Chemistry Hall

  • About
  • Contact Us
  • Contribute: Publishing Guidelines

Chemistry Hall – From Cutting-Edge Research Highlights to Educational Resources

Chemistry Hall From Cutting-Edge Research Highlights to Home Chemistry Experiments
You are here: Home / Chemistry Research Highlights / Can We See Real Atoms and Molecules? Electron Microscopy at a Glance

Can We See Real Atoms and Molecules? Electron Microscopy at a Glance

June 17, 2019 By C. Hall 2 Comments

A universal challenge that has been keeping chemists busy ever since the modern concepts of “atom” and “molecules” were conceived, is how to actually characterize molecular compounds, either human-made or found on Nature. But, can we see real atoms and molecules?

Confirming the actual structure of a molecule, is still a big challenge now-a-days. The advances in techniques such as NMR (Nuclear Magnetic Resonance) spectroscopy, or single-crystal X-ray diffraction have significantly helped speeding up this problem.

Table of Contents hide
1 Molecular structure determination
2 Can we actually see real molecules or atoms?
3 Seeing atoms in motion
4 The Boy And His Atom: The World’s Smallest Movie
5 Direct observation of chemical reactions
6 AFM in structural determination
7 Taking real pictures of complex chemical reactions
8 The search for the “Holy Grail” of structural determination
9 Is this the future of chemistry?

Molecular structure determination

Every month we get reports of chemical structures whose structures have to be reassigned or revised after some study (either synthetic or just based on characterization techniques) is carried out. On this regard, it is worth remarking the difference between scientific models and reality.

The complex chemical structure of maitotoxin

Truth is, even today, the methods for the characterization of molecules available to use routinely (which are explained in the most basic chemical bibliography), can be consider rather rudimentary, and of difficult interpretation for non-experts. Let me be honest, I am a trained PhD organic chemist and if I had to take a look at the NMR spectra of a complex natural product such as maitotoxin, I would probably have no clue what I am looking at.

Single crystal X-ray diffraction is probably the closest method to easily visualize the structure of a molecule in 3D. However, this is not a bulletproof method. The sample preparation (growing single crystals) required for this indirect technique, renders it useless for a wide variety of chemical compounds.

Can we actually see real molecules or atoms?

Accordingly, I would say that by today, there should already be a method that allows taking a direct microscopic “picture” of any compound you like, and immediately visualizing its structure in a screen. Apparently we are not quite there yet (in regards to “any compound”, keep reading). However, the answer may come under the name of atomic microscopy, and all of its variations.

Block diagram of atomic force microscopy

Atomic force microscopy (AFM) or scanning force microscopy (SFM) is a very high resolution probe-microscopy technique. It allows us to actually “see” or “take real pictures” at the nanometer-scale, in which the molecular realm lies. A picture is worth 1000 words. In the example below, scientists make use of this technique to get pictures of a compound called naphthalenetetracarboxylic diimide. We can actually see a real molecule.

Can we see real atoms and molecules?
Credit to P. Moriarty and coworkers (Mapping the force field of a hydrogen-bonded assembly.  doi: 10.1038/ncomms4931)

Much more recently, researchers at Oxford and IBM used STM-AFM to generate and visualize in situ the first cyclic allotrope of carbon, cyclo[18]carbon.

Seeing atoms in motion

The world of visualizing at the atomic level took a leap more than ten years ago. In 2008, a research group reported the imaging for the first time of light atoms and molecules on graphene. Subsequently, the same team managed to observe for the first time the actual movement of insolated graphene atoms in real time. The following movie from the Berkeley team shows the growth of a hole in a graphene sheet. For this experiment, a beam of electrons is focused to a specific spot on the graphene sheet, blowing out the focused carbon atoms making a hole. Besides, it can also be observed how the carbon atoms rearrange themselves (edge reconstruction) to adapt a more stable configuration.

Credit to A. Zettl and coworkers (Graphene at the Edge: Stability and Dynamics, doi: 10.1126/science.1166999).

The Boy And His Atom: The World’s Smallest Movie

The Guinness World Record for the “Smallest Stop-Motion Film” is held by a movie recorded by IBM scientists. Sometimes, nanophysicists also need to have a bit of fun, and what they decided is to “film” a movie by using scanning tunneling microscopy, a the result is in the following video:

By the use of this technique, the scientists managed to move a lot of molecules of carbon dioxide following their will. The result is a movie you can only see using a microscope that magnifies one hundred million times.

Direct observation of chemical reactions

Obviously, taking real pictures of molecules and atoms was just not enough for the scientific community. If we fast-forward to year 2013, atomic microscopy, more specifically, non-contact atomic force microscopy, allowed the direct imaging of molecular structures during a chemical reaction. Some results of these experiments published in the journal Science are displayed below. We cannot only see actual atoms molecules, we can observe directly chemical reactions!

Can we see actual atoms and molecules?
Credit to F. R. Fischer and coworkers (Direct Imaging of Covalent Bond Structure in Single-Molecule Chemical Reactions, doi: 10.1126/science.1238187)

AFM in structural determination

This field started as a cluster of isolated cases, but as the years went by, more and more examples of the application of this set of physical techniques are being constantly reported. The level at which the studied molecules can be observed is rather impressive. A recent example is the actual structural determination of a natural compound, breitfussin A. Several functional groups of the molecule were derived from classical spectroscopic data (a). Then, an AFM image (c) allowed observing the real structure of the molecule, placing each piece of the puzzle (a) in the correct spot. This established the previously unknown structure of the molecule (b).

Can we see real atoms and molecules?
Credit to M. Jaspars, J. Isaksson and coworkers (A Combined Atomic Force Microscopy and Computational Approach for the Structural Elucidation of Breitfussin A and B: Highly Modified Halogenated Dipeptides from Thuiaria breitfussi, doi: 10.1002/anie.201203960)

Taking real pictures of complex chemical reactions

On the reactivity side of things, much more recently, it was possible to directly image the course of a reaction called the Bergman cyclization. This is one of the most fascinating rearrangements in chemistry. The chemical transformation is directly induced in the metal surface in which the atomic microscopy procedure is carried out.

Can we actually see real chemical reactions?
Credit to L. Gross and coworkers (Reversible Bergman cyclization by atomic manipulation, doi: 10.1038/nchem.2438).

However, as stated at the end of the introduction, not every molecule or reaction can be a candidate for a STM study as these. Several conditions need to be met. One of them (which might have already called your attention) is that the analyzed compounds need to be near-planar. These techniques rely on depositing the molecules of the compound in a planar metal surface, so planar molecules are the ones that give more interpretable data.

The search for the “Holy Grail” of structural determination

To finish this short essay that does not make justice to the whole field of molecular imaging, a recent application of what is called micro-electron diffraction (MicroED) will be discussed. This brilliant application of electron diffraction, allows overcoming probably the biggest problem on classical X-ray diffraction methods: the requirement of crystalline material of the molecule which structure wants to be elucidated.

Credit to B. M. Stoltz, J. A. Rodriguez, H. M. Nelson, T. Gonen and coworkers (The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination, doi: 10.1021/acscentsci.8b00760).

This technique allows taking simple powder of any non-crystalline solid, without almost any sample preparation, and getting 3D structures of the powder nano-crystals in a matter of minutes, with extremely high resolutions. The structure of molecules with very high complexity, as thiostrepton, could be obtained unequivocally.

Credit to T. Gonen and coworkers (doi: 10.1021/acscentsci.8b00760).

Is this the future of chemistry?

Can we see real atoms and molecules at this point? I would say that we definitely can. All the results that have been described in this article were published only over the last decade. Atomic microscopy seems to be here to stay, and it might be one of the tools that finally allows chemists to stop relying in rudimentary techniques for the determination of molecular structures. Only time will tell.

Stay tuned for more posts about the future of chemistry, share, and post your thoughts in the comment section!

Filed Under: Chemistry Research Highlights, Featured Tagged With: inorganic chemistry, physical chemistry

Comments

  1. mahabet says

    June 21, 2019 at 6:07 pm

    Awesome article.

    Reply
  2. scott says

    November 1, 2023 at 7:18 am

    I’m confused still. Not a scientist but curious. Can we see an atom? Like we can see an object with our eyes but with the use of microscope? Not by inference but actually see the atom.

    Reply

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

RSS Feed Subscribe to our RSS Feed
Twitter Follow us on Twitter

why do chemicals react

Why Do Chemicals React? Kinetics and Thermodynamics

April 10, 2021 By C. Hall 4 Comments

Chemistry is the science of change. But why do chemical reactions take place? Why do chemicals react with each other? The answer is in thermodynamics and kinetics. These … [Read More...]

How to Learn Chemistry

How To Learn Chemistry at Any Level

January 31, 2020 By C. Hall 2 Comments

Have you ever wanted to learn chemistry, but just didn’t know how to go about doing it? Taking college courses and you don't know how to find resources? There is so much to … [Read More...]

tlc guide

Thin Layer Chromatography: A Complete Guide to TLC

January 2, 2020 By C. Hall 31 Comments

If there is one technique or experiment that every chemist, or student learning chemistry should know, it is Thin Layer Chromatography (or TLC for short). If you want to … [Read More...]

best chemistry set for kids

The Best Chemistry Set for Kids (and Adults!)

January 1, 2020 By Emily McPeek 1 Comment

There’s no better way to learn about chemistry than with fun, hands-on experiments and science projects. Teachers and parents, read on to learn the best chemistry set for kids … [Read More...]

best chemistry textbook

The Best General Chemistry Textbook

August 23, 2019 By C. Hall 1 Comment

The new academic year has already begun in many parts of the world, but it’s never too early to start planning for next year. Time to get your hands into the best general … [Read More...]

best inorganic chemistry textbook

The Best Inorganic Chemistry Textbooks

August 5, 2019 By C. Hall 14 Comments

Inorganic chemistry is one of the cornerstones of the central science. For many is the most fun, but it covers an extremely wide range of topics. For this reason, you need to … [Read More...]

top 100 chemistry facts

100 Fun Chemistry Facts (With Awesome Explanations!)

July 18, 2019 By C. Hall 9 Comments

You probably agree with me on the first fact: chemistry is fascinating. There are plenty of unanswered mysteries within this science, but there are also many interesting and … [Read More...]

Cracking the AP Chemistry Exam

The Best AP Chemistry Review Book

July 5, 2019 By C. Hall 2 Comments

Summer vacation is a time to relax and unwind, but students enrolled in advanced placement (or AP for short) classes for the coming school year are already planning for the … [Read More...]

Clayden Organic Chemistry Textbook

The Best Organic Chemistry Textbook [A Definitive Guide]

June 27, 2019 By C. Hall 28 Comments

Let's face it, organic chemistry can seem difficult to learn. Especially from a beginner's point of view. For exactly that reason we have put together the definitive guide for … [Read More...]

Home Chemistry Lab Experiments

Chemistry Experiments at Home: Setting Up a Home Lab

June 22, 2019 By C. Hall Leave a Comment

Not everybody has access to a professional chemistry lab, so setting up a home chemistry lab is your best bet if you want to do chemistry experiments at home. Chemistry is … [Read More...]

Can we see atoms and molecules?

Can We See Real Atoms and Molecules? Electron Microscopy at a Glance

June 17, 2019 By C. Hall 2 Comments

A universal challenge that has been keeping chemists busy ever since the modern concepts of “atom” and “molecules” were conceived, is how to actually characterize molecular … [Read More...]

TLC Lab Hacks

Lab Hacks – How to Increase your Productivity in the Lab

November 19, 2016 By C. Hall 4 Comments

I have been working in a chemistry laboratory for some years and still every once in a while I learn new amazing tricks or lab hacks that leave me open-mouthed. Also, it has … [Read More...]

LSD

LSD Synthesis and Discovery: What You May Not Know About It

December 14, 2014 By C. Hall 28 Comments

Disclaimer: This article is purely informative, and it does not contain information about how to actually carry out experimental procedures for the synthesis of LSD or any … [Read More...]

More Posts from this Category

Categories

  • Chemistry Experiments
  • Chemistry Lab
  • Chemistry Research Highlights
  • Education and Concepts
  • Everyday Life Chemistry
  • Featured
  • General Science
  • Tools for Chemists
  • Uncategorized

Chemistry Hall

Privacy Policy - Terms of Service - Disclaimer

Contact

Contact Us - Contribute - Twitter

AFFILIATE DISCLAIMER

Chemistry Hall is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon websites, including, but not limited to amazon.com

Copyright © 2024 Chemistry Hall · All Rights Reserved · Log in
Copyright by Chemistry Hall or by third-party sources, where indicated. All rights controlled by their respective owners.
Views expressed here do not necessarily reflect those of Chemistry Hall, all of its staff, contributors or partners.
Content on this website is for informational purposes only.

This website uses cookies to improve your experience. We'll assume you're ok with this, but you can opt-out if you wish. Cookie settingsACCEPT
Privacy & Cookies Policy

Privacy Overview

This website uses cookies to improve your experience while you navigate through the website. Out of these cookies, the cookies that are categorized as necessary are stored on your browser as they are as essential for the working of basic functionalities of the website. We also use third-party cookies that help us analyze and understand how you use this website. These cookies will be stored in your browser only with your consent. You also have the option to opt-out of these cookies. But opting out of some of these cookies may have an effect on your browsing experience.
Necessary
Always Enabled
Necessary cookies are absolutely essential for the website to function properly. This category only includes cookies that ensures basic functionalities and security features of the website. These cookies do not store any personal information.
SAVE & ACCEPT