a shape that causes all the individual bond dipoles to cancel We will have more to say about this m Section 1 11 after we have developed a feeling for the three dimensional shapes of molecules... 

Protein tertiary structure is also influenced by the environment In water a globu lar protein usually adopts a shape that places its hydrophobic groups toward the interior with Its polar groups on the surface where they are solvated by water molecules About 65% of the mass of most cells is water and the proteins present m cells are said to be m their native state—the tertiary structure m which they express their biological activ ity When the tertiary structure of a protein is disrupted by adding substances that cause the protein chain to unfold the protein becomes denatured and loses most if not all of Its activity Evidence that supports the view that the tertiary structure is dictated by the primary structure includes experiments m which proteins are denatured and allowed to stand whereupon they are observed to spontaneously readopt their native state confer matron with full recovery of biological activity... 

The above discussion points out the difficulty associated with using the linear dimensions of a molecule as a measure of its size It is not the molecule alone that determines its dimensions, but also the shape in which it exists. Linear arrangements of the sort described above exist in polymer crystals, at least for some distance, although not over the full length of the chain. We shall take up the structure of polymer crystals in Chap. 4. In the solution and bulk states, many polymers exist in the coiled form we have also described. Still other structures are important, notably the helix, which we shall discuss in Sec. 1.11. The overall shape assumed by a polymer molecule is greatly affected... 

Cyclodextrins are macrocyclic compounds comprised of D-glucose bonded through 1,4-a-linkages and produced enzymatically from starch. The greek letter which proceeds the name indicates the number of glucose units incorporated in the CD (eg, a = 6, /5 = 7, 7 = 8, etc). Cyclodextrins are toroidal shaped molecules with a relatively hydrophobic internal cavity (Fig. 6). The exterior is relatively hydrophilic because of the presence of the primary and secondary hydroxyls. The primary C-6 hydroxyls are free to rotate and can partially block the CD cavity from one end. The mouth of the opposite end of the CD cavity is encircled by the C-2 and C-3 secondary hydroxyls. The restricted conformational freedom and orientation of these secondary hydroxyls is thought to be responsible for the chiral recognition inherent in these molecules (77). 

Antibodies are large Y-shaped molecules having a molecular mass of 000 ia which the domains forming the tips of the arm biad to the... 

Molecules of nematic Hquid crystals also are aligned in flow fields which results in a viscosity that is lower than that of the isotropic Hquid the rod-shaped molecules easily stream past one another when oriented. Flow may be impeded if an electric or magnetic field is appHed to counter the flow orientation the viscosity then becomes an anisotropic property. 

Disk-shaped molecules based on a metal atom possess discotic Hquid crystal phases. An example is octasubstituted metaHophthalocyanine. FiaaHy, metallomesogens which combine both rod-like and disk-like features iato a single molecule adopt the biaxial nematic phase. In addition to there being a preferred direction for orientation of the longest molecular axis as is tme for the nematic phase, perpendicular to this direction is another preferred direction for orientation of the shortest molecular axis (12). NonmetaHomesogens which combine both rod- and disk-like features iato a single molecule also adopt a biaxial nematic phase, but at least ia one case the amount of biaxiaHty is very small (15). 

Bulky, even if highly polari2able, functional groups or atoms that are attached anywhere but on the end of a rod-shaped molecule usually are less favorable for Hquid crystal formation. Enhanced intermolecular attractions are more than countered as the molecule deviates from the required linearity. For example, the inclusion of the bromine atom at position three of 4-decyloxy-3-bromoben2oic acid [5519-23-3] (9) prevents mesomorphic behavior. In other cases the Hquid crystal phases do not disappear, but their ranges are narrower. 

The formation of photodimers of the cyclobutane type from thymine (111 R = Me) occurs most effectively when a frozen aqueous solution of the substrate is irradiated. After the independent recognition of such dimers in two laboratories about 1960, it was some six years before the main constituent was identified beyond doubt (66JCS(C)2239) as the cis-syn entity (113), a U-shaped molecule in which the planes of the six-membered rings... 

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