Hydrogen Bonding
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chemistry Chemistry is the science, scientific study of the properties and behavior of matter. It is a natural science that covers the Chemical element, elements that make up matter to the chemical compound, compounds made of atoms, molecules and ions ...
, a hydrogen bond (or H-bond) is a primarily
electrostatic Electrostatics is a branch of physics that studies electric charges at rest (static electricity). Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for amber ...
force of attraction between a
hydrogen Hydrogen is the chemical element with the symbol H and atomic number 1. Hydrogen is the lightest element. At standard conditions hydrogen is a gas of diatomic molecules having the formula . It is colorless, odorless, tasteless, non-toxic, an ...
(H) atom which is covalently bound to a more
electronegative Electronegativity, symbolized as , is the tendency for an atom of a given chemical element to attract shared electrons (or electron density) when forming a chemical bond. An atom's electronegativity is affected by both its atomic number and the d ...
"donor" atom or group (Dn), and another electronegative atom bearing a
lone pair In chemistry, a lone pair refers to a pair of valence electrons that are not shared with another atom in a covalent bondIUPAC ''Gold Book'' definition''lone (electron) pair''/ref> and is sometimes called an unshared pair or non-bonding pair. Lone ...
of electrons—the hydrogen bond acceptor (Ac). Such an interacting system is generally denoted , where the solid line denotes a polar
covalent bond A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atoms ...
, and the dotted or dashed line indicates the hydrogen bond. The most frequent donor and acceptor atoms are the second-row elements
nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...
(N),
oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as wel ...
(O), and
fluorine Fluorine is a chemical element with the symbol F and atomic number 9. It is the lightest halogen and exists at standard conditions as a highly toxic, pale yellow diatomic gas. As the most electronegative reactive element, it is extremely reacti ...
(F). Hydrogen bonds can be
intermolecular An intermolecular force (IMF) (or secondary force) is the force that mediates interaction between molecules, including the electromagnetic forces of attraction or repulsion which act between atoms and other types of neighbouring particles, e.g. a ...
(occurring between separate molecules) or intramolecular (occurring among parts of the same molecule). The energy of a hydrogen bond depends on the geometry, the environment, and the nature of the specific donor and acceptor atoms and can vary between 1 and 40 kcal/mol. This makes them somewhat stronger than a
van der Waals interaction In molecular physics, the van der Waals force is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds, these attractions do not result from a chemical electronic bond; they are comparatively weak and the ...
, and weaker than fully
covalent A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atoms ...
or
ionic bond Ionic bonding is a type of chemical bonding that involves the electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities, and is the primary interaction occurring in ionic compounds. ...
s. This type of bond can occur in inorganic molecules such as water and in organic molecules like DNA and proteins. Hydrogen bonds are responsible for holding materials such as
paper Paper is a thin sheet material produced by mechanically or chemically processing cellulose fibres derived from wood, rags, grasses or other vegetable sources in water, draining the water through fine mesh leaving the fibre evenly distributed ...
and felted wool together, and for causing separate sheets of paper to stick together after becoming wet and subsequently drying. The hydrogen bond is responsible for many of the physical and chemical properties of compounds of N, O, and F that seem unusual compared with other similar structures. In particular, intermolecular hydrogen bonding is responsible for the high boiling point of
water Water (chemical formula ) is an inorganic, transparent, tasteless, odorless, and nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of all known living organisms (in which it acts as a ...
(100 °C) compared to the other group-16 hydrides that have much weaker hydrogen bonds. Intramolecular hydrogen bonding is partly responsible for the secondary and
tertiary Tertiary ( ) is a widely used but obsolete term for the geologic period from 66 million to 2.6 million years ago. The period began with the demise of the non-avian dinosaurs in the Cretaceous–Paleogene extinction event, at the start ...
structures of
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
s and
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cl ...
s. It also plays an important role in the structure of
polymer A polymer (; Greek '' poly-'', "many" + ''-mer'', "part") is a substance or material consisting of very large molecules called macromolecules, composed of many repeating subunits. Due to their broad spectrum of properties, both synthetic a ...
s, both synthetic and natural.


Bonding


Definitions and general characteristics

In a hydrogen bond, the electronegative atom not covalently attached to the hydrogen is named the proton acceptor, whereas the one covalently bound to the hydrogen is named the proton donor. While this nomenclature is recommended by the IUPAC, In the hydrogen bond donor, the H center is protic. The donor is a Lewis base. Hydrogen bonds are represented as system, where the dots represent the hydrogen bond. Liquids that display hydrogen bonding (such as water) are called associated liquids. Hydrogen bonds arise from a combination of electrostatics (multipole-multipole and multipole-induced multipole interactions), covalency (charge transfer by orbital overlap), and dispersion ( London forces). Weaker hydrogen bonds are known for hydrogen atoms bound to elements such as sulfur (S) or chlorine (Cl); even carbon (C) can serve as a donor, particularly when the carbon or one of its neighbors is electronegative (e.g., in chloroform, aldehydes and terminal acetylenes). Gradually, it was recognized that there are many examples of weaker hydrogen bonding involving donor other than N, O, or F and/or acceptor Ac with electronegativity approaching that of hydrogen (rather than being much more electronegative). Although weak (≈1 kcal/mol), , "non-traditional" hydrogen bonding interactions are ubiquitous and influence structures of many kinds of materials. The definition of hydrogen bonding has gradually broadened over time to include these weaker attractive interactions. In 2011, an
IUPAC The International Union of Pure and Applied Chemistry (IUPAC ) is an international federation of National Adhering Organizations working for the advancement of the chemical sciences, especially by developing nomenclature and terminology. It is ...
Task Group recommended a modern evidence-based definition of hydrogen bonding, which was published in the IUPAC journal ''
Pure and Applied Chemistry ''Pure and Applied Chemistry'' is the official journal for the International Union of Pure and Applied Chemistry (IUPAC). It is published monthly by Walter de Gruyter Walter de Gruyter GmbH, known as De Gruyter (), is a German scholarly publ ...
''. This definition specifies:


Bond strength

Hydrogen bonds can vary in strength from weak (1–2 kJ/mol) to strong (161.5 kJ/mol in the
bifluoride The bifluoride ion is an inorganic anion with the chemical formula . The anion is colorless. Salts of bifluoride are commonly encountered in the reactions of fluoride salts with hydrofluoric acid. The commercial production of fluorine involves e ...
ion, ). Typical enthalpies in vapor include: * (161.5 kJ/mol or 38.6 kcal/mol), illustrated uniquely by * (29 kJ/mol or 6.9 kcal/mol), illustrated water-ammonia * (21 kJ/mol or 5.0 kcal/mol), illustrated water-water, alcohol-alcohol * (13 kJ/mol or 3.1 kcal/mol), illustrated by ammonia-ammonia * (8 kJ/mol or 1.9 kcal/mol), illustrated water-amide * (18 kJ/mol or 4.3 kcal/mol) The strength of intermolecular hydrogen bonds is most often evaluated by measurements of equilibria between molecules containing donor and/or acceptor units, most often in solution. The strength of intramolecular hydrogen bonds can be studied with equilibria between conformers with and without hydrogen bonds. The most important method for the identification of hydrogen bonds also in complicated molecules is
crystallography Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. Crystallography is a fundamental subject in the fields of materials science and solid-state physics (condensed matter physics). The wor ...
, sometimes also NMR-spectroscopy. Structural details, in particular distances between donor and acceptor which are smaller than the sum of the van der Waals radii can be taken as indication of the hydrogen bond strength. One scheme gives the following somewhat arbitrary classification: those that are 15 to 40 kcal/mol, 5 to 15 kcal/mol, and >0 to 5 kcal/mol are considered strong, moderate, and weak, respectively.


Resonance assisted hydrogen bond

The resonance assisted hydrogen bond (commonly abbreviated as RAHB) is a strong type of hydrogen bond. It is characterized by the π-delocalization that involves the hydrogen and cannot be properly described by the
electrostatic Electrostatics is a branch of physics that studies electric charges at rest (static electricity). Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for amber ...
model alone. This description of the hydrogen bond has been proposed to describe unusually short distances generally observed between or .


Structural details

The distance is typically ≈110  pm, whereas the distance is ≈160 to 200 pm. The typical length of a hydrogen bond in water is 197 pm. The ideal bond angle depends on the nature of the hydrogen bond donor. The following hydrogen bond angles between a hydrofluoric acid donor and various acceptors have been determined experimentally:


Spectroscopy

Strong hydrogen bonds are revealed by downfield shifts in the 1H NMR spectrum. For example, the acidic proton in the enol tautomer of
acetylacetone Acetylacetone is an organic compound with the chemical formula . It is a colorless liquid, classified as a 1,3-diketone. It exists in equilibrium with a tautomer . These tautomers interconvert so rapidly under most conditions that they are tre ...
appears at  15.5, which is about 10 ppm downfield of a conventional alcohol. In the IR spectrum, hydrogen bonding shifts the stretching frequency to lower energy (i.e. the vibration frequency decreases). This shift reflects a weakening of the bond. Certain hydrogen bonds - improper hydrogen bonds - show a blue shift of the stretching frequency and a decrease in the bond length. H-bonds can also be measured by IR vibrational mode shifts of the acceptor. The amide I mode of backbone carbonyls in α-helices shifts to lower frequencies when they form H-bonds with side-chain hydroxyl groups.


Theoretical considerations

Hydrogen bonding is of persistent theoretical interest. According to a modern description integrates both the intermolecular O:H lone pair ":" nonbond and the intramolecular polar-covalent bond associated with repulsive coupling. Quantum chemical calculations of the relevant interresidue potential constants (
compliance constants Compliance Constants are the elements of an inverted Hessian matrix. The calculation of compliance constants provides an alternative description of chemical bonds in comparison with the widely used force constants explicitly ruling out the depende ...
) revealed large differences between individual H bonds of the same type. For example, the central interresidue hydrogen bond between guanine and cytosine is much stronger in comparison to the bond between the adenine-thymine pair. Theoretically, the bond strength of the hydrogen bonds can be assessed using NCI index, non-covalent interactions index, which allows a visualization of these
non-covalent interactions In chemistry, a non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule. The c ...
, as its name indicates, using the electron density of the system. From interpretations of the
anisotropies Anisotropy () is the property of a material which allows it to change or assume different properties in different directions, as opposed to isotropy. It can be defined as a difference, when measured along different axes, in a material's physic ...
in the Compton profile of ordinary ice that the hydrogen bond is partly covalent. However, this interpretation was challenged. Most generally, the hydrogen bond can be viewed as a
metric Metric or metrical may refer to: * Metric system, an internationally adopted decimal system of measurement * An adjective indicating relation to measurement in general, or a noun describing a specific type of measurement Mathematics In mathem ...
-dependent
electrostatic Electrostatics is a branch of physics that studies electric charges at rest (static electricity). Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for amber ...
scalar field In mathematics and physics, a scalar field is a function (mathematics), function associating a single number to every point (geometry), point in a space (mathematics), space – possibly physical space. The scalar may either be a pure Scalar ( ...
between two or more intermolecular bonds. This is slightly different from the intramolecular
bound states Bound or bounds may refer to: Mathematics * Bound variable * Upper and lower bounds, observed limits of mathematical functions Physics * Bound state, a particle that has a tendency to remain localized in one or more regions of space Geography * ...
of, for example,
covalent A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atoms ...
or
ionic bond Ionic bonding is a type of chemical bonding that involves the electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities, and is the primary interaction occurring in ionic compounds. ...
s; however, hydrogen bonding is generally still a
bound state Bound or bounds may refer to: Mathematics * Bound variable * Upper and lower bounds, observed limits of mathematical functions Physics * Bound state, a particle that has a tendency to remain localized in one or more regions of space Geography * ...
phenomenon, since the
interaction energy In physics, interaction energy is the contribution to the total energy that is caused by an interaction between the objects being considered. The interaction energy usually depends on the relative position of the objects. For example, Q_1 Q_2 / ( ...
has a net negative sum. The initial theory of hydrogen bonding proposed by
Linus Pauling Linus Carl Pauling (; February 28, 1901August 19, 1994) was an American chemist, biochemist, chemical engineer, peace activist, author, and educator. He published more than 1,200 papers and books, of which about 850 dealt with scientific top ...
suggested that the hydrogen bonds had a partial covalent nature. This interpretation remained controversial until NMR techniques demonstrated information transfer between hydrogen-bonded nuclei, a feat that would only be possible if the hydrogen bond contained some covalent character.


History

The concept of hydrogen bonding once was challenging.
Linus Pauling Linus Carl Pauling (; February 28, 1901August 19, 1994) was an American chemist, biochemist, chemical engineer, peace activist, author, and educator. He published more than 1,200 papers and books, of which about 850 dealt with scientific top ...
credits T. S. Moore and T. F. Winmill with the first mention of the hydrogen bond, in 1912. Moore and Winmill used the hydrogen bond to account for the fact that trimethylammonium hydroxide is a weaker base than
tetramethylammonium hydroxide Tetramethylammonium hydroxide (TMAH or TMAOH) is a quaternary ammonium salt with molecular formula N(CH3)4+ OH−. It is commonly encountered in form of concentrated solutions in water or methanol. TMAH in solid state and its aqueous soluti ...
. The description of hydrogen bonding in its better-known setting, water, came some years later, in 1920, from Latimer and Rodebush. In that paper, Latimer and Rodebush cite work by a fellow scientist at their laboratory,
Maurice Loyal Huggins Maurice Loyal Huggins (19 September 1897, Berkeley County, West Virginia – 17 December 1981) was a scientist who independently conceived the idea of hydrogen bonding and who was an early advocate for their role in stabilizing protein secondary st ...
, saying, "Mr. Huggins of this laboratory in some work as yet unpublished, has used the idea of a hydrogen kernel held between two atoms as a theory in regard to certain organic compounds."


Hydrogen bonds in small molecules


Water

A ubiquitous example of a hydrogen bond is found between
water Water (chemical formula ) is an inorganic, transparent, tasteless, odorless, and nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of all known living organisms (in which it acts as a ...
molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. The simplest case is a pair of
water Water (chemical formula ) is an inorganic, transparent, tasteless, odorless, and nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of all known living organisms (in which it acts as a ...
molecules with one hydrogen bond between them, which is called the
water dimer The water dimer consists of two water (molecule), water molecules loosely bound by a hydrogen bond. It is the smallest water cluster. Because it is the simplest model system for studying hydrogen bonding in water, it has been the target of many ...
and is often used as a model system. When more molecules are present, as is the case with 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 a hydrogen on another water molecule. This can repeat such 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). Hydrogen bonding strongly affects the
crystal structure In crystallography, crystal structure is a description of the ordered arrangement of atoms, ions or molecules in a crystal, crystalline material. Ordered structures occur from the intrinsic nature of the constituent particles to form symmetric pat ...
of
ice Ice is water frozen into a solid state, typically forming at or below temperatures of 0 degrees Celsius or Depending on the presence of impurities such as particles of soil or bubbles of air, it can appear transparent or a more or less opaq ...
, helping to create an open hexagonal lattice. The density of ice is less than the density of water at the same temperature; thus, the solid phase of water floats on the liquid, unlike most other substances.
Liquid A liquid is a nearly incompressible fluid that conforms to the shape of its container but retains a (nearly) constant volume independent of pressure. As such, it is one of the four fundamental states of matter (the others being solid, gas, a ...
water's high
boiling point The boiling point of a substance is the temperature at which the vapor pressure of a liquid equals the pressure surrounding the liquid and the liquid changes into a vapor. The boiling point of a liquid varies depending upon the surrounding envir ...
is due to the high number of hydrogen bonds each molecule can form, relative to its low
molecular mass The molecular mass (''m'') is the mass of a given molecule: it is measured in daltons (Da or u). Different molecules of the same compound may have different molecular masses because they contain different isotopes of an element. The related quanti ...
. Owing to the difficulty of breaking these bonds, water has a very high boiling point, melting point, and viscosity compared to otherwise similar liquids not conjoined by hydrogen bonds. Water is unique because its oxygen atom has two lone pairs and two hydrogen atoms, meaning that the total number of bonds of a water molecule is up to four. The number of hydrogen bonds formed by a molecule of liquid water fluctuates with time and 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. Another study found a much smaller number of hydrogen bonds: 2.357 at 25 °C. The differences may be due to the use of a different method for defining and counting the hydrogen bonds. Where the bond strengths are more equivalent, one might instead find the atoms of two interacting water molecules partitioned into two
polyatomic ion A polyatomic ion, also known as a molecular ion, is a covalent bonded set of two or more atoms, or of a metal complex, that can be considered to behave as a single unit and that has a net charge that is not zero. The term molecule may or may no ...
s of opposite charge, specifically
hydroxide Hydroxide is a diatomic anion with chemical formula OH−. It consists of an oxygen and hydrogen atom held together by a single covalent bond, and carries a negative electric charge. It is an important but usually minor constituent of water. I ...
() and
hydronium In chemistry, hydronium (hydroxonium in traditional British English) is the common name for the aqueous cation , the type of oxonium ion produced by protonation of water. It is often viewed as the positive ion present when an Arrhenius acid is d ...
(). (Hydronium ions are also known as "hydroxonium" ions.) :H-O^- \quad H3O+ Indeed, in pure water under conditions of
standard temperature and pressure Standard temperature and pressure (STP) are standard sets of conditions for experimental measurements to be established to allow comparisons to be made between different sets of data. The most used standards are those of the International Union o ...
, this latter formulation is applicable only rarely; on average about one in every 5.5 molecules gives up a proton to another water molecule, in accordance with the value of the
dissociation constant In chemistry, biochemistry, and pharmacology, a dissociation constant (K_D) is a specific type of equilibrium constant that measures the propensity of a larger object to separate (dissociate) reversibly into smaller components, as when a complex fa ...
for water under such conditions. It is a crucial part of the uniqueness of water. Because water may form hydrogen bonds with solute proton donors and acceptors, it may competitively inhibit the formation of solute intermolecular or intramolecular hydrogen bonds. Consequently, hydrogen bonds between or within solute molecules dissolved in water are almost always unfavorable relative to hydrogen bonds between water and the donors and acceptors for hydrogen bonds on those solutes. Hydrogen bonds between water molecules have an average lifetime of 10−11 seconds, or 10 picoseconds.


Bifurcated and over-coordinated hydrogen bonds in water

A single hydrogen atom can participate in two hydrogen bonds, rather than one. This type of bonding is called "bifurcated" (split in two or "two-forked"). It can exist, for instance, in complex natural or synthetic organic molecules. It has been suggested that a bifurcated hydrogen atom is an essential step in water reorientation.
Acceptor-type hydrogen bonds (terminating on an oxygen's lone pairs) are more likely to form bifurcation (it is called overcoordinated oxygen, OCO) than are donor-type hydrogen bonds, beginning on the same oxygen's hydrogens.


Other liquids

For example,
hydrogen fluoride Hydrogen fluoride (fluorane) is an inorganic compound with the chemical formula . This colorless gas or liquid is the principal industrial source of fluorine, often as an aqueous solution called hydrofluoric acid. It is an important feedstock i ...
—which has three lone pairs on the F atom but only one H atom—can form only two bonds; (
ammonia Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogenous was ...
has the opposite problem: three hydrogen atoms but only one lone pair). :H-F***H-F***H-F


Further manifestations of solvent hydrogen bonding

* Increase in the
melting point The melting point (or, rarely, liquefaction point) of a substance is the temperature at which it changes state from solid to liquid. At the melting point the solid and liquid phase exist in equilibrium. The melting point of a substance depends ...
,
boiling point The boiling point of a substance is the temperature at which the vapor pressure of a liquid equals the pressure surrounding the liquid and the liquid changes into a vapor. The boiling point of a liquid varies depending upon the surrounding envir ...
,
solubility In chemistry, solubility is the ability of a substance, the solute, to form a solution with another substance, the solvent. Insolubility is the opposite property, the inability of the solute to form such a solution. The extent of the solubil ...
, and viscosity of many compounds can be explained by the concept of hydrogen bonding. * Negative azeotropy of mixtures of HF and water. * The fact that ice is less dense than liquid water is due to a crystal structure stabilized by hydrogen bonds. * Dramatically higher boiling points of , , and HF compared to the heavier analogues , , and HCl, where hydrogen-bonding is absent. * Viscosity of anhydrous
phosphoric acid Phosphoric acid (orthophosphoric acid, monophosphoric acid or phosphoric(V) acid) is a colorless, odorless phosphorus-containing solid, and inorganic compound with the chemical formula . It is commonly encountered as an 85% aqueous solution, w ...
and of
glycerol Glycerol (), also called glycerine in British English and glycerin in American English, is a simple triol compound. It is a colorless, odorless, viscous liquid that is sweet-tasting and non-toxic. The glycerol backbone is found in lipids known ...
. * Dimer formation in
carboxylic acid In organic chemistry, a carboxylic acid is an organic acid that contains a carboxyl group () attached to an R-group. The general formula of a carboxylic acid is or , with R referring to the alkyl, alkenyl, aryl, or other group. Carboxylic ...
s and hexamer formation in
hydrogen fluoride Hydrogen fluoride (fluorane) is an inorganic compound with the chemical formula . This colorless gas or liquid is the principal industrial source of fluorine, often as an aqueous solution called hydrofluoric acid. It is an important feedstock i ...
, which occur even in the gas phase, resulting in gross deviations from the
ideal gas law The ideal gas law, also called the general gas equation, is the equation of state of a hypothetical ideal gas. It is a good approximation of the behavior of many gases under many conditions, although it has several limitations. It was first stat ...
. * Pentamer formation of water and alcohols in apolar solvents.


Hydrogen bonds in polymers

Hydrogen bonding plays an important role in determining the three-dimensional structures and the properties adopted by many synthetic and natural proteins. Compared to the , , and bonds that comprise most polymers, hydrogen bonds are far weaker, perhaps 5%. Thus, hydrogen bonds can be broken by chemical or mechanical means while retaining the basic structure of the polymer backbone. This hierarchy of bond strengths (covalent bonds being stronger than hydrogen-bonds being stronger than van der Waals forces) is key to understanding the properties of many materials.


DNA

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. For example, the double helical structure of DNA is due largely to hydrogen bonding between its
base pair A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...
s (as well as
pi stacking In chemistry, pi stacking (also called π–π stacking) refers to the presumptive attractive, noncovalent pi interactions ( orbital overlap) between the pi bonds of aromatic rings. However this is a misleading description of the phenomena sinc ...
interactions), which link one complementary strand to the other and enable replication.


Proteins

In the
secondary structure of proteins Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...
, hydrogen bonds form between the backbone oxygens and
amide In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula , where R, R', and R″ represent organic groups or hydrogen atoms. The amide group is called a peptide bond when it is ...
hydrogens. When the spacing of the
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
residues participating in a hydrogen bond occurs regularly between positions ''i'' and , an
alpha helix The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues e ...
is formed. When the spacing is less, between positions ''i'' and , then a 310 helix is formed. When two strands are joined by hydrogen bonds involving alternating residues on each participating strand, a
beta sheet The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a g ...
is formed. Hydrogen bonds also play a part in forming the tertiary structure of protein through interaction of R-groups. (See also
protein folding Protein folding is the physical process by which a protein chain is translated to its native three-dimensional structure, typically a "folded" conformation by which the protein becomes biologically functional. Via an expeditious and reproduci ...
). Bifurcated H-bond systems are common in alpha-helical
transmembrane proteins A transmembrane protein (TP) is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequentl ...
between the backbone amide of residue ''i'' as the H-bond acceptor and two H-bond donors from residue : the backbone amide and a side-chain hydroxyl or thiol . The energy preference of the bifurcated H-bond hydroxyl or thiol system is -3.4 kcal/mol or -2.6 kcal/mol, respectively. This type of bifurcated H-bond provides an intrahelical H-bonding partner for polar side-chains, such as
serine Serine (symbol Ser or S) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated − form under biological conditions), a carboxyl group (which is in the deprotonated − form un ...
,
threonine Threonine (symbol Thr or T) is an amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH form under biological conditions), a carboxyl group (which is in the deprotonated −COO ...
, and
cysteine Cysteine (symbol Cys or C; ) is a semiessential proteinogenic amino acid with the formula . The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile. When present as a deprotonated catalytic residue, sometime ...
within the hydrophobic membrane environments. The role of hydrogen bonds in protein folding has also been linked to osmolyte-induced protein stabilization. Protective osmolytes, such as
trehalose Trehalose (from Turkish '' tıgala'' – a sugar derived from insect cocoons + -ose) is a sugar consisting of two molecules of glucose. It is also known as mycose or tremalose. Some bacteria, fungi, plants and invertebrate animals synthesize it ...
and
sorbitol Sorbitol (), less commonly known as glucitol (), is a sugar alcohol with a sweet taste which the human body metabolizes slowly. It can be obtained by reduction of glucose, which changes the converted aldehyde group (−CHO) to a primary alcohol g ...
, shift the protein folding equilibrium toward the folded state, in a concentration dependent manner. While the prevalent explanation for osmolyte action relies on excluded volume effects that are entropic in nature, circular dichroism (CD) experiments have shown osmolyte to act through an enthalpic effect. The molecular mechanism for their role in protein stabilization is still not well established, though several mechanisms have been proposed. Computer
molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the ...
simulations suggest that osmolytes stabilize proteins by modifying the hydrogen bonds in the protein hydration layer. Several studies have shown that hydrogen bonds play an important role for the stability between subunits in multimeric proteins. For example, a study of sorbitol dehydrogenase displayed an important hydrogen bonding network which stabilizes the tetrameric quaternary structure within the mammalian sorbitol dehydrogenase protein family. A protein backbone hydrogen bond incompletely shielded from water attack is a
dehydron A solvation shell or solvation sheath is the solvent interface of any chemical compound or biomolecule that constitutes the solute. When the solvent is water it is called a hydration shell or hydration sphere. The number of solvent molecules sur ...
. Dehydrons promote the removal of water through proteins or
ligand binding In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. The etymology stems from ''ligare'', which means 'to bind'. In protein-ligand binding, the ligand is usually a mo ...
. The exogenous dehydration enhances the
electrostatic Electrostatics is a branch of physics that studies electric charges at rest (static electricity). Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for amber ...
interaction between the
amide In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula , where R, R', and R″ represent organic groups or hydrogen atoms. The amide group is called a peptide bond when it is ...
and
carbonyl In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O. It is common to several classes of organic compounds, as part of many larger functional groups. A compound containing a ...
groups by de-shielding their
partial charges A partial charge is a non- integer charge value when measured in elementary charge units. Partial charge is more commonly called net atomic charge. It is represented by the Greek lowercase letter 𝛿, namely 𝛿− or 𝛿+. Partial charges are ...
. Furthermore, the dehydration stabilizes the hydrogen bond by destabilizing the nonbonded state consisting of dehydrated isolated charges.
Wool Wool is the textile fibre obtained from sheep and other mammals, especially goats, rabbits, and camelids. The term may also refer to inorganic materials, such as mineral wool and glass wool, that have properties similar to animal wool. As ...
, being a protein fibre, is held together by hydrogen bonds, causing wool to recoil when stretched. However, washing at high temperatures can permanently break the hydrogen bonds and a garment may permanently lose its shape.


Cellulose

Hydrogen bonds are important in the structure of
cellulose Cellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to many thousands of β(1→4) linked D-glucose units. Cellulose is an important structural component of the primary cell wall ...
and derived polymers in its many different forms in nature, such as
cotton Cotton is a soft, fluffy staple fiber that grows in a boll, or protective case, around the seeds of the cotton plants of the genus ''Gossypium'' in the mallow family Malvaceae. The fiber is almost pure cellulose, and can contain minor perce ...
and
flax Flax, also known as common flax or linseed, is a flowering plant, ''Linum usitatissimum'', in the family Linaceae. It is cultivated as a food and fiber crop in regions of the world with temperate climates. Textiles made from flax are known in ...
.


Synthetic polymers

Many
polymer A polymer (; Greek '' poly-'', "many" + ''-mer'', "part") is a substance or material consisting of very large molecules called macromolecules, composed of many repeating subunits. Due to their broad spectrum of properties, both synthetic a ...
s are strengthened by hydrogen bonds within and between the chains. Among the synthetic polymers, a well characterized example is
nylon Nylon is a generic designation for a family of synthetic polymers composed of polyamides ( repeating units linked by amide links).The polyamides may be aliphatic or semi-aromatic. Nylon is a silk-like thermoplastic, generally made from petro ...
, where hydrogen bonds occur in the
repeat unit In polymer chemistry, a repeat unit or repeating unit (or mer) is a part of a polymer whose repetition would produce the complete polymer chain (except for the end-groups) by linking the repeat units together successively along the chain, like the ...
and play a major role in
crystallization Crystallization is the process by which solid forms, where the atoms or molecules are highly organized into a structure known as a crystal. Some ways by which crystals form are precipitating from a solution, freezing, or more rarely deposi ...
of the material. The bonds occur between
carbonyl In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O. It is common to several classes of organic compounds, as part of many larger functional groups. A compound containing a ...
and
amine In chemistry, amines (, ) are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia (), wherein one or more hydrogen atoms have been replaced by a substituen ...
groups in the
amide In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula , where R, R', and R″ represent organic groups or hydrogen atoms. The amide group is called a peptide bond when it is ...
repeat unit. They effectively link adjacent chains, which help reinforce the material. The effect is great in
aramid Aramid fibers, short for aromatic polyamide, are a class of heat-resistant and strong synthetic fibers. They are used in aerospace and military applications, for ballistic-rated body armor fabric and ballistic composites, in marine cordage, ma ...
fibre Fiber or fibre (from la, fibra, links=no) is a natural or artificial substance that is significantly longer than it is wide. Fibers are often used in the manufacture of other materials. The strongest engineering materials often incorporate ...
, where hydrogen bonds stabilize the linear chains laterally. The chain axes are aligned along the fibre axis, making the fibres extremely stiff and strong. The hydrogen-bond networks make both natural and synthetic polymers sensitive to
humidity Humidity is the concentration of water vapor present in the air. Water vapor, the gaseous state of water, is generally invisible to the human eye. Humidity indicates the likelihood for precipitation, dew, or fog to be present. Humidity depe ...
levels in the atmosphere because water molecules can diffuse into the surface and disrupt the network. Some polymers are more sensitive than others. Thus
nylon Nylon is a generic designation for a family of synthetic polymers composed of polyamides ( repeating units linked by amide links).The polyamides may be aliphatic or semi-aromatic. Nylon is a silk-like thermoplastic, generally made from petro ...
s are more sensitive than
aramid Aramid fibers, short for aromatic polyamide, are a class of heat-resistant and strong synthetic fibers. They are used in aerospace and military applications, for ballistic-rated body armor fabric and ballistic composites, in marine cordage, ma ...
s, and
nylon 6 Nylon 6 or polycaprolactam is a polymer, in particular semicrystalline polyamide. Unlike most other nylons, nylon 6 is not a condensation polymer, but instead is formed by ring-opening polymerization; this makes it a special case in the comparis ...
more sensitive than
nylon-11 Nylon 11 or Polyamide 11 (PA 11) is a polyamide, bioplastic and a member of the nylon family of polymers produced by the polymerization of 11-aminoundecanoic acid. It is produced from castor beans by Arkema under the trade name Rilsan. Nylon 11 ...
.


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
three-center four-electron bond The 3-center 4-electron (3c–4e) bond is a model used to explain bonding in certain hypervalent molecules such as tetratomic and hexatomic interhalogen compounds, sulfur tetrafluoride, the xenon fluorides, and the bifluoride ion. It is also know ...
. This type of bond is much stronger than a "normal" hydrogen bond. The effective bond order is 0.5, so 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 Hydrofluoric acid is a Solution (chemistry), solution of hydrogen fluoride (HF) in water. Solutions of HF are colourless, acidic and highly Corrosive substance, corrosive. It is used to make most fluorine-containing compounds; examples include th ...
and
formic acid Formic acid (), systematically named methanoic acid, is the simplest carboxylic acid, and has the chemical formula HCOOH and structure . It is an important intermediate in chemical synthesis and occurs naturally, most notably in some ants. Es ...
at high pressure. It is also seen in the
bifluoride The bifluoride ion is an inorganic anion with the chemical formula . The anion is colorless. Salts of bifluoride are commonly encountered in the reactions of fluoride salts with hydrofluoric acid. The commercial production of fluorine involves e ...
ion . Due to severe steric constraint, the protonated form of Proton Sponge (1,8-bis(dimethylamino)naphthalene) and its derivatives also have symmetric hydrogen bonds (), although in the case of protonated Proton Sponge, the assembly is bent.


Dihydrogen bond

The hydrogen bond can be compared with the closely related
dihydrogen bond In chemistry, a dihydrogen bond is a kind of hydrogen bond, an interaction between a metal hydride bond and an OH or NH group or other proton donor. With a van der Waals radius of 1.2 Å, hydrogen atoms do not usually approach other hydrogen ato ...
, which is also an
intermolecular An intermolecular force (IMF) (or secondary force) is the force that mediates interaction between molecules, including the electromagnetic forces of attraction or repulsion which act between atoms and other types of neighbouring particles, e.g. a ...
bonding interaction involving hydrogen atoms. These structures have been known for some time, and well characterized by
crystallography Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. Crystallography is a fundamental subject in the fields of materials science and solid-state physics (condensed matter physics). The wor ...
; however, an understanding of their relationship to the conventional hydrogen bond,
ionic bond Ionic bonding is a type of chemical bonding that involves the electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities, and is the primary interaction occurring in ionic compounds. ...
, and
covalent bond A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atoms ...
remains unclear. Generally, the hydrogen bond is characterized by a proton acceptor that is a lone pair of electrons in nonmetallic atoms (most notably in the
nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...
, and
chalcogen The chalcogens (ore forming) ( ) are the chemical elements in group 16 of the periodic table. This group is also known as the oxygen family. Group 16 consists of the elements oxygen (O), sulfur (S), selenium (Se), tellurium (Te), and the radioac ...
groups). In some cases, these proton acceptors may be pi-bonds or metal complexes. In the dihydrogen bond, however, a metal hydride serves as a proton acceptor, thus forming a hydrogen-hydrogen interaction.
Neutron diffraction Neutron diffraction or elastic neutron scattering is the application of neutron scattering to the determination of the atomic and/or magnetic structure of a material. A sample to be examined is placed in a beam of thermal or cold neutrons to o ...
has shown that the
molecular geometry Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determ ...
of these complexes is similar to hydrogen bonds, in that the bond length is very adaptable to the metal complex/hydrogen donor system.


Dynamics probed by spectroscopic means

The dynamics of hydrogen bond structures in water can be probed by the IR spectrum of OH stretching vibration. In the hydrogen bonding network in protic organic ionic plastic crystals (POIPCs), which are a type of phase change material exhibiting solid-solid phase transitions prior to melting, variable-temperature infrared spectroscopy can reveal the temperature dependence of hydrogen bonds and the dynamics of both the anions and the cations. The sudden weakening of hydrogen bonds during the solid-solid phase transition seems to be coupled with the onset of orientational or rotational disorder of the ions.


Application to drugs

Hydrogen bonding is a key to the design of drugs. According to
Lipinski's rule of five Lipinski's rule of five, also known as Pfizer's rule of five or simply the rule of five (RO5), is a rule of thumb to evaluate druglikeness or determine if a chemical compound with a certain pharmacological or biological activity has chemical pro ...
the majority of orally active drugs tend to have no more than five hydrogen bond donors and less than ten hydrogen bond acceptors. These interactions exist between
nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...
hydrogen Hydrogen is the chemical element with the symbol H and atomic number 1. Hydrogen is the lightest element. At standard conditions hydrogen is a gas of diatomic molecules having the formula . It is colorless, odorless, tasteless, non-toxic, an ...
and
oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as wel ...
–hydrogen centers. However, up to half of new drugs do not obey these "rules".


References


Further reading

* George A. Jeffrey. ''An Introduction to Hydrogen Bonding (Topics in Physical Chemistry)''. Oxford University Press, USA (March 13, 1997).


External links


The Bubble Wall
(Audio slideshow from the National High Magnetic Field Laboratory explaining cohesion, surface tension and hydrogen bonds)
isotopic effect on bond dynamics
{{DEFAULTSORT:Hydrogen Bonds Chemical bonding Hydrogen physics Supramolecular chemistry Intermolecular forces