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An example of a quadruple hydrogen bond between a self-assembled dimer complex reported by Meijer and coworkers.
An example of a quadruple hydrogen bond between a self-assembled dimer complex reported by Meijer and coworkers. Molecular self-assembly is the process by which Molecules adopt a defined arrangement without guidance or management from an outside source [1]
Intramolecular hydrogen bonding in acetylacetone helps stabilize the enol tautomer
Intramolecular hydrogen bonding in acetylacetone helps stabilize the enol tautomer
Carboxylic acids often form dimers in vapor phase.
Carboxylic acids often form dimers in vapor phase. Acac redirects here For other uses see ACAC. Acetylacetone is an Organic compound with molecular formula C5H8O2 Enols (also known as alkenols) are Alkenes with a Hydroxyl group affixed to one of the carbon atoms composing the Double bond. Carboxylic acids are Organic acids characterized by the presence of a Carboxyl group, which has the formula -C(=OOH usually written -COOH or -CO2H

A hydrogen bond is a special type of dipole-dipole force that exists between an electronegative atom and a hydrogen atom bonded to Nitrogen, Oxygen or Fluorine. In Physics, Chemistry, and Biology, intermolecular forces are forces that act between stable Molecules or between functional groups of " Electronegativity " is the opposite of " Electropositivity," which describes an element's ability to donate electrons Hydrogen (ˈhaɪdrədʒən is the Chemical element with Atomic number 1 Nitrogen (ˈnaɪtɹəʤɪn is a Chemical element that has the symbol N and Atomic number 7 and Atomic weight 14 Oxygen (from the Greek roots ὀξύς (oxys (acid literally "sharp" from the taste of acids and -γενής (-genēs (producer literally begetteris the Fluorine, fluorum meaning "to flow" is the Chemical element with the symbol F and Atomic number 9 This type of force always involves a hydrogen atom and the energy of this attraction is close to that of weak covalent bonds (155 kJ/mol), thus the name - Hydrogen Bonding. A covalent bond is only 20 times stronger than an intermolecular hydrogen bond. These attractions can occur between molecules (intermolecularly), or within different parts of a single molecule (intramolecularly). [2] The hydrogen bond is a very strong fixed dipole-dipole van der Waals-Keesom force, but weaker than covalent, ionic and metallic bonds. The Van der Waals equation is an Equation of state that can be derived from a special form of the potential between a pair of molecules (hard-sphere repulsion An ionic bond (or electrovalent bond) is a type of Chemical bond that can often form between Metal and Non-metal Ions (or Although the term metallic bond is often used in contrast to the term Covalent bond it is better to speak of metallic bonding, because this type of bonding is The hydrogen bond is somewhere between a covalent bond and an electrostatic intermolecular attraction. In Physics, Chemistry, and Biology, intermolecular forces are forces that act between stable Molecules or between functional groups of

Intermolecular hydrogen bonding is responsible for the high boiling point of water (100 °C). Water is a common Chemical substance that is essential for the survival of all known forms of Life. This is because of the strong hydrogen bond, as opposed to other group 16 hydrides. See also Gold chalcogenides Periodic table Hydride is the name given to the negative Ion of Hydrogen, H− Intramolecular hydrogen bonding is partly responsible for the secondary, tertiary, and quaternary structures of proteins and nucleic acids. In Biochemistry and Structural biology, secondary structure is the general three-dimensional form of local segments of Biopolymers such as In Biochemistry and Chemistry, the tertiary structure of a Protein or any other Macromolecule is its three-dimensional structure as defined In Biochemistry, quaternary structure is the arrangement of multiple folded Protein molecules in a multi-subunit complex Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information

Contents

Bonding

A hydrogen atom attached to a relatively electronegative atom is a hydrogen bond donor. " Electronegativity " is the opposite of " Electropositivity," which describes an element's ability to donate electrons This electronegative atom is usually fluorine, oxygen, or nitrogen. Fluorine, fluorum meaning "to flow" is the Chemical element with the symbol F and Atomic number 9 Oxygen (from the Greek roots ὀξύς (oxys (acid literally "sharp" from the taste of acids and -γενής (-genēs (producer literally begetteris the Nitrogen (ˈnaɪtɹəʤɪn is a Chemical element that has the symbol N and Atomic number 7 and Atomic weight 14 An electronegative atom such as fluorine, oxygen, or nitrogen is a hydrogen bond acceptor, regardless of whether it is bonded to a hydrogen atom or not. An example of a hydrogen bond donor is ethanol, which has a hydrogen bonded to oxygen; an example of a hydrogen bond acceptor which does not have a hydrogen atom bonded to it is the oxygen atom on diethyl ether. Diethyl ether, also known as ether and ethoxyethane, is a clear colorless and highly Flammable liquid with a low Boiling point and a

Carbon can also participate in hydrogen bonding, especially when the carbon atom is bound to several electronegative atoms, as is the case in chloroform, CHCl3. Carbon (kɑɹbən is a Chemical element with the symbol C and its Atomic number is 6 Chloroform, also known as trichloromethane and methyl trichloride, is a Chemical compound with formula C[[Hydrogen H]] Cl The electronegative atom attracts the electron cloud from around the hydrogen nucleus and, by decentralizing the cloud, leaves the atom with a positive partial charge. Because of the small size of hydrogen relative to other atoms and molecules, the resulting charge, though only partial, nevertheless represents a large charge density. A hydrogen bond results when this strong positive charge density attracts a lone pair of electrons on another heteroatom, which becomes the hydrogen-bond acceptor. lone pair is a (valence electron pair without bonding or sharing with other Atoms They are found in the outermost Electron shell of an atom so lone pairs In the nomenclature of Organic chemistry, a heteroatom (from Ancient Greek heteros, different + atomos) is any Atom that

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. In Chemistry, valence, also known as valency or valency number, is a measure of the number of Chemical bonds formed by the Atoms 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. The nucleus of an Atom is the very dense region consisting of Nucleons ( Protons and Neutrons, at the center of an atom . . Y system: X-H distance is typically ~1. 1 Å, whereas H. An ångström or angstrom (symbol Å) (ˈɔːŋstrəm Swedish: ˈɔ̀ŋstrœm is an internationally recognized non- SI unit of length equal . . Y distance is ~ 1. 6 to 2. 0 Å. An ångström or angstrom (symbol Å) (ˈɔːŋstrəm Swedish: ˈɔ̀ŋstrœm is an internationally recognized non- SI unit of length equal 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. The bifluoride, or hydrogen(difluoride, ion is the species HF2− [3] Typical values include:

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). A dielectric is a nonconducting substance ie an insulator. The term was coined by William Whewell in response to a request from Michael Faraday. The typical length of a hydrogen bond in water is 1. 97 Å (197 pm).

History

In his book The Nature of the Chemical Bond, Linus Pauling credits T. S. Moore and T. F. Winmill with the first mention of the hydrogen bond, in 1912 (J. Chem. Soc. 101, 1635). Moore and Winmill used the hydrogen bond to account for the fact that trimethylammonium hydroxide is a weaker base than tetramethylammonium hydroxide. The description of hydrogen bonding in its more well-known setting, water, came some years later, in 1920, from Latimer and Rodebush (JACS, 42, 1419).

Hydrogen bonds in water

Snapshot from a simulation of liquid water. The dashed blue lines from the molecule in the center of the picture represent hydrogen bonds.
Snapshot from a simulation of liquid water. Water is a common Chemical substance that is essential for the survival of all known forms of Life. The dashed blue lines from the molecule in the center of the picture represent hydrogen bonds.

The most ubiquitous, and perhaps simplest, example of a hydrogen bond is found between water molecules. Water is a common Chemical substance that is essential for the survival of all known forms of Life. 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. Water is a common Chemical substance that is essential for the survival of all known forms of Life. The water dimer consists of two water molecules loosely bound by a Hydrogen bond. 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. )

Liquid water's high boiling point is due to the high number of hydrogen bonds each molecule can have relative to its low molecular mass, not to mention the great strength of these hydrogen bonds. Liquid is one of the principal States of matter. A liquid is a Fluid that has the particles loose and can freely form a distinct surface at the boundaries of The boiling point of a liquid is the temperature at which the Vapor pressure of the liquid equals the environmental pressure surrounding the liquid The molecular mass (abbreviated m of a substance, more commonly referred to as molecular weight and abbreviated as MW, is the Mass of one Realistically the water molecule has a very high boiling point, melting point and viscosity compared to other similar substances not conjoined by hydrogen bonds. The reasoning for these attributes is the inability to, or the difficulty in, breaking these 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. For example, hydrogen fluoride—which has three lone pairs on the F atom but only one H atom—can have a total of only two bonds (ammonia has the opposite problem: three hydrogen atoms but only one lone pair). Ammonia is a compound with the formula N[[hydrogen H3]] It is normally encountered as a Gas with a characteristic pungent Odor

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. Computational chemistry, classical water models are used for the simulation of Water clusters liquid water, and aqueous solutions with explicit solvent 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.

Where the bond strengths are more equivalent, one might instead find the atoms of two interacting water molecules partitioned into two polyatomic ions of opposite charge, specifically hydroxide (OH) and hydronium (H3O+). A polyatomic ion is a charged species ( Ion) composed of two or more atoms covalently bonded or of a metal complex that can be considered as acting In Chemistry, hydroxide is the most common name for the diatomic Anion OH− consisting of Oxygen and Hydrogen In Chemistry, hydronium is the obsolete name for the Cation H 3 O + derived from Protonation of Water (Hydronium ions are also known as 'hydroxonium' ions. )

H-O H3O+

Indeed, in pure water under conditions of standard temperature and pressure, this latter formulation is applicable only rarely; on average about one in every 5. In Physical sciences standard conditions for temperature and pressure are Standard sets of conditions for experimental measurements to allow comparisons to be made 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.

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 between guanine and cytosine, one of two types of base pairs in DNA.
Hydrogen bonding between guanine and cytosine, one of two types of base pairs in DNA. Guanine is one of the five main Nucleobases found in the Nucleic acids DNA and RNA, the others being Adenine, Cytosine, Cytosine is one of the five main bases found in DNA and RNA. It is a Pyrimidine derivative with a Heterocyclic Aromatic ring In Molecular biology, two Nucleotides on opposite complementary DNA or RNA strands that are connected via Hydrogen bonds are called

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 DNA, for example, is due largely to hydrogen bonding between the base pairs, which link one complementary strand to the other and enable replication. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known In Molecular biology, two Nucleotides on opposite complementary DNA or RNA strands that are connected via Hydrogen bonds are called DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules

In proteins, hydrogen bonds form between the backbone oxygens and amide hydrogens. When the spacing of the amino acid residues participating in a hydrogen bond occurs regularly between positions i and i + 4, an alpha helix is formed. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this A common motif in the Secondary structure of Proteins the alpha helix (α-helix is a right-handed coiled conformation resembling a spring, in which When the spacing is less, between positions i and i + 3, then a 310 helix is formed. A 310 helix is a type of Secondary structure found (rarely in Proteins Structure The amino acids in a 310-helix are When two strands are joined by hydrogen bonds involving alternating residues on each participating strand, a beta sheet is formed. The β sheet (also β-pleated sheet) is the second form of regular Secondary structure in Proteins consisting of beta strands connected laterally 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 Polypeptide folds into its characteristic and functional three-dimensional structure.

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 2-electron bond. This type of bond is much stronger than "normal" hydrogen bonds. 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 and formic acid at high pressure. It is also seen in the bifluoride ion [F-H-F]. The bifluoride, or hydrogen(difluoride, ion is the species HF2−

Symmetric hydrogen bonds have been observed recently spectroscopically in formic acid at high pressure (>GPa). A symmetric hydrogen bond is a special type of Hydrogen bond in which the Proton is spaced exactly halfway between two identical atoms Formic acid (systematically called methanoic acid) is the simplest Carboxylic acid. Each hydrogen atom forms a partial covalent bond with two atoms rather than one. Symmetric hydrogen bonds have been postulated in ice at high pressure (ice-X). Low-barrier hydrogen bonds form when the distance between two heteroatoms is very small. A Low-barrier hydrogen bond or LBHB is a special type of Hydrogen bond.

Dihydrogen bond

The hydrogen bond can be compared with the closely related dihydrogen bond, which is also an intermolecular bonding interaction involving hydrogen atoms. 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 another Proton In Physics, Chemistry, and Biology, intermolecular forces are forces that act between stable Molecules or between functional groups of These structures have been known for some time, and well characterized by crystallography; however, an understanding of their relationship to the conventional hydrogen bond, ionic bond, and covalent bond remains unclear. X-ray crystallography is a method of determining the arrangement of Atoms within a Crystal, in which a beam of X-rays strikes a crystal and scatters An ionic bond (or electrovalent bond) is a type of Chemical bond that can often form between Metal and Non-metal Ions (or 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, and chalcogen groups). See also Gold chalcogenides Periodic table In some cases, these proton acceptors may be pi-bonds or metal complexes. In Chemistry, pi bonds ( π bonds) are covalent Chemical bonds where two lobes of one involved electron orbital overlap two lobes The term complex in Chemistry is usually used to describe molecules or ensembles formed by the combination of Ligands and metal Ions. In the dihydrogen bond, however, a metal hydride serves as a proton acceptor; thus forming a hydrogen-hydrogen interaction. Neutron diffraction has shown that the 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. Neutron diffraction is a crystallographic method for the determination of the atomic and/or magnetic structure of a material Molecular geometry or molecular structure is the three- Dimensional arrangement of the Atoms that constitute a Molecule.

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. Anisotropy (pronounced with stress on the third syllable ˌænaɪˈsɒtrəpi is the property of being directionally dependent as opposed to Isotropy, which means homogeneity 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. In Mathematics, a metric or distance function is a function which defines a Distance between elements of a set. Electrostatics is the branch of Science that deals with the Phenomena arising from what seems to be stationary Electric charges Since Classical In Mathematics and Physics, a scalar field associates a scalar value which can be either mathematical in definition or physical, to every point This is slightly different from the intramolecular bound states of, for example, covalent or ionic bonds; however, hydrogen bonding is generally still a bound state phenomenon, since the interaction energy has a net negative sum. Intramolecular in Chemistry describes a process or characteristic limited within the structure of a single Molecule; a property or phenomenon limited to the extent In Physics, a bound state is a composite of two or more building blocks ( particles or bodies) that behaves as a single object An ionic bond (or electrovalent bond) is a type of Chemical bond that can often form between Metal and Non-metal Ions (or In Physics, a bound state is a composite of two or more building blocks ( particles or bodies) that behaves as a single object In Physics, interaction energy is the contribution to the total Energy that is caused by an Interaction between the objects being considered The initial theory of hydrogen bonding proposed by Linus Pauling suggested that the hydrogen bonds had a partial covalent nature. Linus Carl Pauling (February 28 1901 – August 19 1994 was an American Scientist, Peace activist, Author and educator. This remained a controversial conclusion until the late 1990's when NMR techniques were employed by F. Cordier et al. to transfer information between hydrogen-bonded nuclei, a feat that would only be possible if the hydrogen bond contained some covalent character. While a lot of experimental data has been recovered for hydrogen bonds in water, for example, that provide good resolution on the scale of intermolecular distances and molecular thermodynamics, the kinetic and dynamical properties of the hydrogen bond in dynamic systems remains unchanged. Water ( H2[[oxygen O]] H OH) is the most abundant Molecule on Earth 's surface composing of about 70% of the Earth's surface as In Physics, thermodynamics (from the Greek θερμη therme meaning " Heat " and δυναμις dynamis meaning " Kinetic theory (or kinetic theory of gases) attempts to explain Macroscopic properties of Gases such as pressure temperature or volume by considering In Mathematics, chaos theory describes the behavior of certain dynamical systems – that is systems whose state evolves with time – that may exhibit dynamics that In physics the term dynamics customarily refers to the time evolution of physical processes

Hydrogen bonding phenomena

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. Angewandte Chemie is a weekly Peer-reviewed Chemistry journal that covers all disciplines of chemistry doi:10.1002/(SICI)1521-3773(19980202)37:1/2%3C75::AID-ANIE75%3E3.0.CO;2-R. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.  
  2. ^ International Union of Pure and Applied Chemistry. The International Union of Pure and Applied Chemistry ( IUPAC) (aɪjuːpæk or ay-yoo-pec) is an international Non-governmental organization "hydrogen bond". Compendium of Chemical Terminology Internet edition. Compendium of Chemical Terminology (ISBN 0-86542-684-8 is a book published by IUPAC containing internationally accepted definitions for terms in Chemistry.
  3. ^ Emsley, J. (1980). "Very Strong Hydrogen Bonds". Chemical Society Reviews 9: 91-124. Chemical Society Reviews is a peer-reviewed Scientific journal publishing review articles on topics of current interest in the chemical  
  4. ^ Omer Markovitch and Noam Agmon (2007). "Structure and energetics of the hydronium hydration shells". J. Phys. Chem. A 111 (12): 2253 - 2256. The Journal of Physical Chemistry A is a scientific journal which reports Research on the Chemistry of Molecules - including their dynamics doi:10.1021/jp068960g. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.  
  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. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.  
  6. ^ Jan Zielkiewicz (2005). "Structural properties of water: Comparison of the SPC, SPCE, TIP4P, and TIP5P models of water". J. Chem. Phys. 123: 104501. The Journal of Chemical Physics is a Scientific journal that publishes research papers on all areas of Chemical physics. doi:10.1063/1.2018637. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.  .
  7. ^ Damien Laage and James T. Hynes (2006). "A Molecular Jump Mechanism for Water Reorientation". Science 311: 832. Science is the Academic journal of the American Association for the Advancement of Science and is considered one of the world's most prestigious Scientific doi:10.1126/science.1122154. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.  
  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

Dictionary

hydrogen bond

-noun

  1. (chemistry) A weak bond in which a hydrogen atom in one molecule is attracted to an electronegative atom (usually nitrogen or oxygen) in the same or different molecule.

-verb

  1. (chemistry) To bond to another species by means of hydrogen bonds. E.g. Water hydrogen bonds with itself.
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