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Method for Molecular Structure Identification with the Atomic Force Microscope

IP.com Disclosure Number: IPCOM000245120D
Publication Date: 2016-Feb-10
Document File: 5 page(s) / 713K

Publishing Venue

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Abstract

Here we present a method for molecular structure determination with elemental specificity using atomic force microscopy. Molecular identification is performed based on atomic force microscopy images of an individual molecule using different tip functionalizations and employing a library of molecular substructures measured by AFM with these different tip functionalizations and theoretical calculations of the substructures.

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Method for Molecular Structure Identification with the Atomic Force Microscope

Identification of molecular structures is of great importance in chemistry (e.g. in molecular synthesis), pharmacy (for the search of new cures), life sciences (for the investigation of inner cell processes and substances), energy and environmental sciences (for the chemical analysis of fuels and pollutants), and technology applications (e.g. for the development of molecular electronics, molecular machines, and organic photovoltaics). We will propose research collaborations using our method for molecule identification with the AFM, i.e., analysis of samples and instrumentation training to industry partners. Possible partners will include oil majors and petrochemical industries (study of asphaltenes for enhanced oil recovery and improved upstream and downstream fuel production), automotive and plane manufacturers (fuel pyrolysis analysis), chemical industries (characterization of reactions, reactive intermediates and catalysis) and pharmaceutical industries (identification of natural products for new medicines).

Elemental specificity is the most desirable goal, to enable wide applicability of structure identification of individual molecules by AFM. Here we present a method for molecular structure determination with elemental specificity using AFM.

Instead of direct element specification we propose the identification of molecular substructures based on a database containing measured substructures and/or substructures calculated computationally. Entries of the database will be AFM and KPFM maps of common molecular substructures obtained with different tip functionalizations.

Main Claim :

Molecular identification is performed based on atomic force microscopy images of an individual molecule with different tip functionalizations employing a library of molecular substructures measured by AFM with these different tip functionalizations or theoretical calculations of the substructures.

Known molecules will be measured in order to fill the database with information. E.g. planar systems containing a polycyclic aromatic hydrocarbon (PAH) backbone. Commonly encountered side groups connected to the PAH core will be measured, e.g. H, CH2, CH3, NH2, OH, O, NO2 , F, Cl, I, Br, alkyl, alkenyl or alkynyl substituents. Typical heteroatoms in the PAH core will be studied, e.g. different aromatic heterocycles comprising B, N, O, S and/or P atoms.

Tip functionalizations include for example termination with CO, Xe, Kr, Br, I.

The tip-independent contrast from Kelvin probe force microscopy can be employed to provide a reference for the comparison of images with different tips.

STM orbital imaging in conjunction with DFT calculations can be used to confirm the molecular structure.

The molecule could be imaged in different adsorption conformations (exposing different sides/facets).

Analysis will be done by using image recognition algorithms and simulations of AFM images to iden...