The mechanism of high-resolution STM/AFM imaging with functionalized tips

High resolution Atomic Force Microscopy (AFM) and Scanning Tunnelling Microscopy (STM) imaging with functionalized tips is well established, but a detailed understanding of the imaging mechanism is still missing. We present a numerical STM/AFM model, which takes into account the relaxation of the probe due to the tip-sample interaction. We demonstrate that the model is able to reproduce very well not only the experimental intra- and intermolecular contrasts, but also their evolution upon tip approach. At close distances, the simulations unveil a significant probe particle relaxation towards local minima of the interaction potential. This effect is responsible for the sharp sub-molecular resolution observed in AFM/STM experiments. In addition, we demonstrate that sharp apparent intermolecular bonds should not be interpreted as true hydrogen bonds, in the sense of representing areas of increased electron density. Instead they represent the ridge between two minima of the potential energy landscape due to neighbouring atoms

Molecular sensitised probe for amino acid recognition within peptide sequences

The combination of low-temperature scanning tunnelling microscopy with a mass-selective electro-spray ion-beam deposition established the investigation of large biomolecules at nanometer and sub-nanometer scale. Due to complex architecture and conformational freedom, however, the chemical identification of building blocks of these biopolymers often relies on the presence of markers, extensive simulations, or is not possible at all. Here, we present a molecular probe-sensitisation approach addressing the identification of a specific amino acid within different peptides. A selective intermolecular interaction between the sensitiser attached at the tip-apex and the target amino acid on the surface induces an enhanced tunnelling conductance of one specific spectral feature, which can be mapped in spectroscopic imaging. Density functional theory calculations suggest a mechanism that relies on conformational changes of the sensitiser that are accompanied by local charge redistributions in the tunnelling junction, which, in turn, lower the tunnelling barrier at that specific part of the peptide

Attomolar detection of hepatitis C virus core protein powered by molecular antenna-like effect in a graphene field-effect aptasensor

Biosensors based on graphene field-effect transistors have become a promising tool for detecting a broad range of analytes. However, their performance is substantially affected by the functionalization protocol. In this work, we use a controlled in-vacuum physical method for the covalent functionalization of graphene to construct ultrasensitive aptamer-based biosensors (aptasensors) able to detect hepatitis C virus core protein. These devices are highly specific and robust, achieving attomolar detection of the viral protein in human blood plasma. Such an improved sensitivity is rationalized by theoretical calculations showing that induced polarization at the graphene interface, caused by the proximity of covalently bound molecular probe, modulates the charge balance at the graphene/aptamer interface. This charge balance causes a net shift of the Dirac cone providing enhanced sensitivity for the attomolar detection of the target proteins. Such an unexpected effect paves the way for using this kind of graphene-based functionalized platforms for ultrasensitive and real-time diagnostics of different diseases.EU Graphene Flagship funding (Grant Graphene Core3 881603), the Ministerio de Ciencia e Innovación of Spain: PID2020-113142RB-C21, the European Structural Funds via FotoArt-CM project (P2018/NMT-4367) and the Portuguese Foundation for Science and Technology (FCT) via the Strategic Funding UIDB/04650/2020. Work at CAB was funded by the Spanish Ministerio de Ciencia e Innovación (MICINN) grant no. PID2019-104903RB-I00 and the Spanish Agencia Estatal de Investigación (AEI) Project no. MDM-2017-0737 - Unidad de Excelencia “María de Maeztu,” and it also benefits from the interdisciplinary framework provided by CSIC through “LifeHUB.CSIC” initiative (PIE 202120E047-CONEXIONES-LIFE). CIBERehd is funded by Instituto de Salud Carlos III (ISCIII). A.N. is supported by the predoctoral fellowship PRE-CAB-BIOMOLECULAS 2 from INTA. B.T-V. is supported by the predoctoral fellowship TS17/16 from INTA and by the CSIC “Garantía Juvenil” contract CAM19_PRE_CAB_001 funded by Comunidad de Madrid (CAM). FCT supports T.D. and P.C. under Ph.D. grants SFRH/BD/08181/2020 and SFRH/BD/128579/2017. M.M. would like to thank Comunidad de Madrid for the predoctoral grant IND2020/BIO-17523. P.A. and C.B. also acknowledge the support provided by La Caixa Foundation through Project LCF/PR/HR21/52410023. L. V. would like to thank Comunidad de Madrid (TRANSNANOAVANSENS program: S2018-NMT-4349) and E.V. García-Frutos for her assistance during the AFM experiments

Chemisorption-induced formation of biphenylene dimer on Ag(111)

We report an example that demonstrates the clear interdependence between surface-supported reactions and molecular-adsorption configurations. Two biphenyl-based molecules with two and four bromine substituents, i.e., 2,2′-dibromobiphenyl (DBBP) and 2,2′,6,6′-tetrabromo-1,1′-biphenyl (TBBP), show completely different reaction pathways on a Ag(111) surface, leading to the selective formation of dibenzo[e,l]pyrene and biphenylene dimer, respectively. By combining low-temperature scanning tunneling microscopy, synchrotron radiation photoemission spectroscopy, and density functional theory calculations, we unravel the underlying reaction mechanism. After debromination, a biradical biphenyl can be stabilized by surface Ag adatoms, while a four-radical biphenyl undergoes spontaneous intramolecular annulation due to its extreme instability on Ag(111). Such different chemisorption-induced precursor states between DBBP and TBBP consequently lead to different reaction pathways after further annealing. In addition, using bond-resolving scanning tunneling microscopy and scanning tunneling spectroscopy, we determine with atomic precision the bond-length alternation of the biphenylene dimer product, which contains 4-, 6-, and 8-membered rings. The 4-membered ring units turn out to be radialene structures.This work was financially supported by the National Natural Science Foundation of China (21773222, 51772285, 21872131, U1732272, and U1932214), the National Key R&D Program of China (2017YFA0403402, 2017YFA0403403, and 2019YFA0405601), and Users with Excellence Program of Hefei Science Center CAS (2020HSC-UE004). The work at Washington State University was primarily funded through the National Science Foundation CAREER program under Contract no. CBET-1653561. This work was also partially funded by the Joint Center for Deployment and Research in Earth Abundant Materials (JCDREAM) in Washington State. Most of the computational resources were provided by the Kamiak HPC under the Center for Institutional Research Computing at Washington State University. This research also used resources of the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility operated under Contract no. DE-AC02-05CH11231. The work at Donostia International Physics Center was primarily funded through the Juan de la Cierva Grant (no. FJC2019-041202-I) from Spanish Ministry of Economy and Competitiveness, the European Union’s Horizon 2020 Research and Innovation program (Marie Skłodowska-Curie Actions Individual Fellowship (no. 101022150), and the MCIN/AEI/ 10.13039/501100011033 (Grant no. PID2019-107338RB-C63).Peer reviewe