Interactions between molecules hydrogen-bonding

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 ). 

By decreasing the alternation of hydrogen bond donors and acceptors on the same molecule, the hydrogen bonds become stronger due to less repulsive interactions between neighboring hydrogen bonds. 

Perhaps the most important noncovalent interaction in biological molecules is tbe hydrogen bond, an attractive interaction between a hydrogen bonded to an electronegative O or N atom and an unshared electron pair on another O or N atom. In essence, a hydrogen bond is a very strong dipole-dipole interaction... 

The origin of a torsional barrier can be studied best in simple cases like ethane. Here, rotation about the central carbon-carbon bond results in three staggered and three eclipsed stationary points on the potential energy surface, at least when symmetry considerations are not taken into account. Quantum mechanically, the barrier of rotation is explained by anti-bonding interactions between the hydrogens attached to different carbon atoms. These interactions are small when the conformation of ethane is staggered, and reach a maximum value when the molecule approaches an eclipsed geometry. 

Effect of Temperature and pH. The temperature dependence of enzymes often follows the rule that a 10°C increase in temperature doubles the activity. However, this is only tme as long as the enzyme is not deactivated by the thermal denaturation characteristic for enzymes and other proteins. The three-dimensional stmcture of an enzyme molecule, which is vital for the activity of the molecule, is governed by many forces and interactions such as hydrogen bonding, hydrophobic interactions, and van der Waals forces. At low temperatures the molecule is constrained by these forces as the temperature increases, the thermal motion of the various regions of the enzyme increases until finally the molecule is no longer able to maintain its stmcture or its activity. Most enzymes have temperature optima between 40 and 60°C. However, thermostable enzymes exist with optima near 100°C. 

If the protein of interest is a heteromultimer (composed of more than one type of polypeptide chain), then the protein must be dissociated and its component polypeptide subunits must be separated from one another and sequenced individually. Subunit associations in multimeric proteins are typically maintained solely by noncovalent forces, and therefore most multimeric proteins can usually be dissociated by exposure to pEI extremes, 8 M urea, 6 M guanidinium hydrochloride, or high salt concentrations. (All of these treatments disrupt polar interactions such as hydrogen bonds both within the protein molecule and between the protein and the aqueous solvent.) Once dissociated, the individual polypeptides can be isolated from one another on the basis of differences in size and/or charge. Occasionally, heteromultimers are linked together by interchain S—S bridges. In such instances, these cross-links must be cleaved prior to dissociation and isolation of the individual chains. The methods described under step 2 are applicable for this purpose. 

Hydrophilic hydration signifies that a strong energetically favored direct interaction exists between dissolved polar or ionic particle and the surrounding water molecules by ion-dipole-, dipole-dipole-interactions and/or hydrogen bonds. 

When thinking about chemical reactivity, chemists usually focus their attention on bonds, the covalent interactions between atoms within individual molecules. Also important, hotvever, particularly in large biomolecules like proteins and nucleic acids, are a variety of interactions between molecules that strongly affect molecular properties. Collectively called either intermolecular forces, van der Waals forces, or noncovalent interactions, they are of several different types dipole-dipole forces, dispersion forces, and hydrogen bonds. 

Noncovalcnt interaction (Section 2.13) An interaction between molecules, commonly called intermolecular forces or van der VVaals forces. Hydrogen bonds, dipole-dipole forces, and dispersion forces are examples. 

Where no specific interaction such as hydrogen-bonding can occur between the polymer and the solvent, the intermolecular attraction between the dissimilar molecules is intermediate between the intermolecular forces of the similar species, i.e. 

In order to do this, experimental determinations of the intrinsic viscosities of both the standards and the fractions from the unknown polymer are required. It is possible to obtain commercial gel permeation chromatographs that will do this routinely, and hence to exploit the concept of universal cali-hration. Care must he taken, though, to ensure that the separation of the polymer molecules occurs purely as a result of size exclusion. If there are any other specific interactions, e.g. hydrogen bonding, between the polymer and the column packing, such as may occur with water-soluhle polymers, Benoit s approach does not work and the universal cafihrafion plot is not valid. 

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