Simulating noncontact atomic force microscopy images

Chelikowsky, James R.; Fan, Dingxin; Lee, Alex J.; Sakai, Yuki

doi:10.1103/physrevmaterials.3.110302

Cited by 11 publications

(11 citation statements)

References 112 publications

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Nonetheless, a systematic way to discriminate atomic species is lacking. Here, we extend previous work [12] for the identification of heteroatoms.We employ ab initio real-space pseudopotentials to accurately simulate nc-AFM images of four molecules: DBT, ITP, ACR, and FePc, which contain the heteroatoms S, I, and N. We find S and I atoms can be easily identified from C, which is not surprising given their different atomic structure. We also propose a new method, scanning with a chemically inert tip followed by a chemically active tip, to effectively determine the structures of N containing molecules.

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supporting

confidence: 77%

“…Nonetheless, a systematic way to discriminate atomic species is lacking. Here, we extend previous work [12] for the identification of heteroatoms.…”

supporting

confidence: 77%

“…[2] Numerous studies [3][4][5][6][7][8] have demonstrated that nc-AFM has the capability to discriminate carbon-carbon bond order, bond length, and molecular adsorption geometry on various substrates. With respect to the identification of atomic species, previous work [9][10][11][12] has shown the possibility of discriminating atom species under certain conditions. For example, Group IV elements such as Si, Sn, and Pb atoms may be readily discriminated against first row elements like C, based on their relative size and atomic structure.…”

Section: Introductionmentioning

confidence: 99%

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Atomic Fingerprinting of Heteroatoms Using Noncontact Atomic Force Microscopy

Fan

Chelikowsky

2021

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…”

supporting

confidence: 77%

“…Nonetheless, a systematic way to discriminate atomic species is lacking. Here, we extend previous work [12] for the identification of heteroatoms.…”

supporting

confidence: 77%

Section: Introductionmentioning

confidence: 99%

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Atomic Fingerprinting of Heteroatoms Using Noncontact Atomic Force Microscopy

Fan

Chelikowsky

2021

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“…Here, we report the realization of a system containing an individual CO and FePc and subsequent AFM studies of the bond rupture process under vacuum conditions, so as to minimize the effects of environmental perturbations. Together with real-space pseudopotential density functional theory (DFT) calculations [22][23][24] modeling the events, this work advances our understanding of the origins of the measured forces in dative bond breaking.…”

Section: Introductionmentioning

confidence: 95%

Breaking a Dative Bond with Mechanical Forces

Chen

Fan

Zhang

et al. 2021

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Bond breaking and forming is essential in every chemical reaction. Here, we report a single dative bond breaking process revealing an unprecedented level of detail using noncontact atomic force microscopy. The dative bond between carbon monoxide and ferrous phthalocyanine was ruptured via mechanical forces applied by atomic force microscope tips; the process was quantitatively measured and characterized both experimentally and via first principles quantum mechanics modeling. Our results show that the bond can be ruptured either by applying an attractive force of ~150 pN (pulling) or by a repulsive force of ~220 pN (pushing), accompanied by changes of the spin state of the system. Our combined experimental and computational studies provide a deeper understanding of the chemical bond breaking process.

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“…Dative bonds are commonly found in transition metal complexes and play vital roles in catalysis, organometallic chemistry, and biochemistry. Here, we focus on understanding the breaking of a single chemical bond between a CO molecule and a ferrous phthalocyanine (FePc) complex using AFM together with real-space pseudopotential density functional theory (DFT) calculations [20][21][22] . Our results reveal detailed mechanisms of bond breaking by both repulsive and attractive forces.…”

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confidence: 99%

Breaking a dative bond with mechanical forces

et al. 2021

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Bond breaking and forming are essential components of chemical reactions. Recently, the structure and formation of covalent bonds in single molecules have been studied by non-contact atomic force microscopy (AFM). Here, we report the details of a single dative bond breaking process using non-contact AFM. The dative bond between carbon monoxide and ferrous phthalocyanine was ruptured via mechanical forces applied by atomic force microscope tips; the process was quantitatively measured and characterized both experimentally and via quantum-based simulations. Our results show that the bond can be ruptured either by applying an attractive force of ~150 pN or by a repulsive force of ~220 pN with a significant contribution of shear forces, accompanied by changes of the spin state of the system. Our combined experimental and computational studies provide a deeper understanding of the chemical bond breaking process.

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Simulating noncontact atomic force microscopy images

Cited by 11 publications

References 112 publications

Atomic Fingerprinting of Heteroatoms Using Noncontact Atomic Force Microscopy

Atomic Fingerprinting of Heteroatoms Using Noncontact Atomic Force Microscopy

Breaking a Dative Bond with Mechanical Forces

Breaking a dative bond with mechanical forces

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