Biological Sciences
Hydrogen Bonding in Water
Hydrogen bonding in water refers to the attractive force between the hydrogen atom of one water molecule and the oxygen atom of another. This unique type of bonding gives water its high surface tension, cohesion, and ability to moderate temperature. In biological systems, hydrogen bonding in water is essential for maintaining the structure and function of biomolecules.
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11 Key excerpts on "Hydrogen Bonding in Water"
eBook - PDF- Alexander Gavrilyuk(Author)
- 2013(Publication Date)
- Jenny Stanford Publishing(Publisher)
These bonds can occur between molecules (intermolecularly), or within different parts of a single molecule (intramolecularly). This type of bond occurs both in inorganic molecules such as water and organic molecules such as DNA. New knowledge on the nature of the hydrogen bond made it possible to pose the question concerning its redefinition. In the following table there are two definitions of hydrogen bond: the current one adopted by the IUPAC and another proposed by Prof. Desiraju [33], which has good chances to substitute the current one. In the table there are abstracts both from the current and proposed definitions. Considering both definitions it is possible to conclude that the proposed definition is more “liberal” since it does not demand the necessity of an electrostatic interaction. Current definition Proposed definition A form of association between an electronegative atom and a hy-drogen atom attached to a second, relatively electronegative atom. It is best considered as an electro-static interaction, heightened by the small size of hydrogen, which permits proximity of the interact-ing dipoles or charges. The hydrogen bond is an attractive interaction between a hydro-gen atom from a molecule or a molecular fragment X–H in which X is more electronegative than H, and an atom or a group of atoms in the same or a different molecule, in which there is evidence of bond formation. 2.4 Importance of the Hydrogen Bond In the world scientific literature there is bewildering amount of publications concerning the hydrogen bond, which currently grows at a great rate. Among numerous publications the classical monographs can be recommended [34–38]. Natural scientists from various branches are continuously interested in hydrogen bonding. 29 The hydrogen bond X-H···Y-Z is an attractive interaction in which an electropositive H atom intercedes between two electronegative species X and Y and brings them closer together.
eBook - PDFWater and Life
The Unique Properties of H2O
- Ruth M. Lynden-Bell, Simon Conway Morris, John D. Barrow, John L. Finney, Charles Harper, Ruth M. Lynden-Bell, Simon Conway Morris, John D. Barrow, John L. Finney, Charles Harper(Authors)
- 2010(Publication Date)
- CRC Press(Publisher)
86 5.1 INTRODUCTION TO THE HYDROGEN BOND IN WATER Latimer and Rodebush first described hydrogen bonding in 1920. It occurs when an atom of hydro-gen is attracted by strong forces to two atoms instead of only one, as its single valence electron implies. The hydrogen atom thus acts to form a divalent bond between the two other atoms (Pauling, 1948). Such hydrogen bonds in liquid water are central to water’s life-providing properties. This paper sets out to investigate the consequences if the hydrogen bond strength of water was to differ from its natural value. From this, an estimate is made as to how far the hydrogen bond strength of water may be varied from its naturally found value but still be supportive of life, in a similar man-ner to the apparent tuning of physical cosmological constants to the existence of the universe (Rees, 2003). Hydrogen bonds arise in water where each partially positively charged hydrogen atom is cova-lently attached to a partially negatively charged oxygen atom from a water molecule with bond energy of about 492 kJ mol – 1 and is also attracted, but much more weakly, to a neighboring par-tially negatively charged oxygen atom from another water molecule. This weaker bond is known as the hydrogen bond and is found to be strongest in hexagonal ice (ordinary ice) where each water molecule takes part in four tetrahedrally arranged hydrogen bonds, two of which involve each of its two hydrogen atoms and two of which involve the hydrogen atoms of neighboring water mol-ecules. There is no standard definition for the hydrogen bond energy. In liquid water, the energy 70 Water and Life: The Unique Properties of H 2 O of attraction between water molecules (hydrogen bond enthalpy) is optimally about 23.3 kJ mol – 1 (Suresh and Naik, 2000) and almost five times the average thermal collision fluctuation at 25°C.
eBook - PDFWater
The Forgotten Biological Molecule
- Denis Le Bihan, Hidenao Fukuyama, Denis Le Bihan, Hidenao Fukuyama(Authors)
- 2016(Publication Date)
- Jenny Stanford Publishing(Publisher)
The hydrogen bond in water is part (about 90%) electrostatic and part (about 10%) covalent. On forming the hydrogen bond, the donor hydrogen atom stretches away from its covalently bonded oxygen atom and the acceptor lone pair stretches away from its oxygen atom and toward the donor hydrogen atom, both oxygen atoms being pulled toward each other. The hydrogen-bonded proton has lower electron density relative to the other protons. Note that, even at temperatures as low as a few kelvin, there are considerable oscillations (
- Steven Emerson, John Hedges(Authors)
- 2008(Publication Date)
- Cambridge University Press(Publisher)
Hydrogen bonding can be thought of as an intermolecular attraction of the hydrogen atoms of water molecules. The hydrogen atoms of each individual water molecule interact along an O–H bond that is aligned with one of the two non-bonding orbitals of the oxygen in an adjacent H 2 O molecule. Hydrogen bonds are weaker than ordinary intramolecular bonds but are generally the strongest type of 104.5 H δ + δ + H O δ – δ – Figure 3:1: The three- dimensional structure of a water molecule. The sphere in the middle represents the oxygen atom and the dark circles are hydrogen atoms. Ovals represent electron orbitals of the outer shell electrons; ds indicate net charges. 64 THERMODYNAMICS BACKGROUND intermolecular attraction. The resulting intermolecular interaction has a characteristic distance of 1.8 Angstroms (1 ¯ ¼ 10 10 cm) between the oxygen of one water molecule and the hydrogen of an adjacent water molecule and exhibits a strength of c. 19 kJ mol 1 . By contrast, in an H–O bond the covalent bond distance is approxi- mately 1.0 ¯ and has a strength of 463 kJ mol 1 (1 kcal ¼ 4.184 kJ). Because the joined H 2 O molecules must be aligned along the axes of their bonding orbital, hydrogen bonding causes H 2 O molecules to exist in strongly ordered assemblies. Pervasive hydrogen bonding is evident in all physical properties that reflect the strengths of association among H 2 O molecules in both liquid water and ice. For example, liquid water has the highest heat capacity, heat of vaporization, surface tension, and dielectric constant (ion insulating capability) of all substances. In addition, the amount of heat necessary to go from the solid to the liquid phase is greater for water than for all substances except ammonia.
eBook - PDF- Charlotte W. Pratt, Kathleen Cornely(Authors)
- 2017(Publication Date)
- Wiley(Publisher)
1 Å O H Covalent bond 2.7 Å O H No bond Hydrogen bond 1.8 Å H O (a) (b) (c) Hydrogen bonds usually involve NH and OH groups as hydrogen donors and the electronegative N and O and occasionally S atoms as hydrogen acceptors (electronegativity is a measure of an atom’s affinity for electrons; Table 2.1 ). Water, therefore, can form hydrogen bonds not just with other water molecules but with a wide variety of other compounds that bear N- and O-containing functional groups. FIGURE 2.3 A water strider supported by the surface tension of water. [Hermann Eisenbeiss/Photo Research, Inc.] 400 300 200 100 350 250 150 50 Covalent bond Bond strength (kJ . mol −1 ) Ionic interaction Hydrogen bond van der Waals interaction 0 FIGURE 2.4 Relative strengths of bonds in biological molecules. TABLE 2.1 Electronegativities of Some Elements ELEMENT ELECTRONEGATIVITY C 2.55 F 3.98 H 2.20 N 3.04 O 3.44 S 2.58 Water Molecules and Hydrogen Bonds 27 O O H H H R Water–alcohol O N H H H R R Water–amine Likewise, these functional groups can form hydrogen bonds among themselves. For example, the complementarity of bases in DNA and RNA is determined by their ability to form hydrogen bonds with each other. Here, three NH groups are hydrogen bond donors, and N and O atoms are acceptors: Cytosine Guanine Other electrostatic interactions occur between particles that are polar but not actually charged, for example, two carbonyl groups: C O δ − C O δ + These forces, called van der Waals interactions, are usually weaker than hydrogen bonds. The interaction between two strongly polar groups is known as a dipole–dipole interaction and has a strength of about 9 kJ · mol −1 . Very weak van der Waals interactions, called London dispersion forces, occur between nonpolar molecules as a result of small fluctu- ations in their distribution of electrons that create a temporary separation of charge.
- Nobuhiko Yui(Author)
- 2002(Publication Date)
- CRC Press(Publisher)
. . . . . . . . .52 3.5.1 Biological Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52 3.5.2 Self-Replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53 3.5.3 Electron and Energy Transfer Systems . . . . . . . . . . . . . . . . . . . . . . .53 3.6 Summary and Perspectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .56 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 3.1 INTRODUCTION Hydrogen bonding is probably the most important noncovalent interaction to think about in the development of biological or biomimetic supramolecular architectures. Water, the most ubiquitous medium in nature, forms strong intermolecular hydrogen bonds. However, hydrogen bonding is the major factor in three-dimensional struc-tures of proteins and polynucleotides, the most typical biological macromolecules. The highly selective and directional nature of the hydrogen bonding system is ideal for the construction and stabilization of supramolecular architectures. Hydrogen bonding is a weaker interaction compared with covalent or ionic bond-ing, and can therefore be switched on or off with energies that are within the range 3 0-8493-0965-4/02/$0.00+$1.50 © 2002 by CRC Press LLC 26 Supramolecular Design for Biological Applications of thermal fluctuations at life temperatures. This means that the hydrogen-bonded molecules have dynamic characters around the thermodynamic equilibrium state. The weakness of the individual hydrogen bond is such that the bond is often not suf-ficient to provide the strength and specificity necessary for biological processes; however, this can be overcome by cooperation among and geometrical arrangement of a number of hydrogen bonds.
eBook - PDF- Rose Marie O. Mendoza(Author)
- 2019(Publication Date)
- Arcler Press(Publisher)
In case of water, the hydrogen atom is covalently bonded to the oxygen atom of a water molecule (approximate bond enthalpy 470 kJ mol −1 ), however, it also has a further attraction (around 23 kJ/mol) to a neighboring oxygen atom of an adjacent water molecule. A hydrogen bond is a fraction of (around 90%) electrostatic and a fraction of (around 10%) covalent. The strength of the bond depends on its angle and length. Nonetheless, minor deviations from linearity in the bond angle (roughly equal to 20”) have a comparatively minor impact. The dependence on the length of the bond is quite significant and has been revealed to decay in an exponential manner with distance. There exists a trade-off between the strength of hydrogen bond and covalent bond: H–O hydrogen bond is stronger, whereas, the O–H covalent bond is the weaker one, and the shorter distance is the O … O. In case the hydrogen bond is considerably bent, it then follows that the strength of the bond is weaker; also, the two water oxygen atoms will normally be further apart (Smith, 2014). In water, there are random patterns of the hydrogen bonding (and typical ice); for any molecule of water, if selected at random, contains equal probability (50%) that any hydrogen bond is positioned at each of the four sites surrounding the oxygen. Water molecules which are surrounded by four hydrogen bonds are likely to clump together to form clusters, for both energetic as well as statistical reasons. Chains of hydrogen bonding (that is, O-H … O-H … O) are cooperative; the most difficult part is to break the first bond in the chain, after that the next bond is weakened, and so on. Therefore, unzipping might take place with complex macromolecules (e.g., nucleic acids) which are held together through hydrogen bonding (Smith, 2014). In water, the significant cooperative strengthening of hydrogen bonds depends on long-range interactions.
eBook - PDFStatistical Physics of Biomolecules
An Introduction
- Daniel M. Zuckerman(Author)
- 2010(Publication Date)
- CRC Press(Publisher)
The other two orbitals do not participate in covalent bonds, so these “lone pairs” remain negative (see Figure 8.1). 8.1.2 H YDROGEN B ONDS Hydrogen bonds (“H-bonds”) are critical to the structure and biological behavior of water. A hydrogen bond forms between a positively charged hydrogen atom and a negatively charged atom—generally N, O, or F—that are not covalently bonded. The hydrogen atom is called the “donor” and the other molecule’s negative atom is called the “acceptor.” The donor and acceptor may be part of the same molecule or different molecules. Because H-bonds form between molecular groups that are charge-neutral overall, any charged atom on an H-bonding molecule necessarily is compensated by opposite charge somewhere else on the molecule: hence a dipole is formed. In water, 185 186 Statistical Physics of Biomolecules: An Introduction H O LP LP H FIGURE 8.1 A water molecule is best described as containing five elements: the central oxygen nucleus, two positively charged hydrogen atoms, and two negatively charged “lone pairs” (unpaired electrons, denoted LP). The lone pairs and hydrogens are tetrahedrally oriented around the oxygen. The figure shows that tetrahedral symmetry is readily visualized using nonadjacent corners of a cube. (Adapted from Ben-Naim, A.Y., Statistical Thermodynamics for Chemists and Biochemists , Springer, Berlin, Germany, 1992.) for instance, the partial charges on the hydrogens are compensated by the negative charges on oxygen’s lone pairs. Hydrogen bonds are directional, because the dipoles on each molecule participate. That is, the strength of a hydrogen bond depends strongly on the relative orientations of the participating dipoles. There are two reasons for this. First, the dipoles tend to align along a single axis (see ice structure in Figure 8.2) to maximize electrostatic interactions.
eBook - PDFVibrational Spectroscopy With Neutrons - With Applications In Chemistry, Biology, Materials Science And Catalysis
With Applications in Chemistry, Biology, Materials Science and Catalysis
- Philip C H Mitchell, Stewart F Parker, Timmy A J Ramirez-cuesta(Authors)
- 2005(Publication Date)
- World Scientific(Publisher)
9 Hydrogen Bonding In a hydrogen bond, here written H-bond, a hydrogen atom occupies a more or less central position between, usually, two electronegative atoms. This is conventionally represented as a linear A-H—B combination of the hydrogen donor system, A-H, and the acceptor, B. Relevant properties of the different strengths of H-bonds are given in Table 9.1 [1]. Table 9.1 Properties of strong, moderate and weak H-bonds, after [1]. Properties Strong H-bonds Moderate H-bonds Weak H-bonds Bond energy / kJ mol 1 4 to 10 1 to 3 < 1 Bond nature mostly covalent mostly electrostatic electrostatic Bond linearity, A-H— B always linear mostly linear sometimes linear Bond lengths / A A-H 1.2 to 1.5 ca 1.0 ca 1.0 H—B 1.2 to 1.5 1.5 to 2.2 2.2 to 3.2 A B 2.2 to 2.5 2.5 to 3.2 3.2 to 4.0 The dynamics of the hydrogen atom in an H-bond is controlled by the potential surface between the heavy AB atoms and spectroscopy is undertaken with the objective of elucidating the fine details of that surface. Because of the high cross section of the hydrogen atoms these dynamics are uniquely accessible using INS spectroscopy. (The strong infrared response of the H-bond stretch is, rightly, regarded as an excellent indicator of the presence of H-bonds. However, its very 393 394 Vibrational spectroscopy with neutrons strength introduces opto-electric effects that make the spectra difficult to interpret, neutron spectroscopy avoids this problem.) This chapter focuses on results from INS for the stronger and moderate H-bonds where, as explained below, the dynamics of hydrogen transfer should be accessible. Since most known examples of moderate H-bonds occur in oxygen-oxygen systems they will assume a particular prominence in this chapter. H-bonds also determine, to a great extent, the tertiary and quaternary structure essential to achieve biological activity (§10.3).
eBook - PDFThe Hydrogen Bond and the Water Molecule
The Physics and Chemistry of Water, Aqueous and Bio-Media
- Yves Marechal(Author)
- 2006(Publication Date)
- Elsevier Science(Publisher)
– G. A. Jeffrey and A. Saenger (11) (1994) “Hydrogen Bonding in Biological Structures”. An exhaustive modern compilation of structures of biological interest that involve H-bonds. The crystallographers’ point of view on H-bonds. – G. A. Jeffrey (2) (1997) “An Introduction to Hydrogen Bonding”. A textbook on H-bonds, for a large part is devoted to structural aspect of H-bonds. INTERMOLECULAR AND INTRAMOLECULAR H-BONDS Most H-bonds X H Y are formed between two independent molecules X H and Y, as rep-resented in Figure 1.2. These are “intermolecular H-bonds” and when speaking of H-bonds in the following with no other specification, we always refer to this type of H-bond, which represents the large majority of them. Another category of H-bonds however exists, the “intramolecular H-bonds”, where molecular groups X H and Y are both parts of a same molecule. Even if they represent only a minority of H-bonds, these intramolecular H-bonds include quite a large variety of H-bonds. Two typical examples are shown in Figure 1.3. These two types of H-bonds have macroscopic manifestations that are different: an intramolecular H-bond involves a single molecule, whereas an intermolecular H-bond involves two molecules that become independent upon disruption of the H-bond. As a con-sequence, intermolecular H-bonds, which establish relatively strong interactions between molecules in a liquid, are known to strongly influence the magnitudes of the temperature and heat of evaporation of this liquid. This is particularly marked in the case of liquid water. This is not at all so for intramolecular H-bonds that do not modify the interactions between molecules, which most often remain Van der Waals interactions. In a gas, inter-molecular H-bonds are at the origin of deviations from perfect gas law, which is not so for intramolecular H-bonds. Also, in an intermolecular H-bond the relative positions of the donor and acceptor groups, X H and Y, are only ruled by the H-bond interaction.
eBook - ePubThe Chemical Bond
Chemical Bonding Across the Periodic Table
- Gernot Frenking, Sason Shaik(Authors)
- 2014(Publication Date)
- Wiley-VCH(Publisher)
The Nature of the Chemical Bond) [8], Moore and Winmill made the first mention of the H bond, and Latimer and Rodebush recognized the importance of the H bond. Since those early days, there has been an overwhelming body of research, using X-ray crystallography, spectroscopic methods, and emerging quantum chemistry, that has made significant contributions to the enhancement of our knowledge and understanding of the H bond. However, past studies have also shown that there are many different types of H bonds and that the attributes of H bonding are much more complex and broader than previously assumed. As such, even with its history of around 100 years, the H bond is still a growing research area. The purpose of this chapter is not to discuss the diverse field of H bonding research in a comprehensive or exhaustive manner. Rather, we intend to summarize the nuts and bolts of H bonding, with some emphasis placed on the contributions of theoretical chemistry.17.2 Fundamental Properties of Hydrogen Bonds
Despite its ubiquity, it is not necessarily straightforward to define the H bond without ambiguity. A H bond can be generally described as17.1where X and Y are normally highly electronegative atoms. Although the dotted line in Eq. (17.1 ) constitutes the main part of the H bond, the H bond actually refers to the whole structural moiety composed of the three atoms, X, H, and Y [1e]. Chapter 12 of Pauling's The Nature of the Chemical Bond (third ed.) [8b] opens with the following sentences: “It was recognized some decades ago that under certain conditions an atom of hydrogen is attracted by rather strong forces to two atoms, instead of only one, so that it may be considered to be acting as a bond between them. This is called the hydrogen bond.” According to the definition by Pimentel and McClellan, a H bond exists between X–H and Y when “(a) there is evidence of bond formation (association or chelation) and (b) there is evidence that this new bond linking X–H and Y specifically involves the hydrogen atom already bonded to X [1a]”. More recently, Steiner proposed the following definition: an X–H Y interaction is called a hydrogen bond
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