Biochemistry - Chemical Reactions in Living Cells Volume 1 - D. Metzler 1980

How molecules join together
Forces acting between molecules
Hydrogen bonds and the structure of water

One of the most crucial types of weak bonds between biologically active molecules is the Hydrogen bond (Ch. 2, Sec. A.7). We have already discussed The Role of this type of dipole-dipole interaction in shaping The Structure of Proteins, CARBOHYDRATES, and Nucleic Acids. Let us now examine The Significance of Hydrogen Bonds in the biological solvent—Water.

Biochemists often use METABOLISM/2.html">THE CONCEPT OF "water structure" to describe the ability of large groups of liquid water molecules (clusters) to form ice-like structures via hydrogen bonds. In ordinary ice, all water molecules are linked to one another by hydrogen bonds, with every six molecules forming a six-membered ring resembling a cyclohexane ring. This structure persists throughout the entire ice crystal because hydrogen bonds also form between water molecules of adjacent rings. Each oxygen atom is covalently bonded to two hydrogen atoms and, in addition, forms hydrogen bonds with two hydrogen atoms from other water molecules. (Some of these Hydrogen bonds are indicated by dashed arrows in the figure below.)

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Water molecules in ice crystals can adopt various orientations within the hexagonal structure (see figure). They retain rotational freedom and are therefore able to form hydrogen bonds in multiple directions. This kind of disorder persists even at low temperatures, making ice one of the few substances that possess residual Entropy at absolute zero. Another unusual property of ice is that its constituent water molecules are not packed in the densest possible arrangement, but instead form an "open" structure. The diameter of the cavity inside the hexagon, which also extends through the centers of underlying hexagons, is approximately 0,06 nm.

Although many questions regarding the structure of liquid water remain unresolved, the existence of ice-like clusters that continuously break down and reform is firmly established; these clusters are frequently referred to as flickering clusters.

Water molecules form hydrogen bonds not only with each other, but also with polar groups of dissolved compounds. At the same time, any group capable of forming a hydrogen bond with another group can form hydrogen bonds of approximately the same strength with water molecules as well. For this very reason, hydrogen bonds do not always promote the association of small molecules In aqueous solutions. The fact that certain polar molecules bind strongly to one another via hydrogen bonds in a nonpolar solvent does not at all imply that they will associate in water. What, then, leads biochemists to assert that hydrogen bonds play a vital role in macromolecular Structuring and the interaction of biologically important compounds? The key is that the equilibrium between states in which interacting molecular pairs in water are hydrogen-bonded to each other or dissociated is easily shifted in either direction. For instance, proteins and nucleic acids can form compact structures through intramolecular hydrogen bonds between specific groups, or they can denature As a result of hydrogen bonding between those same groups and water molecules, with the Free energy difference between these two states being relatively small.

Perhaps the primary reason for the profound significance of hydrogen bonds in biochemistry is that they frequently ensure the complementarity of interacting molecular surfaces. In other words, the spatial arrangement of hydrogen-bonding groups on the surfaces of interacting molecules serves as a crucial "blueprint" ensuring the precise alignment of these surfaces. However, the forces driving the aggregation of many organic molecules and their binding to one another in aqueous solutions are not limited to hydrogen bonds alone.