Organic structure determination using atomic-resolution scanning probe microscopy

Abstract

Nature offers a huge and only partially explored variety of small molecules with potential pharmaceutical applications. Commonly used characterization methods for natural products include spectroscopic techniques such as nuclear magnetic resonance spectroscopy and mass spectrometry. In some cases, however, these techniques do not succeed in the unambiguous determination of the chemical structure of unknown compounds. To validate the usefulness of scanning probe microscopy as an adjunct to the other tools available for organic structure analysis, we used the natural product cephalandole A, which had previously been misassigned, and later corrected. Our results, corroborated by density functional theory, demonstrate that direct imaging of an organic compound with atomic-resolution force microscopy facilitates the accurate determination of its chemical structure. We anticipate that our method may be developed further towards molecular imaging with chemical sensitivity, and will become generally useful in solving certain classes of natural product structures.

Single cycle and transient force measurements in dynamic atomic force microscopy

“…The eigenfunctions describe the cantilever motion as a coordinate system as is seen in (13). Substituting into (12) …”

“…The instrument is currently employed by researchers in elds ranging from biology 8,9 to semiconductor theory and devices 10 and in hybrid systems. 11 With the AFM one can routinely image single nanostructures, 12,13 map heterogeneous compositional [14][15][16][17][18] and/or nanomechanical [19][20][21] properties and/ or processes, 22,23 study molecular interactions 24,25 and larger biological systems, 26,27 identify single atoms, 28 molecules 29,30 and/or chemical composition 31 and structures, 32 study the friction induced by single atomic motion 33 and, more recently, even discriminate bond order and symmetry. 34,35 The fundamental principle however is relatively straightforward; atoms, nanostructures and surfaces are probed with high precision on the lateral and vertical axes via a nanoscopic tip mounted on a microstructure, typically a micro-cantilever, by monitoring its deection.…”

Communication: Substrate induced dehydrogenation: Transformation of octa-ethyl-porphyrin into tetra-benzo-porphyrin

“…1 Recently, it was shown that the Cu(111) surface can produce almost perfect layers of graphene by the dehydrogenation of hydrocarbon precursor molecules. 2,3 Scanning tunneling microscopy 4 (STM) is a powerful tool to study the adsorption geometry of different molecules on a conducting surface, 5,6 diffusion processes of single molecules 7 or atoms 8 and even to manipulate single molecules with the STM tip. 9,10 Porphyrins and phthalocyanines are the most studied organic molecules in the monolayer and submonolayer regime.…”

Probing Charges on the Atomic Scale by Means of Atomic Force Microscopy

“…Since then, this technique has been widely applied [2][3][4][5][6][7][8][9][10]. AFM-based Kelvin probe force spectroscopy (KPFS) [11] provides the local contact potential difference (LCPD) between tip and sample [12][13][14].…”