Modeling the Self-Assembly of Organic Molecules in 2D Molecular Layers with Different Structures

Lit, Joost van der; Marsman, Jolien L.; Koster, Rik S.; Jacobse, Peter H.; Hartog, Stephan A. den; Vanmaekelbergh, Daniël; Gebbink, Robertus J. M. Klein; Filion, Laura; Swart, Ingmar

doi:10.1021/acs.jpcc.5b09889

Cited by 23 publications

(16 citation statements)

References 41 publications

(65 reference statements)

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“…The self-arrangement of matter and self-assembly of a complex of biomolecular structures is one of the most important and intriguing phenomena in animate and inanimate nature, and is constantly in the focus of attention of researchers in various directions [1][2][3][4][5]. Of no less interest is computer assisted molecular modelling of the self-organization processes of molecular systems at different levels and by different methods [6][7][8][9][10].…”

Section: Introductionmentioning

confidence: 99%

Chiral Peculiar Properties of Self-Organization of Diphenylalanine Peptide Nanotubes: Modeling Of Structure and Properties

Bystrov¹,

Zelenovskiy²,

Nuraeva³

et al. 2019

Math.Biol.Bioinf.

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The structure and properties of diphenylalanine peptide nanotubes based on phenylalanine were investigated by various molecular modeling methods. The main approaches were semi-empirical quantum-chemical methods (PM3 and AM1), and molecular mechanical ones. Both the model structures and the structures extracted from their experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by naturally-occurring self-assembly showed their important differences depending on D- and L-chirality. In both the cases, the effect of chirality on the results of self-assembly of diphenylalanine peptide nanotubes was established: peptide nanotubes based on the D-diphenylalanine (D-FF) has high condensation energy E0 in transverse direction and forms thicker and shorter peptide nanotubes bundles, than that based on L-diphenylalanine (L-FF). A topological difference was established: model peptide nanotubes were optimized into structures consisting of rings, while naturally self-assembled peptide nanotubes consisted of helical coils. The latter were different for the original L-FF and D-FF. They formed helix structures in which the chirality sign changes as the level of the macromolecule hierarchy raises. Total energy of the optimal distances between two units are deeper for L-FF (–1.014 eV) then for D-FF (–0.607 eV) for ring models, while for helix coil are approximately the same and have for L-FF (–6.18 eV) and for D-FF (–6.22 eV) by PM3 method; for molecular mechanical methods energy changes are of the order of 2–3 eV for both the cases. A topological transition between a ring and a helix coil of peptide nanotube structures is discussed: self-assembled natural helix structures are more stable and favourable, they have lower energy in optimal configuration as compared with ring models by a value of the order of 1 eV for molecular mechanical methods and 5 eV for PM3 method.

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Section: Introductionmentioning

confidence: 99%

Chiral Peculiar Properties of Self-Organization of Diphenylalanine Peptide Nanotubes: Modeling Of Structure and Properties

Bystrov¹,

Zelenovskiy²,

Nuraeva³

et al. 2019

Math.Biol.Bioinf.

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“…An alternative approach which enables facile optimization of molecular systems on surfaces are the computer simulations [9,11,[24][25][26][27][28][29][30][31]. This technique is particularly useful, as it makes it possible to study readily the effect of intrinsic molecular properties on the corresponding superstructures formed under variable conditions (e.g.…”

Section: Introductionmentioning

confidence: 99%

Dichotomous On-Surface Self-Assembly of Tripod Molecules with Anchor Like Interaction Pattern

2018

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Recent development of methods to fabricate low dimensional molecular structures has enabled tailoring their architecture using building blocks with suitably encoded structural and chemical properties. In this contribution we study structure formation in adsorbed assemblies comprising model tripod molecules equipped with terminal arm segments providing short-range directional interactions. The interaction directions were assigned in a specific anchor like pattern which enabled the creation of diverse intermolecular connections. To explore the on-surface self-assembly of these functional units the coarse grained lattice Monte Carlo simulation method was used in which the molecules were represented as collections of interconnected segments adsorbed on a triangular lattice. Our theoretical investigations focus on the effect of symmetry and size of molecular backbone on the outcome of the 2D self-assembly. The simulations revealed the formation of complex superstructures of two types including porous networks with diverse nanocavities and nanoribbons characterized by a constant width. Occurrence of these different assemblies was found to be strongly dependent on the molecular symmetry and aspect ratio, highlighting the decisive role of the arm length distribution in the tripod building block. The theoretical results of this study can be helpful in designing new low-dimensional superstructures which are stabilized be weak intermolecular interactions as well as by covalent bonds formed in on-surface reactions such as the Ullmann coupling.

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“…1 Among these nanomaterials, the 2D supramolecule is made up of one or several types of molecules through the selfassembly process, which forms an ultra-thin lm on a substrate. 2,3 The self-assembled 2D supramolecule nanostructure is generally monotonic and its pattern is also straightforward to control. Accordingly, different 2D supramolecules have been extensively used in many elds, such as for anticancer drug delivery, 4,5 gene delivery, photothermal therapy (PTT), photodynamic therapy (PDT), biosensing, and regenerative medicine.…”

Section: Introductionmentioning

confidence: 99%

Observing the three-dimensional terephthalic acid supramolecular growth mechanism on a stearic acid buffer layer by molecular simulation methods

Chen

Sun

et al. 2020

RSC Adv.

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Modeling the Self-Assembly of Organic Molecules in 2D Molecular Layers with Different Structures

Cited by 23 publications

References 41 publications

Chiral Peculiar Properties of Self-Organization of Diphenylalanine Peptide Nanotubes: Modeling Of Structure and Properties

Chiral Peculiar Properties of Self-Organization of Diphenylalanine Peptide Nanotubes: Modeling Of Structure and Properties

Dichotomous On-Surface Self-Assembly of Tripod Molecules with Anchor Like Interaction Pattern

Observing the three-dimensional terephthalic acid supramolecular growth mechanism on a stearic acid buffer layer by molecular simulation methods

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