Imaging of chemical fingerprints of molecules (with video)

October 30, 2021

(Nanowerk News) Flip through any chemistry textbook and you will see drawings of the chemical structure of molecules, where individual atoms are arranged in space and how they are chemically related to each other. For decades, chemists could only indirectly determine chemical structures based on the response generated when samples interacted with x-rays or particles of light.

For the particular case of molecules on a surface, atomic force microscopy (AFM), invented in the 1980s, provided direct images of the molecules and the patterns they form when they are assembled into two-dimensional (2D) networks.

In 2009, significant advancements in high-resolution AFM (HR-AFM) enabled chemists for the first time to directly image the chemical structure of a single molecule in enough detail to distinguish between different types of binding to the inside the molecule.

AFM “senses” the forces between a sharp probe tip and surface atoms or molecules. The tip scans a sample surface, left to right and top to bottom, to a height of less than one billionth of a meter (nanometer), recording the force at each position. A computer combines these measurements to generate a force map, resulting in a snapshot of the surface. Present in laboratories around the world, AFMs are state-of-the-art instruments, with various applications in science and engineering.

An illustration of a high resolution atomic force microscope probing the chemical properties of hydrogen bonded trimesic acid (TMA) networks (overlaid on a teal blue circle) on a copper surface” border =”0″ align =”middle”/> An illustration of a high resolution atomic force microscope probing the chemical properties of hydrogen bonded trimesic acid (TMA) networks (overlaid on a teal blue circle) on a copper surface. Legend: copper atoms on the apex of the metal tip (orange), carbon atoms (black), oxygen atoms (red) and hydrogen atoms (white). The single carbon monoxide (CO) molecule at the end of the tip apex, with the carbon attached to the copper, is bent slightly in response to the repulsive forces of the nearby oxygen of the TMA molecule.

Only a few HR-AFMs exist in the United States. One is located at the Center for Functional Nanomaterials (CFN), a user facility in the US Department of Energy (DOE) Science Office at the Brookhaven National Laboratory. For several years, physicist Percy Zahl of the CFN Interface Science and Catalysis Group has been upgrading and customizing CFN HR-AFM hardware and software, making it easier to operate and acquire images. As highly specialized instruments, HR-AFMs require expertise to be used. They operate at a very low temperature (just above that needed to liquefy helium). Additionally, HR imaging depends on capturing a single carbon monoxide molecule at the tip end.

As difficult as it may be to prepare and use the instrument for experiments, seeing what molecules look like is just the start. Then the images must be analyzed and interpreted. In other words, how do the characteristics of the image correlate with the chemical properties of the molecules?

Working with theorists from CFN and universities in Spain and Switzerland, Zahl posed this same question for hydrogen bonded networks of trimesic acid molecules (TMAs) on a copper surface. Zahl began to imagine these porous networks, made up of carbon, hydrogen and oxygen, a few years ago. He was interested in their potential to confine atoms or molecules capable of harboring electron spin states for applications in quantum information science (QIS). However, with experience and basic simulations alone, he could not explain their basic structure in detail.

“I suspected that the strong polarity (charge regions) of the TMA molecules was causing what I was seeing in the AFM images”, Zahl said. “But I needed more precise calculations to be sure.”

In AFM, the total force between the tip of the probe and the molecule is measured. However, for an accurate match between experiment and simulation, each individual force in play must be taken into account. Basic models can simulate short-range forces for simple nonpolar molecules, where electric charges are evenly distributed. But for chemically rich structures found in polar molecules like trimesic acid, electrostatic forces (arising from the distribution of electronic charges within the molecule) and van der Waals forces (attraction between molecules) must also be taken into account. To simulate these forces, scientists need the exact molecular geometry showing how atoms are positioned in three dimensions and the exact charge distributions within molecules.

Using DFT calculations at the Swiss National Supercomputing Center, Aliaksandr Yakutovich structurally relaxed the ring with six TMA molecules on a copper plate containing 1,800 copper atoms. In structural relaxation, a basic geometric or structural model is optimized to find the configuration of atoms with the lowest possible energy.

Using DFT calculations at the Swiss National Supercomputing Center, Aliaksandr Yakutovich structurally relaxed the ring with six TMA molecules on a copper plate containing 1,800 copper atoms. In structural relaxation, a basic geometric or structural model is optimized to find the configuration of atoms with the lowest possible energy.

In this study (Nanoscale, “Hydrogen-bonded trimesic acid networks on Cu (111) reveal how basic chemical properties are imprinted in HR-AFM images”), Zahl analyzed the nature of self-assembly of TMA molecules in honeycomb lattice structures on a clean copper crystal. Zahl initially imaged the large-scale structures with a scanning tunneling microscope (STM). This microscope scans a metal tip across a surface while applying electrical voltage between them. To identify how the lattice structure aligned with the substrate, CFN materials scientist Jurek Sadowski bombarded the sample with low-energy electrons and analyzed the pattern of the diffracted electrons. Finally, Zahl performed HR-AFM, which is sensitive to the height of surface characteristics at a submolecular scale.

“With STM, we can see the networks of TMA molecules but cannot easily see the orientation of copper at the same time”, Zahl said. “Low energy electron diffraction can tell us how copper and TMA molecules are oriented relative to each other. AFM allows us to see the detailed chemical structure of molecules. But to understand these details, we need to model the system and figure out exactly where the atoms of TMA molecules are on the copper. ”

For this modeling, the team used density functional theory (DFT) to calculate the most energetically favorable arrangements of TMA molecules on copper. The idea behind DFT is that the total energy of a system is a function of its electron density, or the probability of finding an electron at a particular location around an atom. More electronegative atoms (like oxygen) tend to move electrons away from less electronegative atoms (like carbon and hydrogen) to which they are bonded, like a magnet. Such electrostatic interactions are important for understanding chemical reactivity.

Mark Hybertsen, head of the CFN theory and calculation group, performed the first DFT calculations for an individual TMA molecule and two TMA molecules linked by hydrogen bonds (a dimer). Aliaksandr Yakutovich from [email protected] The Swiss Federal Laboratories for Materials Science and Technology (Empa) laboratory then performed DFT calculations of a larger TMA network consisting of a complete ring of six TMA molecules.

These calculations showed how the inner carbon ring of molecules is distorted from a hexagonal to a triangular shape in the AFM image due to strong polarizations caused by three carboxyl groups (COOH). In addition, all unbound oxygen atoms are pulled a bit towards the surface copper atoms, where more electrons reside. They also calculated the strength of the two hydrogen bonds forming between two TMA molecules. These calculations showed that each bond was about twice as strong as a typical single hydrogen bond.

“By connecting atomic scale models to AFM imaging experiments, we can understand the fundamental chemical characteristics of images”, Hybertsen said.

“This ability can help us identify critical properties of molecules, including reactivity and stability, in complex mixtures (such as petroleum) based on HR-AFM images.”, Zahl added.

To close the loop between modeling and experimentation, collaborators in Spain entered the DFT results into a computer code they developed to generate simulated AFM images. These images corresponded perfectly to the experimental images.

“These precise simulations unveil the subtle interplay of the original molecular structure, the deformations induced by the interaction with the substrate, and the intrinsic chemical properties of the molecule that determine the complex and striking contrast we observe in AFM images.”, said Ruben Perez. of the Universidad Autónoma de Madrid.

From their combined approach, the team also showed that the line-like features appearing between molecules in AFM images of TMA (and other molecules) are not fingerprints of hydrogen bonds. Rather, they are “artifacts” from the curvature of the AFM probe molecule.

“Even though the hydrogen bond is very strong for TMA molecules, the hydrogen bonds are invisible in the experiment and simulation”, Zahl said. “What is visible is the evidence of a strong withdrawal of electrons by the carboxyl groups.”

Next, Zahl plans to continue to study this model system for network self-assembly to explore its potential for QIS applications. It will use a new STM / AFM microscope with additional spectroscopic capabilities, such as those for testing samples with a magnetic field and applying radiofrequency fields to the samples and characterizing their response. These capabilities will allow Zahl to measure the quantum spin states of custom molecules arranged in a perfect lattice to form potential quantum bits.

About Roberto Frank

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