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Zossimova E, Fiedler J, Vollmer F, Walter M. Hybrid quantum-classical polarizability model for single molecule biosensing. Nanoscale 2024; 16:5820-5828. [PMID: 38436120 DOI: 10.1039/d3nr05396b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Optical whispering gallery mode biosensors are able to detect single molecules through effects of their polarizability. We address the factors that affect the polarizability of amino acids, which are the building blocks of life, via electronic structure theory. Amino acids are detected in aqueous environments, where their polarizability is different compared to the gasphase due to solvent effects. Solvent effects include structural changes, protonation and the local field enhancement through the solvent (water). We analyse the impact of these effects and find that all contribute to an increased effective polarizability in the solvent. We also address the excess polarizability relative to the displaced water cavity and develop a hybrid quantum-classical model that is in good agreement with self-consistent calculations. We apply our model to calculate the excess polarizability of 20 proteinogenic amino acids and determine the minimum resolution required to distinguish the different molecules and their ionised conformers based on their polarizability.
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Affiliation(s)
- Ekaterina Zossimova
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, EX4 4QD, Exeter, UK.
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, D-79110 Freiburg, Germany
| | - Johannes Fiedler
- Department of Physics and Technology, University of Bergen, Allégaten 55, 5007 Bergen, Norway
| | - Frank Vollmer
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, EX4 4QD, Exeter, UK.
| | - Michael Walter
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, D-79110 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT, Freiburg, Germany
- Fraunhofer IWM, MikroTribologie Centrum μTC, Freiburg, Germany
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Czernek J, Brus J. Reliable Dimerization Energies for Modeling of Supramolecular Junctions. Int J Mol Sci 2024; 25:602. [PMID: 38203773 PMCID: PMC10778993 DOI: 10.3390/ijms25010602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Accurate estimates of intermolecular interaction energy, ΔE, are crucial for modeling the properties of organic electronic materials and many other systems. For a diverse set of 50 dimers comprising up to 50 atoms (Set50-50, with 7 of its members being models of single-stacking junctions), benchmark ΔE data were compiled. They were obtained by the focal-point strategy, which involves computations using the canonical variant of the coupled cluster theory with singles, doubles, and perturbative triples [CCSD(T)] performed while applying a large basis set, along with extrapolations of the respective energy components to the complete basis set (CBS) limit. The resulting ΔE data were used to gauge the performance for the Set50-50 of several density-functional theory (DFT)-based approaches, and of one of the localized variants of the CCSD(T) method. This evaluation revealed that (1) the proposed "silver standard" approach, which employs the localized CCSD(T) method and CBS extrapolations, can be expected to provide accuracy better than two kJ/mol for absolute values of ΔE, and (2) from among the DFT techniques, computationally by far the cheapest approach (termed "ωB97X-3c/vDZP" by its authors) performed remarkably well. These findings are directly applicable in cost-effective yet reliable searches of the potential energy surfaces of noncovalent complexes.
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Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 16200 Prague, Czech Republic;
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Fang S, Zahl P, Wang X, Liu P, Stacchiola D, Hu YH. Direct Observation of Twin van der Waals Molecular Chains. J Phys Chem Lett 2023; 14:10710-10716. [PMID: 37988703 DOI: 10.1021/acs.jpclett.3c02914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
The van der Waals (vdW) assemblies are the most common structures of materials. However, direct mapping of intermolecular electron clouds of a vdW assembly has never been obtained, even though the intramolecular electron clouds were visualized by atomic-resolution techniques. In this report, we unprecedentedly mapped the intermolecular electron cloud of the assemblies of ethanol molecules via ethyl groups with high-resolution atomic force microscopy and scanning tunneling microscopy at 5 K, leading to the first visualization of vdW molecular chains, in which ethanol molecules assemble into twin vdW molecular chains in a reverse parallel configuration on the Ag(111) plane. Furthermore, spontaneous order-disorder transitions in the chain were dynamically observed, suggesting its unusual properties different from those of 2D vdW materials. These findings provide an "eye" to see the atomic world of vdW materials.
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Affiliation(s)
- Siyuan Fang
- Department of Materials Science and Engineering, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Percy Zahl
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Xuelong Wang
- Chemistry Division, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Ping Liu
- Chemistry Division, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Dario Stacchiola
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yun Hang Hu
- Department of Materials Science and Engineering, Michigan Technological University, Houghton, Michigan 49931, United States
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Maier P, Hourigan NJ, Ruckhofer A, Bremholm M, Tamtögl A. Surface properties of 1T-TaS 2 and contrasting its electron-phonon coupling with TlBiTe 2 from helium atom scattering. Front Chem 2023; 11:1249290. [PMID: 38033467 PMCID: PMC10687202 DOI: 10.3389/fchem.2023.1249290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023] Open
Abstract
We present a detailed helium atom scattering study of the charge-density wave (CDW) system and transition metal dichalcogenide 1T-TaS2. In terms of energy dissipation, we determine the electron-phonon (e-ph) coupling, a quantity that is at the heart of conventional superconductivity and may even "drive" phase transitions such as CDWs. The e-ph coupling of TaS2 in the commensurate CDW phase (λ = 0.59 ± 0.12) is compared with measurements of the topo-logical insulator TlBiTe2 (λ = 0.09 ± 0.01). Furthermore, by means of elastic He diffraction and resonance/interference effects in He scattering, the thermal expansion of the surface lattice, the surface step height, and the three-dimensional atom-surface interaction potential are determined including the electronic corrugation of 1T-TaS2. The linear thermal expansion coefficient is similar to that of other transition-metal dichalcogenides. The He-TaS2 interaction is best described by a corrugated Morse potential with a relatively large well depth and supports a large number of bound states, comparable to the surface of Bi2Se3, and the surface electronic corrugation of 1T-TaS2 is similar to the ones found for semimetal surfaces.
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Affiliation(s)
- Philipp Maier
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | - Noah. J. Hourigan
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | - Adrian Ruckhofer
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | - Martin Bremholm
- Department of Chemistry and iNANO, Aarhus University, Aarhus, Denmark
| | - Anton Tamtögl
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
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Czernek J, Brus J, Czerneková V, Kobera L. Quantifying the Intrinsic Strength of C-H⋯O Intermolecular Interactions. Molecules 2023; 28:molecules28114478. [PMID: 37298953 DOI: 10.3390/molecules28114478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
It has been recognized that the C-H⋯O structural motif can be present in destabilizing as well as highly stabilizing intermolecular environments. Thus, it should be of interest to describe the strength of the C-H⋯O hydrogen bond for constant structural factors so that this intrinsic strength can be quantified and compared to other types of interactions. This description is provided here for C2h-symmetric dimers of acrylic acid by means of the calculations that employ the coupled-cluster theory with singles, doubles, and perturbative triples [CCSD(T)] together with an extrapolation to the complete basis set (CBS) limit. Dimers featuring the C-H⋯O and O-H⋯O hydrogens bonds are carefully investigated in a wide range of intermolecular separations by the CCSD(T)/CBS approach, and also by the symmetry-adapted perturbation theory (SAPT) method, which is based on the density-functional theory (DFT) treatment of monomers. While the nature of these two types of hydrogen bonding is very similar according to the SAPT-DFT/CBS calculations and on the basis of a comparison of the intermolecular potential curves, the intrinsic strength of the C-H⋯O interaction is found to be about a quarter of its O-H⋯O counterpart that is less than one might anticipate.
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Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 162 00 Prague, Czech Republic
| | - Jiří Brus
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 162 00 Prague, Czech Republic
| | - Vladimíra Czerneková
- Institute of Physics, Czech Academy of Science, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Libor Kobera
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 162 00 Prague, Czech Republic
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Emig T, Bimonte G. Multiple Scattering Expansion for Dielectric Media: Casimir Effect. Phys Rev Lett 2023; 130:200401. [PMID: 37267564 DOI: 10.1103/physrevlett.130.200401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 04/03/2023] [Indexed: 06/04/2023]
Abstract
Recent measurements of Casimir forces have provided evidence of an intricate modification of quantum fluctuations of the electromagnetic field in complex geometries. Here we introduce a multiple scattering description for Casimir interactions between bodies of arbitrary shape and material composition, admitting an expansion as a sequence of inter- and intra-body wave scatterings. Interactions in complex geometries can be computed within the current experimental resolution from typically a few wave scatterings, notably without any a priori knowledge of the scattering amplitudes of the bodies. Some first applications demonstrate the power of the approach.
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Affiliation(s)
- Thorsten Emig
- Laboratoire de Physique Théorique et Modèles Statistiques, CNRS UMR 8626, Bâtiment 530, Université Paris-Sud/Saclay, 91405 Orsay cedex, France
| | - Giuseppe Bimonte
- Dipartimento di Fisica E. Pancini, Università di Napoli Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia, I-80126 Napoli, Italy and INFN Sezione di Napoli, I-80126 Napoli, Italy
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