Molecular Level Hydrogen Bonds Have Finally Been Detected

Image credits:University of Basel, Department of Physics

For the first time since its debut in the 1912 book “The Nature of the Chemical Bond”, hydrogen bonds have finally been detected at a molecular scale.

Researchers from the University of Basel’s Swiss Nanoscience Institute carried out a study which examined the detection of a hydrogen bond between a hydrogen atom and an oxygen atom using atomic force microscopy.

Hydrogen is the most abundant element in the universe, making up over 90% of every atom. Due to its enormous abundancy, being able to detect and image the way that it bonds opens huge a plethora of research possibilities.

A hydrogen bond forms between a carbon monoxide microscope tip (upper molecule) and the propellane (lower molecule) Image credits: Department of Physics, University of Basel.

Hydrogen is a very simple molecule, as it is made up of a single proton and a single electron. Having an atomic weight of almost 1, it is the lightest element in our periodic table.

Hydrogen bonds can occur between hydrogen and any element that is suitably electronegative. FYI: Electronegativity is an atomic property that describes how well an atom can attract electrons with the positive attraction of their protons.

Fluorine has the highest electronegativity with a rating of 4.0 and thus forms the strongest hydrogen bond.

Oxygen has the second highest electronegativity at 3.4. The tip of the atomic force microscope was augmented with carbon monoxide for the hydrogen bond to occur.

Although hydrogen bonds are relatively weak in comparison to chemical bonds, they are still extremely useful and influential in compounds.

Hydrogen bonds makes stable double helical DNA double helical structure which is the fundamental building block of life. The monatomic form (H) of hydrogen is the most abundant chemical substance in the entire Universe, constituting roughly 75% of all baryonic mass.

Organic compounds will regularly contain oxygen and hydrogen in close proximity to one another, so the presence of the hydrogen bonds will significantly affect the structure and stability of proteins within the body.


Atomic force microscopy was the imaging technique used in this study. Images are taken from a mechanical probe touching the surface which is used to compile an image. The scanning’s accuracy is achieved by piezoelectric elements that enable accurate imaging.

Trinaphtho[3.3.3]propellane (TNP) and trifluorantheno[3.3.3]propellane (TFAP) molecules were used in this study. They were used due to having C-H bonds perpendicular to the rest of the compound, thus ensuring they were prominently pointing away from the surface.

We use atomic force microscopy (AFM) to resolve the outermost hydrogen atoms of propellane molecules via very weak C═O⋅⋅⋅H–C hydrogen bonding just before the onset of Pauli repulsion,” the report stated.

Regardless to how they adsorbed to the substrate, the C-H bond always faced upwards, allowing for easier manipulation of the hydrogen bonding process.

Propellane organic compunds
2 chemical computational models of the propellane organic compounds, shown from a top down view and a side on view. Image credits: Science Advances.

The C=O tip was lowered near the TNP and TFAP molecules until a hydrogen bond was formed. The atomic force microscope was able to capture images of the bond at varying distances.

hydrogen bonds detected
“(A to F) Series of STM topographies (A, C, and E) of TNP deposited on the Ag(111) surface with increasing coverage and corresponding AFM images (B, D, and F). As the coverage of TNP increases, the ratio of the upright (red arrows) and side-lying (yellow arrow) TNP becomes larger. (G) STM topography of upright TFAP and (H) corresponding AFM image. Measurement parameters: For STM observations, tunneling current I = 1.0 pA and bias voltage V = −300 mV (A), I = 0.8 pA and V = −200 mV (C), I = 0.8 pA and V = −200 mV (E), and I = 0.8 pA and V = 500 mV (G); for AFM observations, oscillation amplitude A = 60 pm and V = 0 mV (B, D, F, and H).” Text and image credits: Science Advances.

The team believe that the findings of this study could be used for the identification of larger molecules, such as polymers and DNA.

Whilst this is a huge advancement in atomic level research and the understanding of atomic level bonding, it’s also a huge testament to how advanced modern day imaging techniques are becoming.

Now that equipment is possible to image these small and weak bonds, it opens up a huge array of possibility for future research.

The research is published in Science Advances.

Source Science Advances

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