Effect of backbone aspect ratio on the surface-confined self-assembly of tetratopic molecular building blocks

Nieckarz, Damian; Rżysko, W.; Lutsyk, Valery; Lisiecki, Jakub; Szabelski, Paweł

doi:10.1016/j.colsurfa.2019.123632

Cited by 4 publications

(5 citation statements)

References 38 publications

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“…The most common are patchy-particle and lattice models. Analysis of the continuous patchy-particle models of SAMs − with a few exceptions , is focused on examining their structural characteristics rather than thermodynamic characteristics. Lattice models of SAMs have become more widespread due to their simplicity.…”

Section: Introductionmentioning

confidence: 99%

Thermodynamics of Rigid Self-Assembled Crystals: Molecular Simulation of Two-Phase Systems under External Fields

2021

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A general methodology for determining the thermodynamic characteristics of orientationally ordered rigid crystals is presented. The basic problem here is associated with a very small flux of primary molecules that are released from a narrow interface and carry main information on thermodynamic properties of the crystal. The proposed approach is based on the kinetic Monte Carlo simulation of the gas−crystal system with an external "damping field" that reduces the intermolecular potential at the crystal edges and switches it off in the gas phase. Such a technique increases the primary molecular flux by several orders of magnitude, which is crucial for accurate determination of thermodynamic functions. In this study, we applied the approach to the thermodynamic analysis of the trimesic acid monolayer, explicitly accounting for hydrogen bonds, the dispersion, and electrostatic potentials. We considered equations of state, heat capacities, Helmholtz free energies, and entropies of three polymorphous structures: honeycomb, flower-like, and hexagonally close-packed structures in a wide range of temperatures and pressures. The calculated free energy and entropy excellently obey the Gibbs−Duhem equation, which confirms the thermodynamic consistency of our approach. The role of hydrogen bonds in the stability of different phases, as well as the condition of phase transitions, was also considered.

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Section: Introductionmentioning

confidence: 99%

Thermodynamics of Rigid Self-Assembled Crystals: Molecular Simulation of Two-Phase Systems under External Fields

2021

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“…All these circumstances stimulated us to address the formation of two ordered structures of BTB molecules, the deprotonated R phase, and the O phase which we treat both intact as well as weakly deprotonated, by using modeling methods of Monte Carlo (MC) and density functional theory (DFT). A computational approach − has been instrumental recently in explaining the formation of self-organized molecular networks. The particular methodology used here was previously developed to handle the triangular- and rectangular-shaped molecules with hydrogen bonds at the vertices and employed for systems such as deprotonated TMA molecules, neutral TMA–BTB mixtures, and host–guest architectures…”

Section: Introductionmentioning

confidence: 99%

Modeling of Ribbon and Oblique Structures of Benzene-1,3,5-triyl-tribenzoic Acid

Ibenskas

Tornau

2020

J. Phys. Chem. C

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We propose two models describing the self-assembly of intact and deprotonated benzene-1,3,5-triyl-tribenzoic acid (BTB) molecules into the oblique (O) and ribbon (R) phases. The models are also extended to describe the formation of the honeycomb (HON) structure. To determine the intermolecular interaction potentials for the R and O phases, we performed the DFT calculations for the clusters of neutral and charged BTB molecules. The obtained values were used as an input in the Monte Carlo (MC) simulations. The model and MC simulations for the R phase demonstrate how ionic interactions between singly deprotonated BTB molecules lead to the formation of ribbons separated by the interribbon gap, and how these ribbons pack into the ordered two-dimensional structure. The O phase is treated in our model as the structure that might be composed of both intact and singly deprotonated molecules, owing to the occurrence of this phase in polarization switching experiments for positive surface bias. The ground-state analysis and MC modeling for the O and HON structures with the DFT-calculated interaction parameters demonstrate that for intact molecules (deprotonation level (DPL) = 0) the energy of the HON structure is always lower than that of the O phase. With an increase of DPL, the difference between the energies of these two structures decreases: while for DPL = 0.5, the possibilities to obtain the HON or O phase are very similar, for DPL = 1 the O phase has a higher probability to exist in comparison to the HON phase.

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“…30 The assemblies of symmetric tetratopic molecular building blocks were also extensively explored in the MC studies. [31][32][33][34] In the current work, we present a rather simple model for the assembly of both metal-organic and covalent single-layer molecular networks, taking Br 4 Py as the prototypical halogenated polyarene. The model is partially based on our previous works which have addressed molecular ensembles of intact 33 and dehalogenated 34 pyrene derivatives.…”

Section: Introductionmentioning

confidence: 99%

“…30 The assemblies of symmetric tetratopic molecular building blocks were also extensively explored in the MC studies. 31–34…”

Section: Introductionmentioning

confidence: 99%

Theoretical insights into the interplay between metal–organic and covalent bonding in single-layer molecular networks formed by halogen dissociation

Ibenskas,

Šimėnas,

Tornau

2024

Phys. Chem. Chem. Phys.

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Effect of backbone aspect ratio on the surface-confined self-assembly of tetratopic molecular building blocks

Cited by 4 publications

References 38 publications

Thermodynamics of Rigid Self-Assembled Crystals: Molecular Simulation of Two-Phase Systems under External Fields

Thermodynamics of Rigid Self-Assembled Crystals: Molecular Simulation of Two-Phase Systems under External Fields

Modeling of Ribbon and Oblique Structures of Benzene-1,3,5-triyl-tribenzoic Acid

Theoretical insights into the interplay between metal–organic and covalent bonding in single-layer molecular networks formed by halogen dissociation

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