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Hydrogen bond

Model of hydrogen bonds (1) between molecules of water

ronment, the hydrogen bond free energy content is be-


tween 1 and 5 kcal/mole. This makes it stronger than a
van der Waals interaction, but weaker than covalent or
ionic bonds. This type of bond can occur in inorganic
molecules such as water and in organic molecules like
DNA and proteins.
Intermolecular hydrogen bonding is responsible for the
high boiling point of water (100 C) compared to the
other group 16 hydrides that have much weaker hydro-
gen bonds.[5] Intramolecular hydrogen bonding is partly
responsible for the secondary and tertiary structures of
proteins and nucleic acids. It also plays an important role
in the structure of polymers, both synthetic and natural.
In 2011, an IUPAC Task Group recommended a modern
AFM image of napthalenetetracarboxylic diimide molecules on evidence-based denition of hydrogen bonding, which
silver-terminated silicon, interacting via hydrogen bonding, taken was published in the IUPAC journal Pure and Applied
at 77 K. It should be noted that the contrast in-between the Chemistry. This denition species:
molecules does not arise from the hydrogen bonding, and instead
arises from an artifact related to the imaging technique [1][2][3]
The hydrogen bond is an attractive interac-
tion between a hydrogen atom from a molecule
A hydrogen bond is the electrostatic attraction between or a molecular fragment XH in which X is
two polar groups that occurs when a hydrogen (H) atom more electronegative than H, and an atom or
covalently bound to a highly electronegative atom such as a group of atoms in the same or a dierent
nitrogen (N) or oxygen (O) experiences the electrostatic molecule, in which there is evidence of bond
eld of another highly electronegative atom nearby. formation.[6]
Hydrogen bonds can occur between molecules (inter-
molecular) or within dierent parts of a single molecule An accompanying detailed technical report provides the
(intramolecular).[4] Depending on geometry and envi- rationale behind the new denition.[7]

1
2 1 BONDING

1 Bonding

An example of intermolecular hydrogen bonding in a self-


assembled dimer complex reported by Meijer and coworkers.[8] Examples of hydrogen bond donating (donors) and hydrogen
The hydrogen bonds are represented by dotted lines. bond accepting groups (acceptors)

Intramolecular hydrogen bonding in acetylacetone helps stabi-


lize the enol tautomer.
Cyclic dimer of acetic acid; dashed green lines represent hydro-
A hydrogen atom attached to a relatively electronegative gen bonds
atom will play the role of the hydrogen bond donor.[9]
This electronegative atom is usually uorine, oxygen, or
nitrogen. A hydrogen attached to carbon can also partici- number of interaction partners, which can be interpreted
pate in hydrogen bonding when the carbon atom is bound as a type of valence. These covalent features are more
to electronegative atoms, as is the case in chloroform, substantial when acceptors bind hydrogens from more
CHCl3 .[10][11][12] An example of a hydrogen bond donor electronegative donors.
is the hydrogen from the hydroxyl group of ethanol, The partially covalent nature of a hydrogen bond raises
which is bonded to an oxygen. the following questions: To which molecule or atom
In a hydrogen bond, the electronegative atom not cova- does the hydrogen nucleus belong?" and Which should
lently attached to the hydrogen is named proton accep- be labeled 'donor' and which 'acceptor'?" Usually, this is
tor, whereas the one covalently bound to the hydrogen is simple to determine on the basis of interatomic distances
named the proton donor. in the XHY system, where the dots represent the hy-
drogen bond: the XH distance is typically 110 pm,
In the donor molecule, the electronegative atom attracts
whereas the HY distance is 160 to 200 pm. Liquids
the electron cloud from around the hydrogen nucleus of
that display hydrogen bonding (such as water) are called
the donor, and, by decentralizing the cloud, leaves the
associated liquids.
atom with a positive partial charge. Because of the small
size of hydrogen relative to other atoms and molecules, Hydrogen bonds can vary in strength from very weak (1
the resulting charge, though only partial, represents a 2 kJ mol1 ) to extremely strong (161.5 kJ mol1 in the
large charge density. A hydrogen bond results when this ion HF
strong positive charge density attracts a lone pair of elec- 2).[13][14] Typical enthalpies in vapor include:
trons on another heteroatom, which then becomes the
hydrogen-bond acceptor. FH:F (161.5 kJ/mol or 38.6 kcal/mol)
The hydrogen bond is often described as an electrostatic
OH:N (29 kJ/mol or 6.9 kcal/mol)
dipole-dipole interaction. However, it also has some fea-
tures of covalent bonding: it is directional and strong, OH:O (21 kJ/mol or 5.0 kcal/mol)
produces interatomic distances shorter than the sum of
the van der Waals radii, and usually involves a limited NH:N (13 kJ/mol or 3.1 kcal/mol)
3

NH:O (8 kJ/mol or 1.9 kcal/mol)

HOH:OH+
3 (18 kJ/mol[15] or 4.3 kcal/mol; data obtained using
molecular dynamics as detailed in the reference and
should be compared to 7.9 kJ/mol for bulk water,
obtained using the same molecular dynamics.)

Quantum chemical calculations of the relevant inter-


residue potential constants (compliance constants) re-
vealed large dierences between individual H bonds of
the same type. For example, the central interresidue
NHN hydrogen bond between guanine and cytosine
is much stronger in comparison to the NHN bond be-
tween the adenine-thymine pair.[16]
The length of hydrogen bonds depends on bond strength, Crystal structure of hexagonal ice. Gray dashed lines indicate
temperature, and pressure. The bond strength itself is de- hydrogen bonds
pendent on temperature, pressure, bond angle, and en-
vironment (usually characterized by local dielectric con-
stant). The typical length of a hydrogen bond in water is water molecule. This can repeat such that every water
197 pm. The ideal bond angle depends on the nature of molecule is H-bonded with up to four other molecules, as
the hydrogen bond donor. The following hydrogen bond shown in the gure (two through its two lone pairs, and
angles between a hydrouoric acid donor and various ac- two through its two hydrogen atoms). Hydrogen bonding
ceptors have been determined experimentally:[17] strongly aects the crystal structure of ice, helping to cre-
ate an open hexagonal lattice. The density of ice is less
than the density of water at the same temperature; thus,
2 History the solid phase of water oats on the liquid, unlike most
other substances.
In the book The Nature of the Chemical Bond, Linus Paul- Liquid waters high boiling point is due to the high num-
ing credits T. S. Moore and T. F. Winmill with the rst ber of hydrogen bonds each molecule can form, relative to
mention of the hydrogen bond, in 1912.[18][19] Moore its low molecular mass. Owing to the diculty of break-
and Winmill used the hydrogen bond to account for the ing these bonds, water has a very high boiling point, melt-
fact that trimethylammonium hydroxide is a weaker base ing point, and viscosity compared to otherwise similar
than tetramethylammonium hydroxide. The description liquids not conjoined by hydrogen bonds. Water is unique
of hydrogen bonding in its better-known setting, wa- because its oxygen atom has two lone pairs and two hy-
ter, came some years later, in 1920, from Latimer and drogen atoms, meaning that the total number of bonds of
Rodebush.[20] In that paper, Latimer and Rodebush cite a water molecule is up to four. For example, hydrogen
work by a fellow scientist at their laboratory, Maurice uoridewhich has three lone pairs on the F atom but
Loyal Huggins, saying, Mr. Huggins of this laboratory only one H atomcan form only two bonds; (ammonia
in some work as yet unpublished, has used the idea of a has the opposite problem: three hydrogen atoms but only
hydrogen kernel held between two atoms as a theory in one lone pair).
regard to certain organic compounds.

HFHFHF
3 Hydrogen bonds in water
The exact number of hydrogen bonds formed by a
The most ubiquitous and perhaps simplest example of a molecule of liquid water uctuates with time and depends
hydrogen bond is found between water molecules. In a on the temperature.[21] From TIP4P liquid water simula-
discrete water molecule, there are two hydrogen atoms tions at 25 C, it was estimated that each water molecule
and one oxygen atom. Two molecules of water can participates in an average of 3.59 hydrogen bonds. At
form a hydrogen bond between them; the simplest case, 100 C, this number decreases to 3.24 due to the in-
when only two molecules are present, is called the water creased molecular motion and decreased density, while
dimer and is often used as a model system. When more at 0 C, the average number of hydrogen bonds increases
molecules are present, as is the case with liquid water, to 3.69.[21] A more recent study found a much smaller
more bonds are possible because the oxygen of one water number of hydrogen bonds: 2.357 at 25 C.[22] The dif-
molecule has two lone pairs of electrons, each of which ferences may be due to the use of a dierent method for
can form a hydrogen bond with a hydrogen on another dening and counting the hydrogen bonds.
4 4 HYDROGEN BONDS IN DNA AND PROTEINS

Where the bond strengths are more equivalent, one might


instead nd the atoms of two interacting water molecules
partitioned into two polyatomic ions of opposite charge,
specically hydroxide (OH ) and hydronium (H3 O+ ).
(Hydronium ions are also known as hydroxonium ions.)

HO H3 O+

Indeed, in pure water under conditions of standard tem-


perature and pressure, this latter formulation is applica-
ble only rarely; on average about one in every 5.5 108
molecules gives up a proton to another water molecule,
in accordance with the value of the dissociation constant
for water under such conditions. It is a crucial part of the
uniqueness of water.
Because water may form hydrogen bonds with solute pro-
ton donors and acceptors, it may competitively inhibit
the formation of solute intermolecular or intramolecu-
lar hydrogen bonds. Consequently, hydrogen bonds be-
tween or within solute molecules dissolved in water are
almost always unfavorable relative to hydrogen bonds be-
tween water and the donors and acceptors for hydrogen
bonds on those solutes.[23] Hydrogen bonds between wa-
ter molecules have an average lifetime of 1011 seconds,
or 10 picoseconds.[24]

3.1 Bifurcated and over-coordinated hy-


drogen bonds in water

A single hydrogen atom can participate in two hydrogen The structure of part of a DNA double helix
bonds, rather than one. This type of bonding is called
bifurcated (split in two or two-forked). It can ex-
ist, for instance, in complex natural or synthetic organic
molecules.[25] It has been suggested that a bifurcated hy-
drogen atom is an essential step in water reorientation.[26]
Acceptor-type hydrogen bonds (terminating on an oxy-
gens lone pairs) are more likely to form bifurcation (it
is called overcoordinated oxygen, OCO) than are donor-
type hydrogen bonds, beginning on the same oxygens
hydrogens.[27]

4 Hydrogen bonds in DNA and Hydrogen bonding between guanine and cytosine, one of two
types of base pairs in DNA.
proteins
Hydrogen bonding also plays an important role in deter- In the secondary structure of proteins, hydrogen bonds
mining the three-dimensional structures adopted by pro- form between the backbone oxygens and amide hydro-
teins and nucleic bases. In these macromolecules, bond- gens. When the spacing of the amino acid residues par-
ing between parts of the same macromolecule cause it ticipating in a hydrogen bond occurs regularly between
to fold into a specic shape, which helps determine the positions i and i + 4, an alpha helix is formed. When the
molecules physiological or biochemical role. For exam- spacing is less, between positions i and i + 3, then a 310
ple, the double helical structure of DNA is due largely helix is formed. When two strands are joined by hydro-
to hydrogen bonding between its base pairs (as well as gen bonds involving alternating residues on each partic-
pi stacking interactions), which link one complementary ipating strand, a beta sheet is formed. Hydrogen bonds
strand to the other and enable replication. also play a part in forming the tertiary structure of pro-
5

tein through interaction of R-groups. (See also protein


folding).
The role of hydrogen bonds in protein folding has also
been linked to osmolyte-induced protein stabilization.
Protective osmolytes, such as trehalose and sorbitol, shift
the protein folding equilibrium toward the folded state, in
a concentration dependent manner. While the prevalent
explanation for osmolyte action relies on excluded vol-
ume eects, that are entropic in nature, recent Circular
dichroism (CD) experiments have shown osmolyte to act
through an enthalpic eect.[28] The molecular mechanism
for their role in protein stabilization is still not well estab-
lished, though several mechanism have been proposed.
Recently, computer molecular dynamics simulations sug-
gested that osmolytes stabilize proteins by modifying the
hydrogen bonds in the protein hydration layer.[29]
Several studies have shown that hydrogen bonds play an A strand of cellulose (conformation I), showing the hydrogen
important role for the stability between subunits in mul- bonds (dashed) within and between cellulose molecules.
timeric proteins. For example, a study of sorbitol de-
hydrogenase displayed an important hydrogen bonding
network which stabilizes the tetrameric quaternary struc- aramid bre, where hydrogen bonds stabilize the linear
ture within the mammalian sorbitol dehydrogenase pro- chains laterally. The chain axes are aligned along the bre
tein family.[30] axis, making the bres extremely sti and strong. Hydro-
A protein backbone hydrogen bond incompletely shielded gen bonds are also important in the structure of cellulose
from water attack is a dehydron. Dehydrons promote and derived polymers in its many dierent forms in na-
the removal of water through proteins or ligand binding. ture, such as wood and natural bres such as cotton and
The exogenous dehydration enhances the electrostatic ax.
interaction between the amide and carbonyl groups by The hydrogen bond networks make both natural and syn-
de-shielding their partial charges. Furthermore, the de- thetic polymers sensitive to humidity levels in the atmo-
hydration stabilizes the hydrogen bond by destabilizing sphere because water molecules can diuse into the sur-
the nonbonded state consisting of dehydrated isolated face and disrupt the network. Some polymers are more
charges.[31] sensitive than others. Thus nylons are more sensitive than
aramids, and nylon 6 more sensitive than nylon-11.

5 Hydrogen bonds in polymers


6 Symmetric hydrogen bond

A symmetric hydrogen bond is a special type of hydro-


gen 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 three-
center four-electron bond. This type of bond is much
stronger than a normal hydrogen bond. The eective
bond order is 0.5, so its strength is comparable to a cova-
lent bond. It is seen in ice at high pressure, and also in the
solid phase of many anhydrous acids such as hydrouoric
Para-aramid structure
acid and formic acid at high pressure. It is also seen in

Many polymers are strengthened by hydrogen bonds in the biuoride ion [FHF] .
their main chains. Among the synthetic polymers, the Symmetric hydrogen bonds have been observed recently
best known example is nylon, where hydrogen bonds spectroscopically in formic acid at high pressure (>GPa).
occur in the repeat unit and play a major role in Each hydrogen atom forms a partial covalent bond with
crystallization of the material. The bonds occur between two atoms rather than one. Symmetric hydrogen bonds
carbonyl and amine groups in the amide repeat unit. They have been postulated in ice at high pressure (Ice X). Low-
eectively link adjacent chains to create crystals, which barrier hydrogen bonds form when the distance between
help reinforce the material. The eect is greatest in two heteroatoms is very small.
6 10 HYDROGEN BONDING PHENOMENA

7 Dihydrogen bond 9 Dynamics probed by spectro-


scopic means
The hydrogen bond can be compared with the closely re- The dynamics of hydrogen bond structures in water
lated dihydrogen bond, which is also an intermolecular can be probed by the IR spectrum of OH stretching
bonding interaction involving hydrogen atoms. These vibration.[35] In terms of hydrogen bonding network in
structures have been known for some time, and well protic organic ionic plastic crystals (POIPCs), which are
characterized by crystallography;[32] however, an under- a type of phase change materials exhibiting solid-solid
standing of their relationship to the conventional hydro- phase transitions prior to melting, variable-temperature
gen bond, ionic bond, and covalent bond remains un- infrared spectroscopy can reveal the temperature depen-
clear. Generally, the hydrogen bond is characterized dence of hydrogen bonds and the dynamics of both the
by a proton acceptor that is a lone pair of electrons in anions and the cations.[36] The sudden weakening of
nonmetallic atoms (most notably in the nitrogen, and hydrogen bonds during the solid-solid phase transition
chalcogen groups). In some cases, these proton accep- seems to be coupled with the onset of orientational or
tors may be pi-bonds or metal complexes. In the dihy- rotational disorder of the ions.[36]
drogen bond, however, a metal hydride serves as a proton
acceptor, thus forming a hydrogen-hydrogen interaction.
Neutron diraction has shown that the molecular geom-
etry of these complexes is similar to hydrogen bonds, in 10 Hydrogen bonding phenomena
that the bond length is very adaptable to the metal com-
plex/hydrogen donor system.[32] Dramatically higher boiling points of NH3 , H2 O,
and HF compared to the heavier analogues PH3 ,
H2 S, and HCl.
Increase in the melting point, boiling point,
solubility, and viscosity of many compounds can be
explained by the concept of hydrogen bonding.
Occurrence of proton tunneling during DNA repli-
cation is believed to be responsible for cell
8 Advanced theory of the hydrogen mutations.[37]
bond Viscosity of anhydrous phosphoric acid and of
glycerol

In 1999, Isaacs et al.[33] showed from interpretations of Dimer formation in carboxylic acids and hexamer
the anisotropies in the Compton prole of ordinary ice formation in hydrogen uoride, which occur even in
that the hydrogen bond is partly covalent. Some NMR the gas phase, resulting in gross deviations from the
data on hydrogen bonds in proteins also indicate covalent ideal gas law.
bonding. Pentamer formation of water and alcohols in apolar
Most generally, the hydrogen bond can be viewed as a solvents.
metric-dependent electrostatic scalar eld between two or
High water solubility of many compounds such as
more intermolecular bonds. This is slightly dierent from
ammonia is explained by hydrogen bonding with
the intramolecular bound states of, for example, covalent
water molecules.
or ionic bonds; however, hydrogen bonding is generally
still a bound state phenomenon, since the interaction en- Negative azeotropy of mixtures of HF and water
ergy has a net negative sum. The initial theory of hydro-
gen bonding proposed by Linus Pauling suggested that Deliquescence of NaOH is caused in part by reaction
the hydrogen bonds had a partial covalent nature. This of OH with moisture to form hydrogen-bonded H
remained a controversial conclusion until the late 1990s 3O
when NMR techniques were employed by F. Cordier et al. 2 species. An analogous process happens between
to transfer information between hydrogen-bonded nuclei, NaNH2 and NH3 , and between NaF and HF.
a feat that would only be possible if the hydrogen bond The fact that ice is less dense than liquid water is due
contained some covalent character.[34] While much ex- to a crystal structure stabilized by hydrogen bonds.
perimental data has been recovered for hydrogen bonds
in water, for example, that provide good resolution on The presence of hydrogen bonds can cause an
the scale of intermolecular distances and molecular ther- anomaly in the normal succession of states of matter
modynamics, the kinetic and dynamical properties of the for certain mixtures of chemical compounds as tem-
hydrogen bond in dynamic systems remain unchanged. perature increases or decreases. These compounds
7

can be liquid until a certain temperature, then solid [8] Beijer, Felix H.; Kooijman, Huub; Spek, Anthony
even as the temperature increases, and nally liq- L.; Sijbesma, Rint P.; Meijer, E. W. (1998).
uid again as the temperature rises over the anomaly Self-Complementarity Achieved through Quadru-
interval[38] ple Hydrogen Bonding. Angew. Chem. Int.
Ed. 37 (12): 7578. doi:10.1002/(SICI)1521-
Smart rubber utilizes hydrogen bonding as its sole 3773(19980202)37:1/2<75::AID-ANIE75>3.0.CO;2-R.
means of bonding, so that it can heal when torn,
[9] Campbell, Neil A.; Brad Williamson; Robin J. Heyden
because hydrogen bonding can occur on the y be- (2006). Biology: Exploring Life. Boston, Massachusetts:
tween two surfaces of the same polymer. Pearson Prentice Hall. ISBN 0-13-250882-6.
Strength of nylon and cellulose bres. [10] Wiley, G.R.; Miller, S.I. (1972). Thermodynamic pa-
rameters for hydrogen bonding of chloroform with Lewis
Wool, being a protein bre, is held together by bases in cyclohexane. Proton magnetic resonance study.
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can permanently break the hydrogen bonds and a
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(2008). Solute-solvent complex switching dynamics of
chloroform between acetone and dimethylsulfoxide-two-
dimensional IR chemical exchange spectroscopy. The
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[38] Law-breaking liquid dees the rules. Physicsworld.com
doi:10.1080/00268970701877921.
(September 24, 2004 )
[28] Politi, Regina; Harries, Daniel (2010). Enthalpi-
cally driven peptide stabilization by protective os-
molytes. ChemComm. 46 (35): 64496451. 12 Further reading
doi:10.1039/C0CC01763A.

[29] Gilman-Politi, Regina; Harries, Daniel (2011). Unravel- George A. Jerey. An Introduction to Hydrogen
ing the Molecular Mechanism of Enthalpy Driven Pep- Bonding (Topics in Physical Chemistry). Oxford
tide Folding by Polyol Osmolytes. Journal of Chem- University Press, USA (March 13, 1997). ISBN 0-
ical Theory and Computation. 7 (11): 38163828. 19-509549-9
doi:10.1021/ct200455n.

[30] Hellgren, M; Kaiser, C; de Haij, S; Norberg, A;


Hg, JO (December 2007). A hydrogen-bonding net- 13 External links
work in mammalian sorbitol dehydrogenase stabilizes
the tetrameric state and is essential for the catalytic The Bubble Wall (Audio slideshow from the Na-
power.. Cellular and molecular life sciences : CMLS. 64
tional High Magnetic Field Laboratory explaining
(23): 312938. doi:10.1007/s00018-007-7318-1. PMID
17952367.
cohesion, surface tension and hydrogen bonds)

[31] Fernndez, A; Rogale K; Scott Ridgway; Scheraga H.A. isotopic eect on bond dynamics
(June 2004). Inhibitor design by wrapping pack-
ing defects in HIV-1 proteins.. Proceedings of the
National Academy of Sciences. 101 (32): 116405.
doi:10.1073/pnas.0404641101. PMID 15289598.
9

14 Text and image sources, contributors, and licenses


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