Noncovalent intramolecular interactions

Density functional theory (DFT) calculations of two types of push-pull chromophores built around thiophene-based 7t-conjugating spacers rigidified by either covalent bonds or noncovalent intramolecular interactions (Figure 6) have been carried out to assign the relevant electronic and vibrational features and to derive useful information about the molecular structure of these NLO-phores <2003CEJ3670>. 

Isotactic vinyl polymers often possess a helical conformation in the solid state however, without bulky substituents present (vide infra) in solution at room temperature, helix—helix reversal takes place fast and no optical activity is observed. Ortiz and Kahn reported a borderline case in which a non-bonded interaction between the monomers leads to the formation of isotactic 39 (Chart 7) by anionic polymerzation at —78 °C. Optically active polymers can be isolated, but in solution the proposed one-handed helicity is lost in less than 1 h.148 An intriguing class of polymers formed by polycondensation of diboronic acid and chiral tetraalcohols has been studied by Mikami and Shinkai and is exemplified by polymer 40 (Chart 7). In this D-mannitol-based polymer, the noncovalent intramolecular interaction between the amines and the boron atoms imposed a sp3-hybridization on boron, which, according to calculations, results in a helical conformation of the macromolecule.149... 

Ozen AS, Atilgan C, Sonmez G (2007) Noncovalent intramolecular interactions in the monomers and oligomers of the acceptor and donor type of low band gap conducting polymers. J Phys Chem C 111 16362... 

So what do CAMs tell us about GPGR activation We have seen how active states can be achieved by destabilizing the normal arrangement of TM domains by mutations at several different sites. As discussed above, TM domains are held in the basal state primarily by a network of noncovalent interactions between side chains. Thus, any compound that disrupts one of the many intramolecular interactions that stabilize the basal state could have, in principle, agonist activity. The process of disrupting a stabilizing... 

Noncovalent interactions are weak inter- or intramolecular interactions that result from a combination of electrostatic interactions (ionic), hydrogen bonding, hydrophobic interactions (stacking or intercalation), and van der Waals interactions (dipole-dipole or induced dipole-induced dipole). Complexes formed by these types of interactions are usually fragile. This property is often essential to their biological function, which depends on the equilibria between the associated and free forms of these molecules. 

We have recently shown that 3,6-dimethoxythieno[3,2-h]thiophene 21 leads to a polymer presenting low oxidation potential and moderate bandgap (1.7 eV) [74]. The advantage of thienothiophene unit compared to bithiophene one resides in the planar structure and absence of positional isomers. Furthermore, the crystallographic structure of the dimer 22 (Figure 13.1), shows a hilly planar conjugated system stabilized by noncovalent intramolecular sulhir-oxygen interactions. 

The self-rigidification associated with noncovalent S-O intramolecular interactions between adjacent EDOT units has been observed for many EDOT-based tr-conjugated systems [60]. 

It seems fair to say that, in general, intermolecular noncovalent interactions, of whatever type, receive more attention than do intramolecular ones. However the latter can also be very important. For instance, intramolecular attractions are responsible for chlorotrinitromethane, C1-C(N02)3, having the shortest C(sp )-Cl bond ever observed crystallographically [36]. Another intramolecular interaction is a key factor in the remarkable increase in detonation sensitivity that occurs when the central carbon in the explosive PETN (2) is replaced by a silicon (3) [37]. 

Contributions from various noncovalent, supramolecular interactions are present in both low molecular weight and polymeric organic materials. Even conventional macromolecules, stabilized by mainchain covalent bonds as originally described by Staudinger, display a variety of supramolecular effects that control their intramolecular conformation and their intermolecular interactions. The selection of systems to be included in a book on supramolecular polymers was therefore a delicate task. 

A number of issues need to be addressed before this method will become a routine tool applicable to problems as the conformational equilibrium of protein kinase. E.g. the accuracy of the force field, especially the combination of Poisson-Boltzmann forces and molecular mechanics force field, remains to be assessed. The energy surface for the opening of the two kinase domains in Pig. 2 indicates that intramolecular noncovalent energies are overestimated compared to the interaction with solvent. 

Noncovalent interactions, both inter- and intramolecular, are of considerable importance in determining the physical properties of molecules. Such interactions can be classified as hydrogen-bonding or non-hydrogen-bonding. In this section we will explore some recent uses of the electrostatic potential in the analysis of both types. 

In p-isosparteine (14) all rings have a chairlike shape (54). Protonation of the N-16 atom makes the distance between N-1 and N-16 equal to 2.61 A, owing to the presence of an intramolecular hydrogen bond. Molecules of sparteine stereoisomers in crystals are sterically conjugated, and in all cases the angles between atoms C-6—C-7—C-17 and C-10—C-9—C-11 were increased to 116-120° (42-50). The B and C rings are flattened at their N termini as a result of noncovalent interaction of atoms with those situated next to them. The conformation of such strained molecules is stabilized by intramolecular hydrogen bonds (46). 

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