Hydrogen bond

Bonding

A hydrogen atom attached to a relatively diethyl ether.

lone pair of electrons on another heteroatom, which becomes the hydrogen-bond acceptor.

The hydrogen bond is often described as an electrostatic dipole-dipole interaction. However, it also has some features of covalent bonding: it is directional, strong, produces interatomic distances shorter than sum of van der Waals radii, and usually involves a limited number of interaction partners, which can be interpreted as a kind of valence. These covalent features are more significant when acceptors bind hydrogens from more electronegative donors.

The partially covalent nature of a hydrogen bond raises the questions: "To which molecule or atom does the hydrogen nucleus belong?" and "Which should be labeled 'donor' and which 'acceptor'?" Usually, this is easy to determine simply based on interatomic distances in the X-H...Y system: X-H distance is typically ~1.1 Å, whereas H...Y distance is ~ 1.6 to 2.0 Å. Liquids that display hydrogen bonding are called associated liquids.

Hydrogen bonds can vary in strength from very weak (1-2 kJ mol⁻¹) to extremely strong (>155 kJ mol⁻¹), as in the ion HF₂⁻.^[3] Typical values include:

• F—H^...:F (155 kJ/mol or 40 kcal/mol)
• O—H^...:N (29 kJ/mol or 6.9 kcal/mol)
• O—H^...:O (21 kJ/mol or 5.0 kcal/mol)
• N—H^...:N (13 kJ/mol or 3.1 kcal/mol)
• N—H^...:O (8 kJ/mol or 1.9 kcal/mol)
• HO—H^...:OH₃⁺ (18 kJ/mol^[4] or 4.3 kcal/mol) {Data obtained using molecular dynamics.}

The length of hydrogen bonds depends on bond strength, temperature, and pressure. The bond strength itself is dependent on temperature, pressure, bond angle, and environment (usually characterized by local dielectric constant). The typical length of a hydrogen bond in water is 1.97 Å (197 pm).

Hydrogen bonds in water

  The most ubiquitous, and perhaps simplest, example of a hydrogen bond is found between water molecules. In a discrete water molecule, water has two hydrogen atoms and one oxygen atom. Two molecules of water can form a hydrogen bond between them; the simplest case, when only two molecules are present, is called the water dimer and is often used as a model system. When more molecules are present, as is the case in liquid water, more bonds are possible because the oxygen of one water molecule has two lone pairs of electrons, each of which can form a hydrogen bond with hydrogens on two other water molecules. This can repeat so that every water molecule is H-bonded with up to four other molecules, as shown in the figure (two through its two lone pairs, and two through its two hydrogen atoms.)

ammonia has the opposite problem: three hydrogen atoms but only one lone pair).

H-F^...H-F^...H-F

The exact number of hydrogen bonds in which a molecule in liquid water participates fluctuates with time and depends on the temperature. From TIP4P liquid water simulations at 25 °C, it was estimated that each water molecule participates in an average of 3.59 hydrogen bonds. At 100 °C, this number decreases to 3.24 due to the increased molecular motion and decreased density, while at 0 °C, the average number of hydrogen bonds increases to 3.69.^[5] A more recent study found a much smaller number of hydrogen bonds: 2.357 at 25 °C.^[6] The differences may be due to the use of a different method for defining and counting the hydrogen bonds.

Were the bond strengths more equivalent, one might instead find the atoms of two interacting water molecules partitioned into two hydronium (H₃O⁺) (Hydronium ions are also known as 'hydroxonium' ions.)

H-O⁻ H₃O⁺

Indeed, in pure water under conditions of dissociation constant for water under such conditions. It is a crucial part of the uniqueness of water.

Bifurcated and over-coordinated hydrogen bonds in water

It can be that a single hydrogen atom participates in two hydrogen bonds, rather than one. This type of bonding is called "bifurcated". It was suggested that a bifurcated hydrogen atom is an essential step in water reorientation;^[7] however, the case of an oxygen lone pair participating in more than two hydrogens bonds is rarely given attention in the scientific literature.

Hydrogen bonds in DNA and proteins

 

Hydrogen bonding also plays an important role in determining the three-dimensional structures adopted by proteins and nucleic bases. In these macromolecules, bonding between parts of the same macromolecule cause it to fold into a specific shape, which helps determine the molecule's physiological or biochemical role. The double helical structure of base pairs, which link one complementary strand to the other and enable replication.

In proteins, hydrogen bonds form between the backbone oxygens and amide hydrogens. When the spacing of the alpha helix is formed. When the spacing is less, between positions i and i + 3, then a 3₁₀ helix is formed. When two strands are joined by hydrogen bonds involving alternating residues on each participating strand, a protein folding).

A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own dehydrons.

Symmetric hydrogen bond

A symmetric hydrogen bond is a special type of hydrogen bond in which the proton is spaced exactly halfway between two identical atoms. The strength of the bond to each of those atoms is equal. It is an example of a 3-center 4-electron bond. This type of bond is much stronger than "normal" hydrogen bonds, in fact, its strength is comparable to a covalent bond. It is seen in ice at high pressure, and also in the solid phase of many anhydrous acids such as hydrofluoric acid and formic acid at high pressure. It is also seen in the ion [F-H-F]−. Much has been done to explain the symmetric hydrogen bond quantum-mechanically, as it seems to violate the duet rule for the first shell: The proton is effectively surrounded by four electrons. Because of this problem, some consider it to be an ionic bond.

Symmetric hydrogen bonds have been observed recently spectroscopically in Low-barrier hydrogen bonds form when the distance between two heteroatoms is very small.

Dihydrogen bond

The hydrogen bond can be compared with the closely related molecular geometry of these complexes are similar to hydrogen bonds, in that the bond length is very adaptable to the metal complex/hydrogen donor system.

Advanced theory of the hydrogen bond

Recently the nature of the bond was elucidated. A widely publicized article^[8] proved from interpretations of the anisotropies in the Compton profile of ordinary ice, that the hydrogen bond is partly covalent. Some NMR data on hydrogen bonds in proteins also indicate covalent bonding.

Most generally, the hydrogen bond can be viewed as a metric-dependent electrostatic scalar field between two or more intermolecular bonds. This is slightly different from the kinetic and dynamical properties of the hydrogen bond in dynamic systems remains unchanged.

Hydrogen bonding phenomena

• Dramatically higher boiling points of NH₃, H₂O, and HF compared to the heavier analogues PH₃, H₂S, and HCl
• Viscosity of anhydrous glycerol
• Dimer formation in ideal gas law.
• High water solubility of many compounds such as ammonia is explained by hydrogen bonding with water molecules.
• Negative azeotropy of mixtures of HF and water
• Deliquescence of NaOH is caused in part by reaction of OH^- with moisture to form hydrogen-bonded H₂O₃^- species. An analogous process happens between NaNH₂ and NH₃, and between NaF and HF.
• The fact that Ice is less dense than liquid water is due to a crystal structure resulting from hydrogen bonds.
• The presence of hydrogen bonds can cause an anomaly in the normal succession of States of matter for certain mixtures of Chemical compounds. These compounds can be liquid until a certain temperature, then solid as it goes up, and finally liquid again as the temperature rises over the "anomaly threshold"^[9]

References

1. ^ Felix H. Beijer, Huub Kooijman, Anthony L. Spek, Rint P. Sijbesma, E. W. Meijer (1998). "Self-Complementarity Achieved through Quadruple Hydrogen Bonding". Angew. Chem. Int. Ed. 37: 75-78. doi:10.1002/(SICI)1521-3773(19980202)37:1/2%3C75::AID-ANIE75%3E3.0.CO;2-R.
2. ^ International Union of Pure and Applied Chemistry. "hydrogen bond". Compendium of Chemical Terminology Internet edition.
3. ^ Emsley, J. (1980). "Very Strong Hydrogen Bonds". Chemical Society Reviews 0: 91-124.
4. ^ Omer Markovitch and Noam Agmon (2007). "Structure and energetics of the hydronium hydration shells". J. Phys. Chem. A 111 (12): 2253 - 2256. doi:10.1021/jp068960g.
5. ^ W. L. Jorgensen and J. D. Madura (1985). "Temperature and size dependence for Monte Carlo simulations of TIP4P water". Mol. Phys. 56 (6): 1381. doi:10.1080/00268978500103111.
6. ^ Jan Zielkiewicz (2005). "Structural properties of water: Comparison of the SPC, SPCE, TIP4P, and TIP5P models of water". J. Chem. Phys. 123: 104501. doi:10.1063/1.2018637..
7. ^ Damien Laage and James T. Hynes (2006). "A Molecular Jump Mechanism for Water Reorientation". Science 311: 832. doi:10.1126/science.1122154.
8. ^ E.D. Isaacs, et al., Physical Review Letters vol. 82, pp 600-603 (1999)
9. ^ Law-breaking liquid defies the rules at physicsworld.com

• George A. Jeffrey. An Introduction to Hydrogen Bonding (Topics in Physical Chemistry). Oxford University Press, USA (March 13, 1997). ISBN 0-19-509549-9
• Acc. Chem. Res. 29 (7): 348-354. doi:10.1021/ar950150s.
• Alexander F. Goncharov, M. Riad Manaa, Joseph M. Zaug, Richard H. Gee, Laurence E. Fried, and Wren B. Montgomery (2005). "Polymerization of Formic Acid under High Pressure". Phys. Rev. Lett. 94 (6): 065505. doi:10.1103/PhysRevLett.94.065505.
• F. Cordier, M. Rogowski, S. Grzesiek and A. Bax (1999). "Observation of through-hydrogen-bond (2h)J(HC') in a perdeuterated protein". J Magn Reson. 140: 510-2.
• R. Parthasarathi, V. Subramanian, N. Sathyamurthy (2006). "Hydrogen Bonding Without Borders: An Atoms-In-Molecules Perspective". J. Phys. Chem. (A) 110: 3349-3351.