Carbon hydrogen bonds

Carbon hydrogen bonds DEFAULT

Carbon–hydrogen bond

The carbon-hydrogen bond is a bond between carbon and hydrogen atoms that can be found in many organic compounds. This bond is a covalent bond meaning that carbon shares its outer valence electrons with up to four hydrogens. This completes both of their outer shells making them stable. Carbon–hydrogen bonds have a bond length of about 1.09 Å and a bond energy of about 413 kJ/mol. Using Pauling's scale—C and H —the electronegativity difference between these two atoms is 0.35. Because of this small difference in electronegativities, the C−H bond is generally regarded as being non-polar. In structural formulas of molecules, the hydrogen atoms are often omitted. Compound classes consisting solely of C–H bonds and C–C bonds are alkanes, alkenes, alkynes, and aromatic hydrocarbons. Collectively they are known as hydrocarbons.
In October 2016, astronomers reported that the very basic chemical ingredients of life—the carbon-hydrogen molecule, the carbon-hydrogen positive ion and the carbon ion —are the result, in large part, of ultraviolet light from stars, rather than in other ways, such as the result of turbulent events related to supernovae and young stars, as thought earlier.

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Learning Objective

  • Describe the properties of hydrogen bonding.

Key Points

    • Hydrogen bonds are strong intermolecular forces created when a hydrogen atom bonded to an electronegative atom approaches a nearby electronegative atom.
    • Greater electronegativity of the hydrogen bond acceptor will lead to an increase in hydrogen-bond strength.
    • The hydrogen bond is one of the strongest intermolecular attractions, but weaker than a covalent or an ionic bond.
    • Hydrogen bonds are responsible for holding together DNA, proteins, and other macromolecules.

Terms

  • hydrogen bondThe attraction between a partially positively charged hydrogen atom attached to a highly electronegative atom (such as nitrogen, oxygen, or fluorine) and another nearby electronegative atom.
  • electronegativityThe tendency of an atom or molecule to draw electrons towards itself, form dipoles, and thus form bonds.
  • intermolecularA type of interaction between two different molecules.

Forming a Hydrogen Bond

A hydrogen bond is the electromagnetic attraction created between a partially positively charged hydrogen atom attached to a highly electronegative atom and another nearby electronegative atom. A hydrogen bond is a type of dipole-dipole interaction; it is not a true chemical bond. These attractions can occur between molecules (intermolecularly) or within different parts of a single molecule (intramolecularly).

Hydrogen Bond Donor

A hydrogen atom attached to a relatively electronegative atom is a hydrogen bond donor. This electronegative atom is usually fluorine, oxygen, or nitrogen. The electronegative atom attracts the electron cloud from around the hydrogen nucleus and, by decentralizing the cloud, leaves the hydrogen 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, is stronger. In the molecule ethanol, there is one hydrogen atom bonded to an oxygen atom, which is very electronegative. This hydrogen atom is a hydrogen bond donor.

Hydrogen Bond Acceptor

A hydrogen bond results when this strong partial positive charge attracts a lone pair of electrons on another atom, which becomes the hydrogen bond acceptor. 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. Greater electronegativity of the hydrogen bond acceptor will create a stronger hydrogen bond. The diethyl ether molecule contains an oxygen atom that is not bonded to a hydrogen atom, making it a hydrogen bond acceptor.

A hydrogen attached to carbon can also participate in hydrogen bonding when the carbon atom is bound to electronegative atoms, as is the case in chloroform (CHCl3). As in a molecule where a hydrogen is attached to nitrogen, oxygen, or fluorine, the electronegative atom attracts the electron cloud from around the hydrogen nucleus and, by decentralizing the cloud, leaves the hydrogen atom with a positive partial charge.

Applications for Hydrogen Bonds

Hydrogen bonds occur in inorganic molecules, such as water, and organic molecules, such as DNA and proteins. The two complementary strands of DNA are held together by hydrogen bonds between complementary nucleotides (A&T, C&G). Hydrogen bonding in water contributes to its unique properties, including its high boiling point (100 °C) and surface tension.

In biology, intramolecular hydrogen bonding is partly responsible for the secondary, tertiary, and quaternary structures of proteins and nucleic acids. The hydrogen bonds help the proteins and nucleic acids form and maintain specific shapes.

 

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Metal-free oxidation of aromatic carbon–hydrogen bonds through a reverse-rebound mechanism

Abstract

Methods for carbon–hydrogen (C–H) bond oxidation have a fundamental role in synthetic organic chemistry, providing functionality that is required in the final target molecule or facilitating subsequent chemical transformations. Several approaches to oxidizing aliphatic C–H bonds have been described, drastically simplifying the synthesis of complex molecules1,2,3,4,5,6. However, the selective oxidation of aromatic C–H bonds under mild conditions, especially in the context of substituted arenes with diverse functional groups, remains a challenge. The direct hydroxylation of arenes was initially achieved through the use of strong Brønsted or Lewis acids to mediate electrophilic aromatic substitution reactions with super-stoichiometric equivalents of oxidants, significantly limiting the scope of the reaction7. Because the products of these reactions are more reactive than the starting materials, over-oxidation is frequently a competitive process. Transition-metal-catalysed C–H oxidation of arenes with or without directing groups has been developed, improving on the acid-mediated process; however, precious metals are required8,9,10,11,12,13. Here we demonstrate that phthaloyl peroxide functions as a selective oxidant for the transformation of arenes to phenols under mild conditions. Although the reaction proceeds through a radical mechanism, aromatic C–H bonds are selectively oxidized in preference to activated –H bonds. Notably, a wide array of functional groups are compatible with this reaction, and this method is therefore well suited for late-stage transformations of advanced synthetic intermediates. Quantum mechanical calculations indicate that this transformation proceeds through a novel addition–abstraction mechanism, a kind of ‘reverse-rebound’ mechanism as distinct from the common oxygen-rebound mechanism observed for metal–oxo oxidants. These calculations also identify the origins of the experimentally observed aryl selectivity.

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Accession codes

Data deposits

Supplementary crystallographic data for compound 2a–int have been deposited at the Cambridge Crystallographic Data Centre under accession number CCDC903297. These data can be obtained free of charge at http://www.ccdc.cam.ac.uk/data_request/cif.

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Acknowledgements

Financial support from the University of Texas at Austin, the Welch Foundation (F-1694 to D.S.), and the US National Science Foundation (CHE-1059084 to K.N.H.) are gratefully acknowledged. Calculations were performed on the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the US National Science Foundation (OCI-1053575).

Author information

Affiliations

  1. Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, 78712, Texas, USA

    Changxia Yuan, Taylor Hernandez, Adrian Berriochoa & Dionicio Siegel

  2. Department of Chemistry and Biochemistry, University of California, Los Angeles, 90095, California, USA

    Yong Liang & Kendall N. Houk

Contributions

C.Y. designed experiments; C.Y., T.H. and A.B. carried out experiments; Y.L. and K.N.H. carried out computational analyses; C.Y., Y.L., K.N.H. and D.S. analysed data; K.N.H. and D.S. supervised research; C.Y., Y.L., K.N.H. and D.S. wrote the paper.

Corresponding author

Correspondence to Dionicio Siegel.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Text and Data sections 1-10 – see contents page for details. The Supplementary Information was amended to include a new safety protocol on 24 September 2013 (PDF 13448 kb)

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Yuan, C., Liang, Y., Hernandez, T. et al. Metal-free oxidation of aromatic carbon–hydrogen bonds through a reverse-rebound mechanism. Nature499, 192–196 (2013). https://doi.org/10.1038/nature12284

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Carbon–hydrogen bond

The carbon-hydrogen bond (C–H bond) is a bond between carbon and hydrogen atoms that can be found in many organic compounds.[1] This bond is a covalent bond meaning that carbon shares its outer valence electrons with up to four hydrogens. This completes both of their outer shells making them stable.[2] Carbon–hydrogen bonds have a bond length of about 1.09 Å (1.09 × 10−10 m) and a bond energy of about 413 kJ/mol (see table below). Using Pauling's scale—C (2.55) and H (2.2)—the electronegativity difference between these two atoms is 0.35. Because of this small difference in electronegativities, the C−H bond is generally regarded as being non-polar. In structural formulas of molecules, the hydrogen atoms are often omitted. Compound classes consisting solely of C–H bonds and C–C bonds are alkanes, alkenes, alkynes, and aromatic hydrocarbons. Collectively they are known as hydrocarbons.

In October 2016, astronomers reported that the very basic chemical ingredients of life—the carbon-hydrogen molecule (CH, or methylidyne radical), the carbon-hydrogen positive ion (CH+) and the carbon ion (C+)—are the result, in large part, of ultraviolet light from stars, rather than in other ways, such as the result of turbulent events related to supernovae and young stars, as thought earlier.[3]

Bond length[edit]

The length of the carbon-hydrogen bond varies slightly with the hybridisation of the carbon atom. A bond between a hydrogen atom and an sp2 hybridised carbon atom is about 0.6% shorter than between hydrogen and sp3 hybridised carbon. A bond between hydrogen and sp hybridised carbon is shorter still, about 3% shorter than sp3 C-H. This trend is illustrated by the molecular geometry of ethane, ethylene and acetylene.

Reactions[edit]

Main article: Carbon–hydrogen bond activation

The C−H bond in general is very strong, so it is relatively unreactive. In several compound classes, collectively called carbon acids, the C−H bond can be sufficiently acidic for proton removal. Unactivated C−H bonds are found in alkanes and are not adjacent to a heteroatom (O, N, Si, etc.). Such bonds usually only participate in radical substitution. Many enzymes are known, however, to affect these reactions.[5]

Although the C−H bond is one of the strongest, it varies over 30% in magnitude for fairly stable organic compounds, even in the absence of heteroatoms.[6][7]

See also[edit]

References[edit]

  1. ^March, Jerry (1985), Advanced Organic Chemistry: Reactions, Mechanisms, and Structure (3rd ed.), New York: Wiley, ISBN 
  2. ^"Life Sciences Cyberbridge". Covalent Bonds. Archived from the original on 2015-09-18. Retrieved 2015-09-15.
  3. ^Landau, Elizabeth (12 October 2016). "Building Blocks of Life's Building Blocks Come From Starlight". NASA. Retrieved 13 October 2016.
  4. ^CRC Handbook of Chemistry and Physics, 88th edition
  5. ^Bollinger, J. M. Jr., Broderick, J. B. "Frontiers in enzymatic C-H-bond activation" Current Opinion in Chemical Biology 2009, vol. 13, page 51-7. doi:10.1016/j.cbpa.2009.03.018
  6. ^"Bond Energies". Organic Chemistry, Michigan State University. Archived from the original on 29 August 2016.
  7. ^Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition
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Hydrogen bonds carbon

1

Now, after nearly 25 years of work by chemists at the University of California, Berkeley, those hydrocarbon bonds -- two-thirds of all the chemical bonds in petroleum and plastics -- have fully yielded, opening the door to the synthesis of a large range of novel organic molecules, including drugs based on natural compounds.

"Carbon-hydrogen bonds are usually part of the framework, the inert part of a molecule," said John Hartwig, the Henry Rapoport Chair in Organic Chemistry at UC Berkeley. "It has been a challenge and a holy grail of synthesis to be able to do reactions at these positions because, until now, there has been no reagent or catalyst that will allow you to add anything at the strongest of these bonds."

Hartwig and other researchers had previously shown how to add new chemical groups at C-H bonds that are easier to break, but they could only add them to the strongest positions of simple hydrocarbon chains.

In the May 15 issue of the journal Science, Hartwig and his UC Berkeley colleagues described how to use a newly designed catalyst to add functional chemical groups to the hardest of the carbon-hydrogen bonds to crack: the bonds, typically at the head or tail of a molecule, where a carbon has three attached hydrogen atoms, what's called a methyl group (CH3).

"The primary C-H bonds, the ones on a methyl group at the end of a chain, are the least electron-rich and the strongest," he said. "They tend to be the least reactive of the C-H bonds."

UC Berkeley postdoctoral fellow Raphael Oeschger discovered a new version of a catalyst based on the metal iridium that opens up one of the three C-H bonds at a terminal methyl group and inserts a boron compound, which can be easily replaced with more complex chemical groups. The new catalyst was more than 50 times more efficient than previous catalysts and just as easy to work with.

"We now have the ability to do these types of reactions, which should enable people to rapidly make molecules that they would not have made before," Hartwig said. "I wouldn't say these are molecules that could not have been made before, but people wouldn't make them because it would take too long, too much time and research effort, to make them."

The payoff could be huge. Each year, nearly a billion pounds of hydrocarbons are used by industry to make solvents, refrigerants, fire retardants and other chemicals and are the typical starting point for synthesizing drugs.

'Expert surgery' on hydrocarbons

To prove the utility of the catalytic reaction, UC Berkeley postdoctoral fellow Bo Su and his coworkers in the lab used it to add a boron compound, or borane, to a terminal, or primary, carbon atom in 63 different molecular structures. The borane can then be swapped out for any number of chemical groups. The reaction specifically targets terminal C-H bonds, but works at other C-H bonds when a molecule doesn't have a terminal C-H.

"We make a boron-carbon bond using boranes as reagents -- they're just a couple steps away from ant poison, boric acid -- and that carbon-boron bond can be converted into many different things," Hartwig said. "Classically, you can make a carbon-oxygen bond from that, but you can also make a carbon-nitrogen bond, a carbon-carbon bond, a carbon-fluorine bond or other carbon-halogen bonds. So, once you make that carbon-boron bond, there are many different compounds that can be made."

Organic chemist Varinder Aggarwal from the University of Bristol referred to the catalytic reaction as "expert surgery" and characterized UC Berkeley's new technique as "sophisticated and clever," according to the magazine Chemical and Engineering News

One potential application, Hartwig said, is altering natural compounds -- chemicals from plants or animals that have useful properties, such as antibiotic activity -- to make them better. Many pharmaceutical companies today are focused on biologics -- organic molecules, such as proteins, used as drugs -- that could also be altered with this reaction to improve their effectiveness.

"In the normal course, you would have to go back and remake all those molecules from the start, but this reaction could allow you to just make them directly," Hartwig said. "This is one type of chemistry that would allow you to take those complex structures that nature makes that have an inherent biological activity and enhance or alter that biological activity by making small changes to the structure."

He said that chemists could also add new chemical groups to the ends of organic molecules to prep them for polymerization into long chains never before synthesized.

"It could enable you to take molecules that would be naturally abundant, biosourced molecules like fatty acids, and be able to derivatize them at the other end for polymer purposes," he said.

UC Berkeley's long history with C-H bonds

Chemists have long tried to make targeted additions to carbon-hydrogen bonds, a reaction referred to as C-H activation. One still unachieved dream is to convert methane -- an abundant, but often wasted, byproduct of oil extraction and a potent greenhouse gas -- into an alcohol called methanol that can be used as a starting point in many chemical syntheses in industry.

In 1982, Robert Bergman, now a UC Berkeley professor emeritus of chemistry, first showed that an iridium atom could break a C-H bond in an organic molecule and insert itself and an attached ligand between the carbon and hydrogen. While a major advance in organic and inorganic chemistry, the technique was impractical -- it required one iridium atom per C-H bond. Ten years later, other researchers found a way to use iridium and other so-called transition metals, like tungsten, as a catalyst, where a single atom could break and functionalize millions of C-H bonds.

Hartwig, who was a graduate student with Bergman in the late 1980s, continued to bang on unreactive C-H bonds and in 2000 published a paper in Science describing how to use a rhodium-based catalyst to insert boron at terminal C-H bonds. Once the boron was inserted, chemists could easily swap it out for other compounds. With subsequent improvements to the reaction and changing the metal from rhodium to iridium, some manufacturers have used this catalytic reaction to synthesize drugs by modifying different types of C-H bonds. But the efficiency for reactions at methyl C-H bonds at the ends of carbon chains remained low, because the technique required that the reactive chemicals also be the solvent.

With the addition of the new catalytic reaction, chemists can now stick chemicals in nearly any type of carbon-hydrogen bond. In the reaction, iridium snips off a terminal hydrogen atom, and the boron replaces it; another boron compound floats away with the released hydrogen atom. The team attached a new ligand to iridium -- a methyl group called 2-methylphenanthroline -- that accelerated the reaction by 50 to 80 times over previous results.

Hartwig acknowledges that these experiments are a first step. The reactions vary from 29% to 85% in their yield of the final product. But he is working on improvements.

"For us, it shows, yeah, you can do this, but we will need to make even better catalysts. We know that the ultimate goal is attainable if we can further increase our rates by a factor of 10, let's say. Then, we should be able to increase the complexity of molecules for this reaction and achieve higher yields," Hartwig said. "It is a little bit like a four-minute mile. Once you know that something can be accomplished, many people are able to do it, and the next thing you know, we're running a three-and-three-quarter-minute mile."

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Journal Reference:

  1. Raphael Oeschger, Bo Su, Isaac Yu, Christian Ehinger, Erik Romero, Sam He, John Hartwig. Diverse functionalization of strong alkyl C–H bonds by undirected borylation. Science, 2020; 368 (6492): 736 DOI: 10.1126/science.aba6146

Cite This Page:

University of California - Berkeley. "Scientists finally crack nature's most common chemical bond: Carbon-hydrogen bonds in hydrocarbon molecules have resisted functionalization until now." ScienceDaily. ScienceDaily, 21 May 2020. <www.sciencedaily.com/releases/2020/05/200521151915.htm>.

University of California - Berkeley. (2020, May 21). Scientists finally crack nature's most common chemical bond: Carbon-hydrogen bonds in hydrocarbon molecules have resisted functionalization until now. ScienceDaily. Retrieved October 15, 2021 from www.sciencedaily.com/releases/2020/05/200521151915.htm

University of California - Berkeley. "Scientists finally crack nature's most common chemical bond: Carbon-hydrogen bonds in hydrocarbon molecules have resisted functionalization until now." ScienceDaily. www.sciencedaily.com/releases/2020/05/200521151915.htm (accessed October 15, 2021).


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Polar \u0026 Non-Polar Molecules: Crash Course Chemistry #23

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