Illustration of the chemical fingerprints of molecules



Newswise – Flip through any chemistry textbook and you’ll see drawings of the chemical structure of molecules – where individual atoms are arranged in space and how they are chemically linked. For decades, chemists could only indirectly determine chemical structure from the reaction produced when samples interacted with X-rays or light particles. For the special case of molecules on a surface, atomic force microscopy (AFM), invented in the 1980s, provided direct images of molecules and the patterns that they form when they are assembled into two-dimensional (2D) arrangements. In 2009, significant advances in high resolution AFM (HR-AFM) made it possible for chemists, for the first time, to directly map the chemical structure of a single molecule with sufficient detail to distinguish different types of bonds within the molecule.

AFM “feels” the forces between a sharp probe tip and surface atoms or molecules. The tip scans a sample surface from left to right and top to bottom at a height of less than a billionth of a meter (Nanometer), Record the force at each position. A computer combines these measurements to create a force map that results in a snapshot of the surface. AFMs can be found in laboratories around the world and are workhorses with a wide range of applications in science and technology.

There are few HR AFMs in the US. One is on Center for Functional Nanomaterials (CFN) – a US Department of Energy (DOE) scientific user facility at Brookhaven National Laboratory. The physicist Percy Zahl from the CFN Working group interface science and catalysis has updated and adapted the CFN HR-AFM hardware and software, which makes it easier to operate and take pictures. As highly specialized tools, HR AFMs require specialist knowledge. They work at very low temperatures (just above that required to liquefy helium). In addition, HR imaging depends on capturing a single carbon monoxide molecule at the end of the tip.

As challenging as preparing and operating the instrument for experiments may be, seeing what molecules look like is just the beginning. Next, the images need to be analyzed and interpreted. In other words, how do image features correlate with the chemical properties of molecules?

Together with theorists from the CFN and universities in Spain and Switzerland, Zahl asked exactly this question for hydrogen-bonded networks of trimesic acid (TMA) molecules on a copper surface. number started Imaging of these porous networks – made up of carbon, hydrogen, and oxygen – a few years ago. He was interested in their potential to trap atoms or molecules capable of harboring electron spin states for quantum information science (QIS) applications. With experiments and simple simulations alone, however, he could not explain their basic structure in detail.

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

With AFM, the total force between the probe tip and the molecule is measured. For an exact correspondence between experiment and simulation, however, each individual acting force must be taken into account. Basic models can simulate short-range forces for simple non-polar molecules in which electrical charges are evenly distributed. But for chemically rich structures, such as those found in polar molecules like trimesic acid, electrostatic forces (which come from the electronic charge distribution in the molecule) and van der Waals forces (attraction between molecules) must also be considered. In order to simulate these forces, scientists need the exact molecular geometry that shows the position of the atoms in all three dimensions and the exact charge distribution within the molecules.

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

In this study, Zahl analyzed the nature of the self-assembly of TMA molecules into honeycomb network structures on a clean copper crystal. Zahl first mapped the structures over a large area with a scanning tunneling microscope (STM). This microscope scans a metallic tip over a surface while an electrical voltage is applied between them. To find out how the network structure aligns with the substrate, CFN materials scientists studied Jurek Sadowski bombarded the sample with low-energy electrons and analyzed the pattern of the diffracted electrons. Finally, Zahl performed HR-AFM, which responds to the level of surface features on a submolecular scale.

“With STM, we can see the networks of TMA molecules, but not the orientation of copper at the same time,” says Zahl. “Low-energy electron diffraction can tell us how the copper and TMA molecules are oriented relative to one another. AFM allows us to see the detailed chemical structure of the molecules. But to understand these details, we have to model the system and determine exactly where the atoms of the TMA molecules are located on copper. “

For this modeling, the team used density functional theory (DFT) to calculate the energetically most 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 given point around an atom. More electronegative atoms (like oxygen) tend to pull electrons away from less electronegative atoms (like carbon and hydrogen) to which they are attached, much like a magnet. Such electrostatic interactions are important for understanding chemical reactivity.

Mark Hybertsen, Leader of the CFN Theory and calculation group, performed initial DFT calculations for a single TMA molecule and two TMA molecules (a dimer) linked by hydrogen bonds. Aliaksandr Yakutovich from the [email protected] laboratory the Eidgenössische Materialprüfungs- und Forschungsanstalt (Empa) then carried out DFT calculations on a larger TMA network, which consisted of a complete ring of six TMA molecules.

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

“By combining models on an atomic scale with the AFM imaging experiments, we can understand basic chemical features in the images,” said Hybertsen.

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

To close the loop between modeling and experiment, employees in Spain entered the DFT results into computer code they developed to generate simulated AFM images. These images matched the experimental ones perfectly.

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

Using their combined approach, the team also showed that line-like features that appear between molecules in AFM images of TMA (and other molecules) are not fingerprints of hydrogen bonds. Rather, it is a matter of “artifacts” caused by the bending of the AFM probe molecule.

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

Next, Zahl plans to further investigate this model system for network self-construction in order to explore its potential for QIS applications. He will be using a new STM / AFM microscope with additional spectroscopic skills, e.g. B. for controlling samples with a magnetic field and applying radio frequency fields to samples and characterizing their response. These capabilities will allow Numbers to measure the quantum spin states of custom molecules arranged in a perfect array to form potential quantum bits.

This research was supported by the US Department of Energy’s Office of Science (DOE). All imaging experiments were done at CFN. carried out Device for proximal probes. The first calculations at the CFN were carried out on Scientific data and computing center of Computational Science Initiative in the Brookhaven laboratory. The Swiss National Supercomputing Center and the Spanish Supercomputing Network (MareNostrum at the Barcelona Supercomputing Center) supported the larger calculations. The other cooperating institutions are the E´cole Polytechnique Fe´de´rale de Lausanne; Quasar Science Resources, SL; and Universidad Pablo de Olavide. Further funding was made available by the Spanish MINECO; Comunidad de Madrid; Quasar Science Resources, SL; and the Spanish Ministerio de Ciencia e Innovación.

Brookhaven National Laboratory is supported by the US Department of Energy’s Office of Science. The Office of Science is the largest single funder of basic research in the physical sciences in the United States, working to address some of the most pressing challenges of our time. For more information, visit

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