Structural Biochemistry/Chemical Bonding/Hydrogen bonds

A hydrogen bond is formed by a dipole-dipole force between an electronegative atom (the hydrogen acceptor) and a hydrogen atom that attaches covalently with another electronegative atom (the hydrogen donor) of the same molecule or of a different molecule. Only nitrogen, oxygen, and fluorine atoms can interact with hydrogen to form a hydrogen bond donor; this is different than a hydrogen covalent bond. The hydrogen bond acceptor however can be any atom which is in a polar bond, is electronegative, and has a lone pair. In a hydrogen bond, the lone pair electrons on oxygen, nitrogen, or fluorine interact with the partial positive hydrogen that is covalently bonded to one of those atoms. The hydrogen atom in a hydrogen bond is shared by two electronegative atoms such as oxygen or nitrogen.) Hydrogen bonds are responsible for specific base-pair formation in the DNA double helix and a major factor to the stability of the DNA double helix structure. A hydrogen-bond donor includes the hydrogen atom and the atom to which it is most tightly linked with. The hydrogen-bond also play a very important roles in proteins' structure because it stabalizes the secondary, tertiary and quaternary structure of proteins which formed by alpha helix, beta sheets, turns and loops. The hydrogen-bond connected the amino acides between different polypeptide chains in proteins structure.    The hydrogen-bond acceptor is the atom that is less tightly linked to the hydrogen atom.

Hydrogen bonds are fundamentally electrostatic interactions and are much weaker than covalent bonds. They are, however, the strongest kind of dipole-dipole interaction. The electronegative atom to which the hydrogen atom is bonded with pulls electron density away from the hydrogen atom, developing a partial positive charge. Therefore, the hydrogen atom can then interact with a partial negatively charged atom through an electrostatic interaction.



Components
Hydrogen bonding is a form of electrostatic interaction between a hydrogen atom bonded to two electronegative atoms; one of which is the hydrogen-bond donor that has a stronger bond between itself and the hydrogen. These electronegative atoms are nitrogen, oxygen, and fluorine; this electronegative atom pulls electron density away from the hydrogen atom, giving it a partially positive charge. This partial positive charge is attracted to the partial negative charge of the hydrogen bond acceptor (an electron density rich atom). The chemical bond formed between the hydrogen-bond donor, hydrogen atom, and hydrogen-bond acceptor has a straight, linear structure.

H-bonding
Hydrogen bonding (H-bond) is a non-covalent type of bonding between molecules or within them, intermolecularly or intramolecularly. This type of bonding is much weaker and much longer than the covalent bond and ionic bonds, but it is stronger than a van der waals interaction. It also carries some features of covalent bonding: direct and straight. In other words, H-bond donor and H-bond acceptor lie along the straight line. In order to form an H-bond, an H-bond donor and H-bond acceptor are required. The H-bond donor is the molecule that has a hydrogen atom bonded to a highly electronegative, small atom with available valence (N, F, and O follow the above description the best because they are very electronegative, making H, which is covalently attached to them, very positive). The H-O, H-N, and H-F bonds are extremely polar; as a result, the electron density is easily withdrawn from the hydrogen atom towards the electronegative atom. The partially positive hydrogen in one molecule attracts to partially negative lone pair of the electronegative atom on the other molecule and H-bond forms as a result of such an interaction. All the hydrogen bonds vary in strength

Other important facts about hydrogen bonding are as follows. The small sizes of nitrogen, oxygen, and fluorine are essential to H bonding for two reasons. One is that it makes those atoms electronegative that their covalently bonded H is highly positive. Other reason is that it allows the lone pair on the other oxygen, nitrogen, or fluorine to come close to the H. Also, hydrogen bonding has a profound impact in many systems. Hydrogen bonding is also involves in the action of many enzymes [The Molecular Nature of Matter and Change].

Properties of Water Due to Hydrogen Bonding
Ammonia, water, and hydrogen fluoride all have higher boiling points than other similar molecules, which is due to hydrogen bonds. Bonds between hydrogen and these strongly electronegative atoms are very polar, with a partial positive charge on hydrogen. This partially positive hydrogen is strongly attracted to the partially negative oxygen on the adjacent molecule. In general, boiling points rise with the increase molecular weight, both because the additional mass requires higher temperature for rapid movement of the molecules and because heavier molecules have a greater London forces. Water's freezing point is also much higher than other similar molecules. An unusual feature is that it decreases in density when it freezes. The tetrahedral structure around each oxygen atom, with two regular bonds to hydrogen and two to other molecules. This requires a great amount of space between the ice molecules. Clathrates are molecules trapped in holes of solid, like ice, that is theorized to be able to be used as anesthesia.

Hydrogen bond and physical properties
Hydrogen bonding has a significant influence on a molecule's boiling points. The boiling point usually increases with the increase of the molar mass. However, molecules that are involved in intermolecular H-bonding bonding have much higher boiling points in comparison with the molecules of the same molar mass that are not involved in H-bonding. This is because the unusually strong H-bonding forces allow for stronger interaction between water molecules and therefore creating a stronger bond and higher boiling point. In addition, H-bonding is responsible for many unusual proprieties of water, such as its high boiling point, melting point, heat of vaporization, high dielectric constant, surface tension, capillary action etc.

Hydrogen bonding can occur between hydrogen and four other elements. Oxygen(most common), Fluorine, Nitrogen and Carbon. Carbon is the special case in that it only really interacts in hydrogen bonding when it is bound to very electronegative elements such as Fluorine and Chlorine.

Hydrogen bonding is an important component of the three major macromolecules in biochemistry such as proteins, nucleic acids, and carbohydrates. The H-bonding is responsible for the structure and properties of proteins(enzymes). Hydrogen bonding is applicable in these biomolecules because of functional groups present. Some such are the carboxylic acid, alcohol or even amine groups. These provide either an hydrogen, oxygen or nitrogen for possible hydrogen bonds.

Hydrogen bond in proteins
As previously mentioned, hydrogen bond can be intermolecular (ex. the bonding of water molecules) as well as intramolecular (ex. the bonding of protein and DNA). The secondary structure of protein forms as a result of H-bonding between amino acids. For example, an α-helix is a rod-like secondary structure that forms as a result of H-bonding between the carboxyl group of (i) amino acid to the amino group of (i+4) amino acid. The turn (loop family) is a secondary structure which forms as a result of H-bond between carboxyl group of (i) amino acid and amino group of (i+3) amino acid. The β-sheet is a secondary structure which forms as a result of H-bonding between two or more β-strands. An anti-parallel β-strands forms hydrogen bonds that are straight due to the carbonyl group and the amino group being directly aligned, while a parallel β-strand forms hydrogen bonds that are slightly weaker in comparison to the anti-parallel because the carbonyl group and the amino group don't align perfectly, which forms a longer and weaker hydrogen bond.

The solubility of proteins in water is dependent on the ability to form hydrogen bonds with the protein surface. Proteins that have a greater hydrophilic surface content are generally more capable of forming hydrogen bonds with the surrounding water. The alteration of salt concentration of the solution, as is performed in salting out/in, creates a shielding effect that reduces the ability to form an H-bond with the hydrogens in water. The protein precipitation method of salting out utilizes this concept in protein fractionation.

Hydrogen bonding in water


The simplest example of a hydrogen bond can be found in water molecules. A water molecule consists of one oxygen atom attached to two hydrogen atoms. A hydrogen bond can be formed between two molecules of water. In the case of liquid water where there are many water molecules present, each water molecule could potentially hydrogen bond with up to 4 other molecules (2 through its 2 hydrogen atoms with each hydrogen bonding to another oxygen and another 2 through its 2 lone pairs on the oxygen that can hydrogen bond to 2 other hydrogen atoms).

Although water has a low molecular mass, it has an unusually high boiling point. This property can be attributed to the large number of hydrogen bonds that exist within the water. Since these bonds are difficult to break, water’s melting point, viscosity, and boiling point are relatively high in comparison to other liquids that are similar but lack the hydrogen bonding. Water contains substantially more hydrogen bonds (up to 4) relative to certain other liquids that also have hydrogen bonding. An example would be ammonia in which the nitrogen only has one lone pair but 3 hydrogen atoms and thus only capable of forming up to 2 hydrogen bonds.

Hydrogen bonding can also explain why the density of ice is less than the density of liquid water. In water's liquid form, the hydrogen bonding that keeps the molecules close together is constantly being broken and remade repeatedly at room temperature. But as the water turns into ice, the hydrogen bonding causes the water molecules to form a rigid, lattice structure, which causes large gaps between the molecules, resulting in it's smaller density yet larger volume.

Hydrogen bonding also accounts for water's high surface tension. The large availability of hydrogen bonding between water molecules (4 hydrogen bonds to one water molecule) proves how well they can stick to each other, forming a strong and stretchy surface. Common examples from which this characteristic can be observed include a cup filled slightly over the top without spilling over, or small organisms that are able to stay on top of the water without breaking its surface.

Water has a different number of hydrogen bonds depending upon the temperature. It is estimated that at 0oC each water molecule has an average of 3.69 hydrogen bonds, while at 25oC it has an average of 3.59 hydrogen bonds, and at 100oC it has an average of 3.24 bonds. The decreasing hydrogen bonds with an increase in temperature can be attributed due to the increase of molecular motion.

Hydrogen bonding in DNA
DNA contains four bases: Guanine, Cytosine, Adenine, and Thymine. The complementary base pairs of guanine with cytosine and adenine with thymine connect to one another using hydrogen bonds. These hydrogen bonds between complementary nucleotides are what keeps the two strands of a DNA helix together. Each base can also form hydrogen bonds with the external environment such as with water. Although these internal and external hydrogen bonds are fairly weak, the consolidated power of all the millions of hydrogen bonds in DNA make it a stable molecule. Also, the hydrogen bonds on the phosphate groups on each nucleotide interact inducing two strands of DNA to conform to a helical structure.

The base pairing in the DNA (one purine and one pyrimidine base) can be explained in more details. In addition to holding the DNA strands together, the hydrogen bonding between the complementary bases also sequester the bases in the interior of the double helix. Therefore, the hydrogen bonding between the bases reinforces the hydrophobic effects that stabilize the DNA. The hydrophobic bases are again kept in the inside of the helix, whereas the polar exterior is touching the solvent water. The hydrogen bonding is a weak molecular force, but it is an additive effect that stabilizes the DNA molecule. The bases are precisely held by hydrogen bonding with the energy of 1 to 5 kcal/ mol (4 to 21 kJ/mol).

The hydrogen bonding in the DNA bases of one purine (guanine and adenine) and one pyrimidine (cytosine and thymine) creates a similar shape. The pairing of guanine and cytosine shape and structure is very similar to that of the pairing of adenine and thymine. Cytosine and Guanine are held together by three hydrogen bonds. The pairing of adenine and thymine share two hydrogen bonds, thus the bond is slightly weaker and slightly longer.