• This record comes from PubMed

Visualization of π-hole in molecules by means of Kelvin probe force microscopy

. 2023 Aug 16 ; 14 (1) : 4954. [epub] 20230816

Status PubMed-not-MEDLINE Language English Country England, Great Britain Media electronic

Document type Journal Article

Links

PubMed 37587123
PubMed Central PMC10432393
DOI 10.1038/s41467-023-40593-3
PII: 10.1038/s41467-023-40593-3
Knihovny.cz E-resources

Submolecular charge distribution significantly affects the physical-chemical properties of molecules and their mutual interaction. One example is the presence of a π-electron-deficient cavity in halogen-substituted polyaromatic hydrocarbon compounds, the so-called π-holes, the existence of which was predicted theoretically, but the direct experimental observation is still missing. Here we present the resolution of the π-hole on a single molecule using the Kelvin probe force microscopy, which supports the theoretical prediction of its existence. In addition, experimental measurements supported by theoretical calculations show the importance of π-holes in the process of adsorption of molecules on solid-state surfaces. This study expands our understanding of the π-hole systems and, at the same time, opens up possibilities for studying the influence of submolecular charge distribution on the chemical properties of molecules and their mutual interaction.

See more in PubMed

Müller-Dethlefs K, Hobza P. Noncovalent interactions: a challenge for experiment and theory. Chem. Rev. 2000;100:143–168. doi: 10.1021/cr9900331. PubMed DOI

Murray JS, Shields ZPI, Seybold PG, Politzer P. Intuitive and counterintuitive noncovalent interactions of aromatic π regions with the hydrogen and the nitrogen of HCN. J. Comput. Sci. 2015;10:209–216. doi: 10.1016/j.jocs.2015.02.001. DOI

Pluháčková K, Jurečka P, Hobza P. Stabilisation energy of C 6 H 6 ⋯C 6 X 6 (X = F, Cl, Br, I, CN) complexes: complete basis set limit calculations at MP2 and CCSD(T) levels. Phys. Chem. Chem. Phys. 2007;9:755–760. doi: 10.1039/B615318F. PubMed DOI

Murray JS, Lane P, Clark T, Riley KE, Politzer P. σ-Holes, π-holes and electrostatically-driven interactions. J. Mol. Model. 2012;18:541–548. doi: 10.1007/s00894-011-1089-1. PubMed DOI

Politzer P, Murray JS, Clark T. The π-hole revisited. Phys. Chem. Chem. Phys. 2021;23:16458–16468. doi: 10.1039/D1CP02602J. PubMed DOI

Řezáč J, Hobza P. Benchmark calculations of interaction energies in noncovalent complexes and their applications. Chem. Rev. 2016;116:5038–5071. doi: 10.1021/acs.chemrev.5b00526. PubMed DOI

Wang H, Wang W, Jin WJ. σ-hole bond vs π-hole bond: a comparison based on halogen bond. Chem. Rev. 2016;116:5072–5104. doi: 10.1021/acs.chemrev.5b00527. PubMed DOI

Gross L, Mohn F, Moll N, Liljeroth P, Meyer G. The chemical structure of a molecule resolved by atomic force microscopy. Science (1979) 2009;325:1110–1114. PubMed

Jelínek P. High resolution SPM imaging of organic molecules with functionalized tips. J. Phys. Condens. Matter. 2017;29:343002. doi: 10.1088/1361-648X/aa76c7. PubMed DOI

Wäckerlin C, et al. Role of the magnetic anisotropy in atomic-spin sensing of 1D molecular chains. ACS Nano. 2022;16:16402–16413. doi: 10.1021/acsnano.2c05609. PubMed DOI

Mallada B, et al. Real-space imaging of anisotropic charge of σ-hole by means of Kelvin probe force microscopy. Science (1979) 2021;374:863–867. PubMed

Wheeler SE, Houk KN. Through-space effects of substituents dominate molecular electrostatic potentials of substituted arenes. J. Chem. Theory Comput. 2009;5:2301–2312. doi: 10.1021/ct900344g. PubMed DOI PMC

Sadewasser, S. & Glatzel, T. In Kelvin Probe Force Microscopy: from Single Charge Detection to Device Characterization (Springer International Publishing, Cham, 2018).

Sadewasser S, et al. New insights on atomic-resolution frequency-modulation kelvin-probe force-microscopy imaging of semiconductors. Phys Rev. Lett. 2009;103:266103. doi: 10.1103/PhysRevLett.103.266103. PubMed DOI

Gross L, et al. Measuring the charge state of an adatom with noncontact atomic force microscopy. Science (1979) 2009;324:1428–1431. PubMed

Berger J, et al. Quantum dissipation driven by electron transfer within a single molecule investigated with atomic force microscopy. Nat. Commun. 2020;11:1337. doi: 10.1038/s41467-020-15054-w. PubMed DOI PMC

Mohn F, Gross L, Moll N, Meyer G. Imaging the charge distribution within a single molecule. Nat. Nanotechnol. 2012;7:227–231. doi: 10.1038/nnano.2012.20. PubMed DOI

Klein BP, et al. Molecular topology and the surface chemical bond: alternant versus nonalternant aromatic systems as functional structural elements. Phys. Rev. X. 2019;9:011030.

Mallada B, et al. Atomic-scale charge distribution mapping of single substitutional p-and n-Type dopants in graphene. ACS Sustain Chem Eng. 2020;8:3437–3444. doi: 10.1021/acssuschemeng.9b07623. DOI

Mohn F, Schuler B, Gross L, Meyer G. Different tips for high-resolution atomic force microscopy and scanning tunneling microscopy of single molecules. Appl. Phys. Lett. 2013;102:073109. doi: 10.1063/1.4793200. DOI

Moll N, et al. Image distortions of a partially fluorinated hydrocarbon molecule in atomic force microscopy with carbon monoxide terminated tips. Nano Lett. 2014;14:6127–6131. doi: 10.1021/nl502113z. PubMed DOI

Albrecht F, et al. Probing charges on the atomic scale by means of atomic force microscopy. Phys. Rev. Lett. 2015;115:076101. doi: 10.1103/PhysRevLett.115.076101. PubMed DOI

Hapala P, et al. Mechanism of high-resolution STM/AFM imaging with functionalized tips. Phys. Rev. B Condens Matter Mater Phys. 2014;90:085421. doi: 10.1103/PhysRevB.90.085421. DOI

Schuler B, et al. Adsorption geometry determination of single molecules by atomic force microscopy. Phys. Rev. Lett. 2013;111:106103. doi: 10.1103/PhysRevLett.111.106103. PubMed DOI

Gonthier JF, Sherrill CD. Density-fitted open-shell symmetry-adapted perturbation theory and application to π -stacking in benzene dimer cation and ionized DNA base pair steps. J. Chem. Phys. 2016;145:134106. doi: 10.1063/1.4963385. PubMed DOI

Horcas I, et al. WSXM: a software for scanning probe microscopy and a tool for nanotechnology. Rev. Sci. Instrum. 2007;78:013705. doi: 10.1063/1.2432410. PubMed DOI

Blum V, et al. Ab initio molecular simulations with numeric atom-centered orbitals. Comput. Phys. Commun. 2009;180:2175–2196. doi: 10.1016/j.cpc.2009.06.022. DOI

Perdew JP, Burke K, Ernzerhof M. Generalized gradient approximation made simple. Phys. Rev. Lett. 1996;77:3865–3868. doi: 10.1103/PhysRevLett.77.3865. PubMed DOI

Adamo C, Barone V. Toward reliable density functional methods without adjustable parameters: the PBE0 model. J. Chem. Phys. 1999;110:6158. doi: 10.1063/1.478522. DOI

Ren X, et al. Resolution-of-identity approach to Hartree–Fock, hybrid density functionals, RPA, MP2 and GW with numeric atom-centered orbital basis functions. New. J. Phys. 2012;14:053020. doi: 10.1088/1367-2630/14/5/053020. DOI

Tkatchenko A, Scheffler M. Accurate molecular van der Waals interactions from ground-state electron density and free-atom reference data. Phys. Rev. Lett. 2009;102:073005. doi: 10.1103/PhysRevLett.102.073005. PubMed DOI

Krejčí O, Hapala P, Ondráček M, Jelínek P. Principles and simulations of high-resolution STM imaging with a flexible tip apex. Phys. Rev. B. 2017;95:045407. doi: 10.1103/PhysRevB.95.045407. DOI

Dunning TH. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys. 1989;90:1007–1023. doi: 10.1063/1.456153. DOI

Grimme S, Antony J, Ehrlich S, Krieg H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 2010;132:154104. doi: 10.1063/1.3382344. PubMed DOI

Grimme S, Ehrlich S, Goerigk L. Effect of the damping function in dispersion corrected density functional theory. J. Comput. Chem. 2011;32:1456–1465. doi: 10.1002/jcc.21759. PubMed DOI

Weigend F, Ahlrichs R. Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: design and assessment of accuracy. Phys. Chem. Chem. Phys. 2005;7:3297. doi: 10.1039/b508541a. PubMed DOI

Neese F, Wennmohs F, Becker U, Riplinger C. The ORCA quantum chemistry program package. J. Chem. Phys. 2020;152:224108. doi: 10.1063/5.0004608. PubMed DOI

Smith DGA, et al. PSI4 1.4: open-source software for high-throughput quantum chemistry. J. Chem. Phys. 2020;152:184108. doi: 10.1063/5.0006002. PubMed DOI PMC

Peterson KA, Puzzarini C. Systematically convergent basis sets for transition metals. II. Pseudopotential-based correlation consistent basis sets for the group 11 (Cu, Ag, Au) and 12 (Zn, Cd, Hg) elements. Theor. Chem. Acc. 2005;114:283–296. doi: 10.1007/s00214-005-0681-9. DOI

Find record

Citation metrics

Loading data ...

Archiving options

Loading data ...