Browsing by Subject "Real-space pseudopotential density functional theory calculations"

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Seeing molecules : real-space simulations of noncontact atomic force microscopy
(2021-12-07) Fan, Dingxin; Chelikowsky, James R.; Hwang, Gyeong S.; Korgel, Brian A.; Henkelman, Graeme A.
Noncontact atomic force microscopy (nc-AFM) allows researchers to image the chemical structure of single molecules. In 2009, an experimental group obtained atomic resolution nc-AFM images of pentacene by using a carbon monoxide (CO) functionalized tip. This inspired a wide range of applications, including but not limited to directly characterizing molecular structures and atomic level manipulations. However, interpreting nc-AFM images remains a challenge. We employ a real-space pseudopotential constructed within density functional theory code, PARSEC, to simulate nc-AFM images and compute interatomic forces. We first study the effect of using different probe tips (CO, H₂, N₂, Br, and CH₂O). We find the selected tips provide accurate simulations except for the Br atom tip. In addition, we find contrast inversion with CO and N₂ tips at small tip heights and image distortion with CH₂O tips. Second, we simulate nc-AFM images of molecules containing double and triple bonds. We find triple bonds can be unambiguously distinguished based on a characteristic image, and the degree of double bond character can be determined from the image. Third, we study several nonplanar organic molecules on a Cu(111) substrate. This substrate results in significant distortions in molecular structures. Including these distortions in simulated nc-AFM imaging notably improves the agreement between the simulated and measured images. Next, we simulate the nc-AFM images of several heteroatom-containing (S, I, and N) molecules. We find that S and I atoms can be easily identified from C based on their unique features. For N atoms, we propose a use of tip functionalization to effectively discriminate them from C atoms. Finally, in joint experimental-theoretical work, we study the bond-breaking process of a single dative bond between CO and ferrous phthalocyanine. The bond is ruptured via mechanical forces applied by AFM tips. This process is 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