Hydrogen bonds in biomolecules

S—H—O and S—H—hydrogen bonds also can form. Figure 11-14 includes a view of hydrogen bonding between glycine molecules, and we examine more details of hydrogen bonding in biomolecules in Chapter 13. 

These 46 publications include studies of the structure and bonding of molecules, thermochemistry, ioniation potentials and electron affinities, vibrational spectroscopy, internal rotation, hydrogen bonding in both small molecules and in biomolecules, intermolecular interactions, reactive intermediates, polymers and solvation effects. 

The importance of the hydrogen bond in determining the structure and function of Nature s biomolecules (e.g., DNA, RNA, proteins) is well known. We, therefore, restrict our... 

Based on isotopic substitution, a low-frequency band with a maximum around 100 cm" in liquid amides and proteins is assigned to a mode involving motions of atoms in the hydrogen bonds. This motion can drive the making or breaking of hydrogen bonds in amides and proteins and this mode is an example of how a fast dynamical mode can drive a conformational change of a biomolecule. 

In an atomic level simulation, the bond stretch vibrations are usually the fastest motions in the molecular dynamics of biomolecules, so the evolution of the stretch vibration is taken as the reference propagator with the smallest time step. The nonbonded interactions, including van der Waals and electrostatic forces, are the slowest varying interactions, and a much larger time-step may be used. The bending, torsion and hydrogen-bonding forces are treated as intermediate time-scale interactions. 

Absorption, metaboHsm, and biological activities of organic compounds are influenced by molecular interactions with asymmetric biomolecules. These interactions, which involve hydrophobic, electrostatic, inductive, dipole—dipole, hydrogen bonding, van der Waals forces, steric hindrance, and inclusion complex formation give rise to enantioselective differentiation (1,2). Within a series of similar stmctures, substantial differences in biological effects, molecular mechanism of action, distribution, or metaboHc events may be observed. Eor example, (R)-carvone [6485-40-1] (1) has the odor of spearrnint whereas (5)-carvone [2244-16-8] (2) has the odor of caraway (3,4). 

Since hydration of biomolecules is of particular importance in molecular biology, uracil - water (U-W) complexes have been studied by many groups [98 JCS(F) 1277, 98JST307, 99JPC(A)1611, 00PCCP1281]. In the cyclic U-W complex the most stable hydrogen bond is formed at the site characterized by the lowest proton... 

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. 

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