A Combined Atomic Force Microscopy and Computational Approach for the Structural Elucidation of Breitfussin A and B: Highly Modified Halogenated Dipeptides from <i>Thuiaria breitfussi</i>

Hanssen, Kine Østnes; Schuler, Bruno; Williams, Antony J.; Demissie, Taye B.; Hansen, Espen; Andersen, Jeanette H.; Svenson, Johan; Blinov, Kirill A.; Repiský, Michal; Mohn, Fabian; Meyer, Gerhard; Svendsen, John-Sigurd; Ruud, Kenneth; Elyashberg, Mikhail E.; Groß, Leo; Jaspars, Marcel; Isaksson, Johan

doi:10.1002/ange.201203960

Cited by 25 publications

(31 citation statements)

References 22 publications

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“…Nevertheless, the inexpensive two‐component ZORA (Zeroth Order Regular Approximation) method has been implemented within DFT schemes, whereas four‐component methods are relatively less developed and have a huge computational cost. Ironically, it seems that the ZORA method has not yet found widespread use for typical organic molecules, whereas the characterization of breitfussins A and B has been achieved also thanks to the calculation of their conformational space and 13 C shifts with very expensive four‐component relativistics …”

Section: Outlook: Heavy Atomsmentioning

confidence: 99%

Addressing the stereochemistry of complex organic molecules by density functional theory‐NMR

Bagno

Saielli

2014

WIREs Comput Mol Sci

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Determining the stereochemistry of organic molecules is a long-standing problem, with implications for stereoselective reactions, catalysis, and the structure of natural products. NMR spectroscopy is widely employed to this purpose; however, the interpretation of results is often entrusted to empirical methods or expert systems. Quantum chemical calculations, generally based on density functional theory, provide a reliable framework to predict the relevant parameters (chemical shifts and coupling constants, generally involving 1 H and 13 C) of diastereoisomers with useful accuracy. While the approach virtually spans all molecules of interest in organic chemistry, including those that contain heavy atoms, the analysis of results still poses significant challenges.

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Section: Outlook: Heavy Atomsmentioning

confidence: 99%

Addressing the stereochemistry of complex organic molecules by density functional theory‐NMR

Bagno

Saielli

2014

WIREs Comput Mol Sci

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“…Still, changes in the total electron density and electrostatic forces on different atoms are expected to contribute to the image contrast. 18 , 37 , 45 − 48 Consequently, passivated tips enabled elemental contrast also on molecular systems, in both Δ f 29 , 49 − 52 and LCPD. 50 , 53 However, cross-talk between perceived elemental contrast and nonplanar topography, edge effects, and resulting image distortions due to flexibility of the tip apex make systematic studies in molecular systems challenging.…”

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confidence: 99%

Elemental Identification by Combining Atomic Force Microscopy and Kelvin Probe Force Microscopy

et al. 2018

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There are currently no experimental techniques that combine atomic-resolution imaging with elemental sensitivity and chemical fingerprinting on single molecules. The advent of using molecular-modified tips in noncontact atomic force microscopy (nc-AFM) has made it possible to image (planar) molecules with atomic resolution. However, the mechanisms responsible for elemental contrast with passivated tips are not fully understood. Here, we investigate elemental contrast by carrying out both nc-AFM and Kelvin probe force microscopy (KPFM) experiments on epitaxial monolayer hexagonal boron nitride (hBN) on Ir(111). The hBN overlayer is inert, and the in-plane bonds connecting nearest-neighbor boron and nitrogen atoms possess strong covalent character and a bond length of only ∼1.45 Å. Nevertheless, constant-height maps of both the frequency shift Δf and the local contact potential difference exhibit striking sublattice asymmetry. We match the different atomic sites with the observed contrast by comparison with nc-AFM image simulations based on the density functional theory optimized hBN/Ir(111) geometry, which yields detailed information on the origin of the atomic-scale contrast.

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“…12,13 Recently, molecules comprising heteroatoms have been addressed. [14][15][16][17][18][19][20][21][22][23][24] As soon as electrostatic dipoles in the molecule or tip are present, the electrostatic force plays an important role in interpreting the images. 20,22,[24][25][26][27] Thiols are of great interest owing to their capacity to self-assemble and to create various structures thanks to their functionalizing groups.…”

mentioning

confidence: 99%

AFM Imaging of Mercaptobenzoic Acid on Au(110): Submolecular Contrast with Metal Tips

Hauptmann

Robles

Abufager

et al. 2016

J. Phys. Chem. Lett.

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A self-assembled monolayer of mercaptobenzoic acid (MBA) on Au(110) is investigated with scanning tunneling and atomic force microscopy (STM and AFM) and density functional calculations. High-resolution AFM images obtained with metallic tips show clear contrasts between oxygen atoms and phenyl moieties. The contrast above the oxygen atoms is due to attractive covalent interactions, which is different than previously reported high-resolution images, where Pauli repulsion dominated the image contrast. We show that the bonding of MBA to the substrate occurs mainly through dispersion interactions, whereas the thiol-Au bond contributes only a quarter of the adsorption energy. No indication of Au adatoms mediating the thiol-Au interaction was found in contrast to other thiol-bonded systems. However, MBA lifts the Au(110)-(2 × 1) reconstruction.

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A Combined Atomic Force Microscopy and Computational Approach for the Structural Elucidation of Breitfussin A and B: Highly Modified Halogenated Dipeptides from Thuiaria breitfussi

Cited by 25 publications

References 22 publications

Addressing the stereochemistry of complex organic molecules by density functional theory‐NMR

Addressing the stereochemistry of complex organic molecules by density functional theory‐NMR

Elemental Identification by Combining Atomic Force Microscopy and Kelvin Probe Force Microscopy

AFM Imaging of Mercaptobenzoic Acid on Au(110): Submolecular Contrast with Metal Tips

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