Hydrogen bonding secondary interactions

Secondary Bonding. The atoms in a polymer molecule are held together by primary covalent bonds. Linear and branched chains are held together by secondary bonds hydrogen bonds, dipole interactions, and dispersion or van der Waal s forces. By copolymerization with minor amounts of acryhc (CH2=CHCOOH) or methacrylic acid followed by neutralization, ionic bonding can also be introduced between chains. Such polymers are known as ionomers (qv). 

For polar solutes and solvents, particularly those capable of hydrogen bonding, secondary solvent effects due to the specific nature of solute-solvent interactions may also have to be included in the model, since the ass imption that they are identical in the adsorbed and mobile phases, and therefore self-canceling, is no longer necessarily true. The addition of a secondary solvent term... 

The use of templates that can nucleate secondary structures has also been studied [23], The fundamental idea is to attach one or more conformationally flexible peptides to a rigid template that is designed to initiate either a /f-sheet or an a-helix by forming the first crucial hydrogen bonds. These interactions compensate for the loss of entropy associated with the folding process and in particular in the initiation step. This strategy has been used to develop stable helices, sheets, and artificial proteins. 

This indicates that the 170 NMR parameters are potentially sensitive to changes in the conformation of backbone chains in peptides and proteins.74 The prediction from the above results is that the magnitudes of 170 NMR parameters are the sum of intra- (e.g. secondary structures) and inter- (e.g. hydrogen bonds) molecular interactions. Therefore, in a real biological system, the effects of the two interactions on the NMR parameters should be separated from each other. In the above three examples, only the dependence of the Cq values are discussed. Of course,... 

The conformation of a protein in a particular environment affects its functional properties. Conformation is governed by the amino acid composition and their sequence as influenced by the immediate environment. The secondary, tertiary and quaternary structures of proteins are mostly due to non-covalent interactions between the side chains of contiguous amino acid residues. Covalent disulfide bonds may be important in the maintenance of tertiary and quaternary structure. The non-covalent forces are hydrogen bonding, electrostatic interactions, Van der Waals interactions and hydrophobic associations. The possible importance of these in relation to protein structure and function was discussed by Ryan (13). 

Secondary forces Forces generated by the interactions between atoms other than a covalent bond. Secondary forces include hydrogen bonding, ionic interaction, and dispersion forces. 

Primary hydrogen bonds (im) Secondary hydrogen bonds (—) Repulsive interactions (—)... 

There are various levels of structural organization of proteins primary, secondary, tertiary and quaternary. The primary structure has been defined as the sequential order of amino acid residues linked by covalent peptide bonds. The secondary structure refers to the molecular geometry located in the polypeptide chains within ordered structures, such as a-helix, (3-sheet and random coil (unordered). The tertiary structure contains the information on how the elements of the secondary structure are folded. Finally, the quaternary structure of a protein with more than one polypeptide chain shows how the different principal chains are associated and oriented with one another. The structure of proteins is stabilized by different types of interactions covalent and hydrogen bonds, hydrophobic interactions, electrostatic and van der Waals forces [3,4]. 

Various types of bonds hold together the atoms in polymeric materials, unlike in metals, for example, where only one type of bond (metaUic) exists. These types are (1) primary covalent, (2) hydrogen bond, (3) dipole interaction, (4) van der Waals, and (5) ionic. Examples of each are shown in Figure 3.1. Hydrogen bonds, dipole interactions, van der Waals bonds, and ionic bonds are known collectively as secondary (or weak) bonds. The distinctions are not always clear-cut, that is, hydrogen bonds may be considered as the extreme of dipole interactions. The secondary bonds are generally weaker bonds and are responsible for many of the bonds between different polymer chains (intermolecular bonds). 

Nonbonded contacts considerably shorter than predicted by the vdW radii, are often indicative of specific interactions between molecules (hydrogen bonds, secondary coordination, charge-transfer, etc.) and are useful in analysing solid-state properties (e.g of organic conductors, so called organic metals ). 

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