Evaporation and Fragmentation of Organic Molecules in Strong Electric Fields Simulated with DFT

Abstract

Atom probe tomography allows us to measure the three-dimensional composition of materials with up to atomic resolution by evaporating the material using high electric fields. Initially developed for metals, it is increasingly used for covalently bound structures. To aid the interpretation of the obtained fragmentation pattern, we modeled the fragmentation and desorption of self-assembled monolayers of thiolate molecules on a gold surface in strong electrostatic fields using density functional theory. We used a cluster model and a periodic model of amino-undecanethiolate, NH 2 (CH 2 ) 11 S, and fluoro-decanethiolate, CF 3 (CF 2 ) 7 (CH 2 ) 2 S. In the former molecule, the fragment CH 2 NH 2 + was found to evaporate at fields of 5.4−7.7 V/nm. It was followed by different hydrocarbon fragments. Fluorodecanethiolate evaporates CF 3 + at fields of 5.7−6.7 V/nm in the cluster model and at 15.4−23.1 V/nm in the periodic model, followed by CF 2 + and C 2 F 4 2+ . Detailed analysis of the electronic structure during the evaporation process revealed a stepwise accumulation of the charge in the head groups exposed to the strongest fields, followed by dissociation of covalent bonds. These observations will facilitate the analysis of atom probe experiments of covalently bound structures.

Non-covalent interactions between molecular dimers (S66) in electric fields

“…Impressive progress has a) Electronic mail: anatole.vonlilienfeld@univie.ac.at been made due to synergies of experimental and theoretical efforts. [12][13][14][15] Strong electric fields can also occur as an intramolecular effect. An internal electric field can arise in the cavity of frustrated Lewis pairs 16 .…”

Switch Chemistry at Cryogenic Conditions: Quantum Tunnelling under Electric Fields

“…16 From there, the EEF concept has seen many more (mostly theoretical) applications. [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34] According to IUPAC "A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction; the process is called catalysis. The catalyst is both a reactant and product".…”

Understanding Fragmentation of Organic Small Molecules in Atom Probe Tomography

“…Atom probe tomography (APT) is a cornerstone in nanoscale materials characterization, providing subnanometer spatial resolution along with subdalton mass spectral resolution. − These features have permitted new structural and chemical insights in a wide array of metals and ceramics. − APT of organic systems has seen much less development. Polymeric materials often fragment during the evaporation process, − but small-molecule organics with van der Waals intermolecular bonds can evaporate as whole molecules. , This has been explained as the result of a significantly lower intermolecular van der Waals interaction energy when compared to the intramolecular covalent bonds in these small-molecular systems; however, it ignores potential destabilization of molecules upon ionization and raises the question of where the transition lies between whole molecule evaporation and fragmentation in these organic systems; these are the foci of the present study. We look for evidence of post-ionization molecular fragmentation by examining events where multiple ions are detected for a single laser pulse, known as multiple detection events (MDEs).…”

“…To understand why a particular molecule is more or less prone to fragmentation during APT analysis, we use DFT to find evidence of molecular instability. DFT has been used to study fragmentation in APT previously, but only for long-chained organic polymer and self-assembled monolayer systems, and not organic small molecules. ,, …”

“…DFT has been used to study fragmentation in APT previously, but only for long-chained organic polymer and self-assembled monolayer systems, and not organic small molecules. 11,17,18 To assess the thermodynamic favorability of the various fragmentation reactions, the difference in energy between products and reactants must be understood. These energy values were calculated for all potential sites of molecular fragmentation via homolytic bond dissociation for the four different molecules to predict which bonds may be prone to break.…”