Discrimination of Bond Order in Organic Molecules Using Noncontact Atomic Force Microscopy

Abstract

Noncontact atomic force microscopy (nc-AFM) with a CO-functionalized tip can image submolecular structures through high-resolution images with the possibility of discriminating bond order. We employ real-space pseudopotential calculations to simulate nc-AFM images of molecules containing double (dibenzo­(cd,n)­naphtho­(3,2,1,8-pqra)­perylene (DBNP), hexabenzo­(bc,ef,hi,kl,no,qr)­coronene (HBC)) and triple (1,2-bis­[2-(2-ethynylphenyl)­ethynyl]-benzene (BEEB), 6-phenylhexa-1,3,5-triynylbenzene (PHTB)) bonds. We find (1) triple bonds can be unambiguously distinguished from other interatomic interactions based on a characteristic image and (2) the degree of double bond character can be directly determined from the image. We propose that large lateral forces acting on the tip may induce specific image distortions in the cases of DBNP and BEEB.

Adaptive semi-empirical model for non-contact atomic force microscopy

“…[1] The submolecular resolution of organic molecules was achieved by using CO-functionalized tip and qPlus technique. [2,3] The high performance of topography imaging enables its application in atomic recognition, [4,5] surface manipulation, [6,7] bond order recognition, [8][9][10] self-assembly, [11] and tracing reactions on surfaces. [12] The terminating CO molecule is chemically inert, which reduces the manipulation or bonding with the sample molecule.…”

Hydrogen bonded trimesic acid networks on Cu(111) reveal how basic chemical properties are imprinted in HR-AFM images

“…It uses the tip and sample charge densities and the sample electrostatic potential obtained from density functional theory (DFT) calculations as input. Then just two fitting parameters are used to reproduce tip-sample forces retaining DFT accuracy, similarly to other purely first-principles methods [34,35]. The resulting model is able to efficiently compute HR-AFM images, enabling extensive exploration of atomic scale structure and interpretation of the measured images.…”

Atomic Fingerprinting of Heteroatoms Using Noncontact Atomic Force Microscopy

“…[1] Since then, extending nc-AFM to characterize molecular structures, specific chemical bonds and atomic species remains an ongoing challenge for researchers. [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.…”