Thermodynamics of self-assembled molecular layers of trimesic acid from fields-supported kinetic Monte Carlo simulation

Ustinov, E. A.; Горбунов, В. А.; Akimenko, S. S.

doi:10.1039/d2cp03380a

Cited by 6 publications

(22 citation statements)

References 58 publications

(121 reference statements)

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“…The off-lattice models are much more demanding on computational resources and, as a rule, slowly converge to the equilibrium state. Over the past two decades, the off-lattice models of various levels of coarse-graining have been being used to describe the adsorption layers of functional organic molecules. − Continuous models of SMONs are much less common. In a recent work, Baran had studied how the metal/ligand ratio and size of the coordinating metal center affect the self-assembly of SMONs containing linear linker molecules.…”

Section: Introductionmentioning

confidence: 99%

Off-Lattice Coarse-Grained Model of Surface-Confined Metal–Organic Architectures

2023

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An off-lattice model of self-assembling surface-confined metal–organic nanostructures (SMONs) comprising tripod molecules has been developed. The model considers the directionality and saturability of coordination bonding. To parametrize the model, density functional theory methods have been used. Self-assembly of the SMONs has been simulated with Metropolis Monte Carlo method in the canonical ensemble. In this paper, we investigate how the directionality of metal–linker bonding and the linker/metal ratio affect the self-assembly of SMONs containing metal centers with different coordination numbers: M(II), M(III), and M(IV). The directionality of coordination bonding is determined by the functional group of the linker molecule and is defined in the model as the angular diameter of the interaction shell. Regardless of the preferred coordination number of the metal center, even a small change in the angular diameter significantly affects the structure of the SMONs. Depending on the angular diameter and composition of the metal–organic layer, various structures can appear. Using our model, we have simulated the self-assembly of the random porous (or defected honeycomb) and triangular structures, the set of hexagonal phases, amorphous structures of different densities, and metal–organic chains. Relative thermal stabilities of clusters of the main structures have been studied. The model reproduces correctly the main SMONs observed by scanning tunneling microscopy.

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Section: Introductionmentioning

confidence: 99%

Off-Lattice Coarse-Grained Model of Surface-Confined Metal–Organic Architectures

2023

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“…The damping field depends only on the x coordinate of a molecule according to the formula that we had developed in our previous study. 24 There is a step at the l 0 level in the transition zone of the elongated cell. The value of l 0 is chosen to reproduce the required effective temperature T* = l 0 T in the transition zone, where T is the absolute temperature in the crystal.…”

Section: B Damping and External Fieldsmentioning

confidence: 99%

“…The simulation was carried out in a rectangular cell with the linear sizes L x and L y using the Field(s) supported MultiPhase kinetic Monte Carlo (FsMP/kMC) method in a canonical ensemble. 24 Let us briefly describe how we construct the simulation cell and main details of the simulation technique used in this work.…”

Section: Details Of Kinetic Monte Carlo Simulationmentioning

confidence: 99%

“…Previously, we calculated the entropy and free energy for both structures using the FsMP/kMC method and showed that such a transition is entropy driven. 24 In addition, the formation of the dense ''superflower'' structure is not experimentally observed in the TMA layer on the homogeneous graphite surface. Instead, the chicken-wire structure, in which twodimensional (2D) pores are filled with extra TMA molecules, appears.…”

Section: Introductionmentioning

confidence: 99%

“…We used various versions of this approach to describe van der Waals interactions in the simplified models of the trimesic acid (TMA) layer. [21][22][23][24] The previously proposed FsMP/kMC (Fields-supported MultiPhase kinetic Monte Carlo) method was applied to these simplified models and allowed us to calculate the thermodynamic functions of the TMA layer. The simulation data were used to analyze temperature and concentration phase transitions.…”

Section: Introductionmentioning

confidence: 99%

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Equilibrium structure of a dense trimesic acid monolayer on a homogeneous solid surface: from atomistic simulation to thermodynamics

Akimenko,

Gorbunov,

Ustinov

2023

Phys. Chem. Chem. Phys.

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Toward Molecular Fractals on Surfaces: Designing Covalent Structures with the Monte Carlo Simulation Method

Szabelski,

Lisiecki

2023

J. Phys. Chem. C

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Deterministic fractals have long been considered abstract objects with unique structural properties, and their experimental realization by systematic molecular design has been achieved only recently. In this contribution, we demonstrate how the coarse-grained Monte Carlo modeling can be used to predict and optimize the formation of the fractal Sierpinśki-type triangular metal−organic precursors on solid substrates. To that end, a mixture of suitably functionalized polyaromatics differing in size/ shape and bivalent metal atoms adsorbed on a (111) crystalline surface was modeled. These theoretical investigations focused on the surface-assisted self-assembly of labile precursor architectures preceding the covalent linkage of halogenated aryl monomers in Ullmann-type coupling reactions. Our calculations aimed at the identification of all of the isomers from a large group of candidate units capable of forming fractal triangles and classification of these superstructures. With the collected data, it was possible to extract common molecular features, which made the diverse building blocks able to create topologically identical self-assembled constructs. As a result, we formulated a set of elementary prerequirements that have to be met by an arbitrary functional unit to create the Sierpinśki triangles sustained by 2-fold metal−organic nodes (and subsequent covalent bonds). Our findings are quite general and can be applied to various molecular tectons equipped with active groups providing directional interactions of other types (e.g., hydrogen bonding). This information can be helpful in the design and fabrication of new persistent fractal macromolecules with yet unexplored physicochemical properties.

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Thermodynamics of self-assembled molecular layers of trimesic acid from fields-supported kinetic Monte Carlo simulation

Abstract: A technique has been developed for calculating the thermodynamic characteristics of rigid self-assembled organic adsorption layers and the parameters of polymorphic transitions using two types of external fields and the kinetic Monte Carlo method.

Cited by 6 publications

References 58 publications

Off-Lattice Coarse-Grained Model of Surface-Confined Metal–Organic Architectures

Off-Lattice Coarse-Grained Model of Surface-Confined Metal–Organic Architectures

Equilibrium structure of a dense trimesic acid monolayer on a homogeneous solid surface: from atomistic simulation to thermodynamics

Toward Molecular Fractals on Surfaces: Designing Covalent Structures with the Monte Carlo Simulation Method

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