Beruflich Dokumente
Kultur Dokumente
1
2 1 BONDING
1 Bonding
HOH:OH+
3 (18 kJ/mol[15] or 4.3 kcal/mol; data obtained using
molecular dynamics as detailed in the reference and
should be compared to 7.9 kJ/mol for bulk water,
obtained using the same molecular dynamics.)
HFHFHF
3 Hydrogen bonds in water
The exact number of hydrogen bonds formed by a
The most ubiquitous and perhaps simplest example of a molecule of liquid water uctuates with time and depends
hydrogen bond is found between water molecules. In a on the temperature.[21] From TIP4P liquid water simula-
discrete water molecule, there are two hydrogen atoms tions at 25 C, it was estimated that each water molecule
and one oxygen atom. Two molecules of water can participates in an average of 3.59 hydrogen bonds. At
form a hydrogen bond between them; the simplest case, 100 C, this number decreases to 3.24 due to the in-
when only two molecules are present, is called the water creased molecular motion and decreased density, while
dimer and is often used as a model system. When more at 0 C, the average number of hydrogen bonds increases
molecules are present, as is the case with liquid water, to 3.69.[21] A more recent study found a much smaller
more bonds are possible because the oxygen of one water number of hydrogen bonds: 2.357 at 25 C.[22] The dif-
molecule has two lone pairs of electrons, each of which ferences may be due to the use of a dierent method for
can form a hydrogen bond with a hydrogen on another dening and counting the hydrogen bonds.
4 4 HYDROGEN BONDS IN DNA AND PROTEINS
HO H3 O+
A single hydrogen atom can participate in two hydrogen The structure of part of a DNA double helix
bonds, rather than one. This type of bonding is called
bifurcated (split in two or two-forked). It can ex-
ist, for instance, in complex natural or synthetic organic
molecules.[25] It has been suggested that a bifurcated hy-
drogen atom is an essential step in water reorientation.[26]
Acceptor-type hydrogen bonds (terminating on an oxy-
gens lone pairs) are more likely to form bifurcation (it
is called overcoordinated oxygen, OCO) than are donor-
type hydrogen bonds, beginning on the same oxygens
hydrogens.[27]
4 Hydrogen bonds in DNA and Hydrogen bonding between guanine and cytosine, one of two
types of base pairs in DNA.
proteins
Hydrogen bonding also plays an important role in deter- In the secondary structure of proteins, hydrogen bonds
mining the three-dimensional structures adopted by pro- form between the backbone oxygens and amide hydro-
teins and nucleic bases. In these macromolecules, bond- gens. When the spacing of the amino acid residues par-
ing between parts of the same macromolecule cause it ticipating in a hydrogen bond occurs regularly between
to fold into a specic shape, which helps determine the positions i and i + 4, an alpha helix is formed. When the
molecules physiological or biochemical role. For exam- spacing is less, between positions i and i + 3, then a 310
ple, the double helical structure of DNA is due largely helix is formed. When two strands are joined by hydro-
to hydrogen bonding between its base pairs (as well as gen bonds involving alternating residues on each partic-
pi stacking interactions), which link one complementary ipating strand, a beta sheet is formed. Hydrogen bonds
strand to the other and enable replication. also play a part in forming the tertiary structure of pro-
5
In 1999, Isaacs et al.[33] showed from interpretations of Dimer formation in carboxylic acids and hexamer
the anisotropies in the Compton prole of ordinary ice formation in hydrogen uoride, which occur even in
that the hydrogen bond is partly covalent. Some NMR the gas phase, resulting in gross deviations from the
data on hydrogen bonds in proteins also indicate covalent ideal gas law.
bonding. Pentamer formation of water and alcohols in apolar
Most generally, the hydrogen bond can be viewed as a solvents.
metric-dependent electrostatic scalar eld between two or
High water solubility of many compounds such as
more intermolecular bonds. This is slightly dierent from
ammonia is explained by hydrogen bonding with
the intramolecular bound states of, for example, covalent
water molecules.
or ionic bonds; however, hydrogen bonding is generally
still a bound state phenomenon, since the interaction en- Negative azeotropy of mixtures of HF and water
ergy has a net negative sum. The initial theory of hydro-
gen bonding proposed by Linus Pauling suggested that Deliquescence of NaOH is caused in part by reaction
the hydrogen bonds had a partial covalent nature. This of OH with moisture to form hydrogen-bonded H
remained a controversial conclusion until the late 1990s 3O
when NMR techniques were employed by F. Cordier et al. 2 species. An analogous process happens between
to transfer information between hydrogen-bonded nuclei, NaNH2 and NH3 , and between NaF and HF.
a feat that would only be possible if the hydrogen bond The fact that ice is less dense than liquid water is due
contained some covalent character.[34] While much ex- to a crystal structure stabilized by hydrogen bonds.
perimental data has been recovered for hydrogen bonds
in water, for example, that provide good resolution on The presence of hydrogen bonds can cause an
the scale of intermolecular distances and molecular ther- anomaly in the normal succession of states of matter
modynamics, the kinetic and dynamical properties of the for certain mixtures of chemical compounds as tem-
hydrogen bond in dynamic systems remain unchanged. perature increases or decreases. These compounds
7
can be liquid until a certain temperature, then solid [8] Beijer, Felix H.; Kooijman, Huub; Spek, Anthony
even as the temperature increases, and nally liq- L.; Sijbesma, Rint P.; Meijer, E. W. (1998).
uid again as the temperature rises over the anomaly Self-Complementarity Achieved through Quadru-
interval[38] ple Hydrogen Bonding. Angew. Chem. Int.
Ed. 37 (12): 7578. doi:10.1002/(SICI)1521-
Smart rubber utilizes hydrogen bonding as its sole 3773(19980202)37:1/2<75::AID-ANIE75>3.0.CO;2-R.
means of bonding, so that it can heal when torn,
[9] Campbell, Neil A.; Brad Williamson; Robin J. Heyden
because hydrogen bonding can occur on the y be- (2006). Biology: Exploring Life. Boston, Massachusetts:
tween two surfaces of the same polymer. Pearson Prentice Hall. ISBN 0-13-250882-6.
Strength of nylon and cellulose bres. [10] Wiley, G.R.; Miller, S.I. (1972). Thermodynamic pa-
rameters for hydrogen bonding of chloroform with Lewis
Wool, being a protein bre, is held together by bases in cyclohexane. Proton magnetic resonance study.
hydrogen bonds, causing wool to recoil when Journal of the American Chemical Society. 94 (10): 3287.
stretched. However, washing at high temperatures doi:10.1021/ja00765a001.
can permanently break the hydrogen bonds and a
garment may permanently lose its shape. [11] Kwak, K; Rosenfeld, DE; Chung, JK; Fayer, MD
(2008). Solute-solvent complex switching dynamics of
chloroform between acetone and dimethylsulfoxide-two-
dimensional IR chemical exchange spectroscopy. The
11 References Journal of Physical Chemistry B. 112 (44): 13906
15. doi:10.1021/jp806035w. PMC 2646412 . PMID
[1] Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, 18855462.
I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N.R.;
[12] Romaczyk, P. P.; Rado, M.; Noga, K.; Kurek, S. S.
Kantorovich, L.; Moriarty, P. (2014). Mapping the force
(2013). Autocatalytic cathodic dehalogenation triggered
eld of a hydrogen-bonded assembly. Nature Communi-
by dissociative electron transfer through a C-H...O hy-
cations. 5. doi:10.1038/ncomms4931.
drogen bond. Physical Chemistry Chemical Physics. 15:
[2] Hapala, Prokop; Kichin, Georgy; Wagner, Christian; 1752217536. doi:10.1039/C3CP52933A.
Tautz, F. Stefan; Temirov, Ruslan; Jelnek, Pavel (2014-
[13] Larson, J. W.; McMahon, T. B. (1984). Gas-phase bi-
08-19). Mechanism of high-resolution STM/AFM imag-
halide and pseudobihalide ions. An ion cyclotron reso-
ing with functionalized tips. Physical Review B. 90 (8):
nance determination of hydrogen bond energies in XHY-
085421. doi:10.1103/PhysRevB.90.085421.
species (X, Y = F, Cl, Br, CN)". Inorganic Chemistry. 23
[3] Hmlinen, Sampsa K.; van der Heijden, Nadine; van (14): 20292033. doi:10.1021/ic00182a010.
der Lit, Joost; den Hartog, Stephan; Liljeroth, Peter;
[14] Emsley, J. (1980). Very Strong Hydrogen
Swart, Ingmar (2014-10-31). Intermolecular Contrast in
Bonds. Chemical Society Reviews. 9 (1): 91124.
Atomic Force Microscopy Images without Intermolecu-
doi:10.1039/cs9800900091.
lar Bonds. Physical Review Letters. 113 (18): 186102.
doi:10.1103/PhysRevLett.113.186102. [15] Markovitch, Omer; Agmon, Noam (2007). Struc-
ture and energetics of the hydronium hydration
[4] IUPAC, Compendium of Chemical Terminology, 2nd ed. shells. J. Phys. Chem. A. 111 (12): 22532256.
(the Gold Book) (1997). Online corrected version: doi:10.1021/jp068960g. PMID 17388314.
(2006) "hydrogen bond".
[16] Grunenberg, Jrg (2004). Direct Assessment of In-
[5] John R. Sabin (1971). Hydrogen bonds involving sulfur. terresidue Forces in WatsonCrick Base Pairs Using
I. Hydrogen sulde dimer. J. Am. Chem. Soc. 93: 3613 Theoretical Compliance Constants. Journal of the
3620. doi:10.1021/ja00744a012. American Chemical Society. 126 (50): 163101.
doi:10.1021/ja046282a. PMID 15600318.
[6] Arunan, Elangannan; Desiraju, Gautam R.; Klein, Roger
A.; Sadlej, Joanna; Scheiner, Steve; Alkorta, Ibon; Clary, [17] Legon, A. C.; Millen, D. J. (1987). Angular geome-
David C.; Crabtree, Robert H.; Dannenberg, Joseph J.; tries and other properties of hydrogen-bonded dimers: a
Hobza, Pavel; Kjaergaard, Henrik G.; Legon, Anthony C.; simple electrostatic interpretation of the success of the
Mennucci, Benedetta; Nesbitt, David J. (2011). Deni- electron-pair model. Chemical Society Reviews. 16: 467.
tion of the hydrogen bond. Pure Appl. Chem. 83 (8): doi:10.1039/CS9871600467.
16371641. doi:10.1351/PAC-REC-10-01-02.
[18] Pauling, L. (1960). The nature of the chemical bond and
[7] Arunan, Elangannan; Desiraju, Gautam R.; Klein, Roger the structure of molecules and crystals; an introduction to
A.; Sadlej, Joanna; Scheiner, Steve; Alkorta, Ibon; Clary, modern structural chemistry (3rd ed.). Ithaca (NY): Cor-
David C.; Crabtree, Robert H.; Dannenberg, Joseph J.; nell University Press. p. 450. ISBN 0-8014-0333-2.
Hobza, Pavel; Kjaergaard, Henrik G.; Legon, Anthony C.;
Mennucci, Benedetta; Nesbitt, David J. (2011). Dening [19] Moore, T. S.; Winmill, T. F. (1912). The state of
the hydrogen bond: An Account. Pure Appl. Chem. 83 amines in aqueous solution. J. Chem. Soc. 101: 1635.
(8): 16191636. doi:10.1351/PAC-REP-10-01-01. doi:10.1039/CT9120101635.
8 13 EXTERNAL LINKS
[20] Latimer, Wendell M.; Rodebush, Worth H. (1920). Po- [32] Crabtree, Robert H.; Siegbahn, Per E. M.; Eisenstein,
larity and ionization from the standpoint of the Lewis the- Odile; Rheingold, Arnold L.; Koetzle, Thomas F. (1996).
ory of valence.. Journal of the American Chemical Soci- A New Intermolecular Interaction: Unconventional Hy-
ety. 42 (7): 14191433. doi:10.1021/ja01452a015. drogen Bonds with Element-Hydride Bonds as Proton
Acceptor. Acc. Chem. Res. 29 (7): 348354.
[21] Jorgensen, W. L.; Madura, J. D. (1985). Tem- doi:10.1021/ar950150s. PMID 19904922.
perature and size dependence for Monte Carlo
simulations of TIP4P water. Mol. Phys. 56 [33] Isaacs, E.D.; et al. (1999). Covalency of
(6): 1381. Bibcode:1985MolPh..56.1381J. the Hydrogen Bond in Ice: A Direct X-Ray
doi:10.1080/00268978500103111. Measurement. Physical Review Letters. 82
(3): 600603. Bibcode:1999PhRvL..82..600I.
[22] Zielkiewicz, Jan (2005). Structural properties of doi:10.1103/PhysRevLett.82.600.
water: Comparison of the SPC, SPCE, TIP4P, and
TIP5P models of water. J. Chem. Phys. 123 [34] Cordier, F; Rogowski, M; Grzesiek, S; Bax, A
(10): 104501. Bibcode:2005JChPh.123j4501Z. (1999). Observation of through-hydrogen-bond
doi:10.1063/1.2018637. PMID 16178604. (2h)J(HC') in a perdeuterated protein. J Magn Reson.
140 (2): 5102. Bibcode:1999JMagR.140..510C.
[23] Jencks, William; Jencks, William P. (1986). Hydrogen doi:10.1006/jmre.1999.1899. PMID 10497060.
Bonding between Solutes in Aqueous Solution. J. Amer.
Chem. Soc. 108 (14): 4196. doi:10.1021/ja00274a058. [35] Cowan ML; Bruner BD; Huse N; et al. (2005).
Ultrafast memory loss and energy redistribution in
[24] Dillon, P. F. (2012). Biophysics. Cambridge University the hydrogen bond network of liquid H2 O. Nature.
Press. p. 37. ISBN 978-1-139-50462-1. 434 (7030): 199202. Bibcode:2005Natur.434..199C.
[25] Baron, Michel; Giorgi-Renault, Sylviane; Renault, Jean; doi:10.1038/nature03383. PMID 15758995.
Mailliet, Patrick; Carr, Daniel; Etienne, Jean (1984). [36] Luo, Jiangshui; Jensen, Annemette H.; Brooks, Neil
Htrocycles fonction quinone. V. Raction anormale R.; Sniekers, Jeroen; Knipper, Martin; Aili, David; Li,
de la butanedione avec la diamino-1,2 anthraquinone; Qingfeng; Vanroy, Bram; Wbbenhorst, Michael; Yan,
structure cristalline de la naphto \2,3-f] quinoxalinedione- Feng; Van Meervelt, Luc; Shao, Zhigang; Fang, Jian-
7,12 obtenue. Can. J. Chem. 62 (3): 526530. hua; Luo, Zheng-Hong; De Vos, Dirk E.; Binnemans,
doi:10.1139/v84-087. Koen; Fransaer, Jan (2015). 1,2,4-Triazolium per-
[26] Laage, Damien; Hynes, James T. (2006). A Molecu- uorobutanesulfonate as an archetypal pure protic or-
lar Jump Mechanism for Water Reorientation. Science. ganic ionic plastic crystal electrolyte for all-solid-state fuel
311 (5762): 8325. Bibcode:2006Sci...311..832L. cells. Energy & Environmental Science. 8 (4): 1276.
doi:10.1126/science.1122154. PMID 16439623. doi:10.1039/C4EE02280G.
[27] Markovitch, Omer; Agmon, Noam (2008). The [37] Lwdin, P. O. (1963). Proton Tunneling in DNA and
Distribution of Acceptor and Donor Hydrogen- its Biological Implications. Rev. Mod. Phys. 35: 724.
Bonds in Bulk Liquid Water. Molecular Physics. doi:10.1103/RevModPhys.35.724.
106 (2): 485. Bibcode:2008MolPh.106..485M.
[38] Law-breaking liquid dees the rules. Physicsworld.com
doi:10.1080/00268970701877921.
(September 24, 2004 )
[28] Politi, Regina; Harries, Daniel (2010). Enthalpi-
cally driven peptide stabilization by protective os-
molytes. ChemComm. 46 (35): 64496451. 12 Further reading
doi:10.1039/C0CC01763A.
[29] Gilman-Politi, Regina; Harries, Daniel (2011). Unravel- George A. Jerey. An Introduction to Hydrogen
ing the Molecular Mechanism of Enthalpy Driven Pep- Bonding (Topics in Physical Chemistry). Oxford
tide Folding by Polyol Osmolytes. Journal of Chem- University Press, USA (March 13, 1997). ISBN 0-
ical Theory and Computation. 7 (11): 38163828. 19-509549-9
doi:10.1021/ct200455n.
[31] Fernndez, A; Rogale K; Scott Ridgway; Scheraga H.A. isotopic eect on bond dynamics
(June 2004). Inhibitor design by wrapping pack-
ing defects in HIV-1 proteins.. Proceedings of the
National Academy of Sciences. 101 (32): 116405.
doi:10.1073/pnas.0404641101. PMID 15289598.
9
14.2 Images
File:3D_model_hydrogen_bonds_in_water.svg Source: https://upload.wikimedia.org/wikipedia/commons/c/c6/3D_model_hydrogen_
bonds_in_water.svg License: CC BY-SA 3.0 Contributors: File:3D model hydrogen bonds in water.jpg Original artist: User Qwerter at
Czech wikipedia: Qwerter. Transferred from cs.wikipedia; Transfer was stated to be made by User:sevela.p. Translated to english by by
Michal Maas (User:snek01). Vectorized by Magasjukur2
File:ADN_animation.gif Source: https://upload.wikimedia.org/wikipedia/commons/8/81/ADN_animation.gif License: Public domain
Contributors: Own work Original artist: brian0918™
File:Acac.png Source: https://upload.wikimedia.org/wikipedia/commons/9/9e/Acac.png License: Public domain Contributors: Own
work drawn in ChemDraw Original artist: DMacks (<a href='//commons.wikimedia.org/wiki/User_talk:DMacks' title='User talk:
DMacks'>talk</a>)
File:Acetic_Acid_Hydrogenbridge_V.1.svg Source: https://upload.wikimedia.org/wikipedia/commons/b/be/Acetic_Acid_
Hydrogenbridge_V.1.svg License: CC0 Contributors: Own work Original artist: J
File:Base_pair_GC.svg Source: https://upload.wikimedia.org/wikipedia/commons/6/64/Base_pair_GC.svg License: Public domain Con-
tributors: Own work Original artist: Yikrazuul
File:Cellulose_strand.svg Source: https://upload.wikimedia.org/wikipedia/commons/a/a4/Cellulose_strand.svg License: CC-BY-SA-3.0
Contributors: http://commons.wikimedia.org/wiki/File:Cellulose_strand.jpg Original artist: Laghi.l
File:Free-to-read_lock_75.svg Source: https://upload.wikimedia.org/wikipedia/en/8/80/Free-to-read_lock_75.svg License: CC0 Con-
tributors: ? Original artist: ?
File:Hex_ice.GIF Source: https://upload.wikimedia.org/wikipedia/commons/5/5b/Hex_ice.GIF License: Public domain Contributors:
Own work (Original text: I created this work entirely by myself.) Original artist: NIMSoce (talk)
File:Hydrogen_Bond_Quadruple_AngewChemIntEd_1998_v37_p75.jpg Source: https://upload.wikimedia.org/wikipedia/
commons/2/2d/Hydrogen_Bond_Quadruple_AngewChemIntEd_1998_v37_p75.jpg License: CC-BY-SA-3.0 Contributors: Transferred
from en.wikipedia to Commons. Original artist: M stone at English Wikipedia
File:Kevlar_chemical_structure.png Source: https://upload.wikimedia.org/wikipedia/commons/b/bf/Kevlar_chemical_structure.png
License: CC-BY-SA-3.0 Contributors: ? Original artist: ?
File:NTCDI_AFM2a.jpg Source: https://upload.wikimedia.org/wikipedia/commons/0/0c/NTCDI_AFM2a.jpg License: CC BY 3.0
Contributors: http://www.nature.com/ncomms/2014/140530/ncomms4931/full/ncomms4931.html Original artist: A. M. Sweetman et al.
File:WikipediaHDonorAcceptor.png Source: https://upload.wikimedia.org/wikipedia/commons/3/35/WikipediaHDonorAcceptor.png
License: Public domain Contributors: Own work Original artist: Mcpazzo
10 14 TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES