The stabilization potential of a standing molecule

Knol, Marvin; Arefi, Hadi H.; Corken, Daniel; Gardner, J. W.; Tautz, F. Stefan; Maurer, Reinhard J.; Wagner, Christian

doi:10.1126/sciadv.abj9751

Cited by 5 publications

(23 citation statements)

References 39 publications

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“…The weak mechanical coupling between s-PTCDA and the metal, on the other hand, allows the oscillation of the entire molecule with a remarkably low GHz frequency. 17 …”

Section: Results and Discussionmentioning

confidence: 99%

“…Second, a molecule attachment with two Ag–O bonds involving two neighboring O carb atoms, similar to the known vertical conformation of the molecule on the adatom pedestal on Ag(111), which features two Ag–O carb bonds. 11 , 17 ( Figure 1 , left).…”

Section: Results and Discussionmentioning

confidence: 99%

“…Typically, metastable molecular structures have to be fabricated and investigated at cryogenic temperatures of 5 K to suppress instability from thermal fluctuations. 17 If they could, however, reliably withstand higher temperatures, strong electric fields and other effects such as charging, the application range of molecular devices would greatly increase. Here, we demonstrate how computational nanostructure design using density functional theory (DFT) calculations allows us to discover and systematically improve suitable metastable molecular devices.…”

Section: Introductionmentioning

confidence: 99%

“…The standing PTCDA on Ag(111) is characterized by a competition between stabilizing covalent and destabilizing vdW interactions that causes a shallow potential energy minimum and thermally induced collapse between 10 and 14 K. 17 This insight is our starting point for a deeper and more detailed study culminating in the development of practically applicable design rules. To identify global trends, we examine a broad set of possible configurations of standing PTCDA (s-PTCDA), including cases in which PTCDA is attached to the SPM tip as is required for SQDM.…”

Section: Introductionmentioning

confidence: 99%

“…Because the potential energy surface of s -PTCDA is the consequence of a competition between covalent and vdW interactions, 17 the design criteria for enhanced stability can be formulated with regard to these two interaction types. We have organized the paper accordingly: After summarizing the computational methods, discussing the experimentally observed properties of s-PTCDA and defining the set of SPM tip structures used in our analysis, we first analyze the chemical bonding of s-PTCDA to the Ag structures and subsequently the influence of the vdW interactions on stability.…”

Section: Introductionmentioning

confidence: 99%

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Design Principles for Metastable Standing Molecules

et al. 2022

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Molecular nanofabrication with a scanning probe microscope (SPM) is a promising route toward the prototyping of metastable functional molecular structures and devices which do not form spontaneously. The aspect of mechanical stability is crucial for such structures, especially if they extend into the third dimension vertical to the surface. A prominent example is freestanding molecules fabricated on a metal which can function as field emitters or electric field sensors. Improving the stability of such molecular configurations is an optimization task involving many degrees of freedom and therefore best tackled by computational nanostructure design. Here, we use density functional theory to study 3,4,9,10-perylene-tetracarboxylic dianhydride (PTCDA) standing on the Ag(111) surface as well as on the tip of a scanning probe microscope. We cast our results into a simple set of design principles for such metastable structures, the validity of which we subsequently demonstrate in two computational case studies. Our work proves the capabilities of computational nanostructure design in the field of metastable molecular structures and offers the intuition needed to fabricate new devices without tedious trial and error.

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“…The weak mechanical coupling between s-PTCDA and the metal, on the other hand, allows the oscillation of the entire molecule with a remarkably low GHz frequency. 17 …”

Section: Results and Discussionmentioning

confidence: 99%

Section: Results and Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Design Principles for Metastable Standing Molecules

et al. 2022

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Concept for the Real-Time Monitoring of Molecular Configurations during Manipulation with a Scanning Probe Microscope

et al. 2023

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A bold vision in nanofabrication is the assembly of functional molecular structures using a scanning probe microscope (SPM). This approach requires continuous monitoring of the molecular configuration during manipulation. Until now, this has been impossible because the SPM tip cannot simultaneously act as an actuator and an imaging probe. Here, we implement configuration monitoring using experimental data other than images collected during the manipulation process. We model the manipulation as a partially observable Markov decision process (POMDP) and approximate the actual configuration in real time using a particle filter. To achieve this, the models underlying the POMDP are precomputed and organized in the form of a finite-state automaton, allowing the use of complex atomistic simulations. We exemplify the configuration monitoring process and reveal structural motifs behind measured force gradients. The proposed methodology marks an important step toward the piece-by-piece creation of supramolecular structures in a robotic and possibly automated manner.

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Efficient interatomic descriptors for accurate machine learning force fields of extended molecules

et al. 2023

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Machine learning force fields (MLFFs) are gradually evolving towards enabling molecular dynamics simulations of molecules and materials with ab initio accuracy but at a small fraction of the computational cost. However, several challenges remain to be addressed to enable predictive MLFF simulations of realistic molecules, including: (1) developing efficient descriptors for non-local interatomic interactions, which are essential to capture long-range molecular fluctuations, and (2) reducing the dimensionality of the descriptors to enhance the applicability and interpretability of MLFFs. Here we propose an automatized approach to substantially reduce the number of interatomic descriptor features while preserving the accuracy and increasing the efficiency of MLFFs. To simultaneously address the two stated challenges, we illustrate our approach on the example of the global GDML MLFF. We found that non-local features (atoms separated by as far as 15 Å in studied systems) are crucial to retain the overall accuracy of the MLFF for peptides, DNA base pairs, fatty acids, and supramolecular complexes. Interestingly, the number of required non-local features in the reduced descriptors becomes comparable to the number of local interatomic features (those below 5 Å). These results pave the way to constructing global molecular MLFFs whose cost increases linearly, instead of quadratically, with system size.

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The stabilization potential of a standing molecule

Abstract: Competing chemical and van der Waals interactions keep a molecule in the vertical until it is knocked over by heat.

Cited by 5 publications

References 39 publications

Design Principles for Metastable Standing Molecules

Design Principles for Metastable Standing Molecules

Concept for the Real-Time Monitoring of Molecular Configurations during Manipulation with a Scanning Probe Microscope

Efficient interatomic descriptors for accurate machine learning force fields of extended molecules

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