First-principle study of the hydrogen bonds in a thin film of phthalocyanine molecules

Oison, Vincent

doi:10.1016/j.susc.2006.11.054

Cited by 8 publications

(12 citation statements)

References 34 publications

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“…It is worthy to point out that the larger is the number of molecules the sharper is the first order transition and good are the statistics. An ultimate point within this preliminary work is that the intermolecular potential energy is around 20-30 kJ.mol -1 , which is of the order of magnitude binding energies reported for a square phase 61 . More importantly, the 2D-GCMC approach demonstrates its ability to optimize the intermolecular and interfacial properties right after the transition and appears as an efficient numerical tool to look for the most probable configurations at a given temperature.…”

Section: The 2d Grand-canonical Monte-carlo Approachmentioning

confidence: 74%

“…Our interest for this molecule is also for its highly-ordered phases when co-adsorbed on Ag (111) with the aforementioned ZnPcCl 8 66,67 . The following figure shows Oblique packing was reported when fluorinated copper-phthalocyanines molecules are deposited on copper and gold (111) surfaces 68 . The atomic molecular structure of CuPcF 16 is extracted from DFT calculations 69 . We compute the GCMC simulations at 300K on a small simulation box of 30.6 x 26.5 nm 2 .…”

Section: Methods Transferabilitymentioning

confidence: 99%

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Modeling the Self-Assembly of Nano Objects: Applications to Supramolecular Organic Monolayers Adsorbed on Metal Surfaces

Roussel

Vega

2013

J. Chem. Theory Comput.

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We present here the implementation of a code developed for the simulation of the self-assembly of nano objects (SANO). The code has the ability to predict the molecular self-assembly of different structural motifs by tuning the molecular building blocks as well as the metallic substrate. It consists in a two-dimensional grand canonical Monte Carlo (GCMC) approach developed to perform atomistic simulations of thousands of large organic molecules self-assembling on metal surfaces. By computing adsorption isotherms at room temperature and spanning over the characteristic submicrometric scales, we confront the robustness of the approach with three different well-known systems: ZnPcCl8 on Ag(111), CuPcF16 on Au(111), and PTBC on Ag(111). We retrieve respectively their square, oblique, and hexagonal supramolecular tilling. The code incorporates generalized force fields to describe the molecular interactions, which provides transferability to many organic building blocks and metal surfaces. Ultimately, the method is versatile and can be an interesting multiscale approach if one aims to bridge quantum level calculations to the experimental scales and within a treatment in temperature.

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Section: The 2d Grand-canonical Monte-carlo Approachmentioning

confidence: 74%

Section: Methods Transferabilitymentioning

confidence: 99%

Modeling the Self-Assembly of Nano Objects: Applications to Supramolecular Organic Monolayers Adsorbed on Metal Surfaces

Roussel

Vega

2013

J. Chem. Theory Comput.

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“…The electron wave functions were expanded in a plane wave basis set using a 70 Ry cutoff energy. The PBE‐GGA exchange correlation scheme was chosen because of its excellent performance in hydrogen bond description 35–40. The Brillouin zone was sampled by a 1 × 2 × 4 Monkhorst‐Pack mesh 41…”

Section: Methodsmentioning

confidence: 99%

Ab Initio Based conformational study of the crystalline α‐chitin

Petrov¹,

Lymperakis²,

Friák³

et al. 2012

Biopolymers

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The equilibrium structure including the network of hydrogen bonds of an α-chitin crystal is determined combining density-functional theory (DFT), self-consistent DFT-based tight-binding (SCC-DFTB), and empirical forcefield molecular dynamics (MD) simulations. Based on the equilibrium geometry several possible crystal conformations (local energy minima) have been identified and related to hydrogen bond patterns. Our results provide new insight and allow to resolve the contradicting α-chitin structural models proposed by various experiments.

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“…A theoretical study based on density functional theory ͑DFT͒ calculations shows how a conformational change of this molecule makes possible this hexagonal packing. DFT represents a unique tool for the analysis of molecular self-assemblies, in particular when hydrogen bonds are involved [11][12][13] and also for a realistic study of molecule-surface interactions. 14,15 Figure 1 shows the three different metastable conformers of THQ studied in this paper: conformations 1 and 2 are obtained by the rotation in the molecular plane of one or two hydroxyl groups ͑-OH͒, respectively.…”

Section: Introductionmentioning

confidence: 99%

Conformational change of tetrahydroxyquinone molecules deposited on Ag(111)

et al. 2008

Self Cite

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We report a joint experimental and theoretical study of the deposition of tetrahydroxyquinone ͑THQ͒ molecules on a Ag͑111͒ surface. Scanning tunneling microscopy and low-energy electron diffraction experiments at room temperature reveal the formation of large two-dimensional domains composed of flat-lying molecules which match exactly with the surface network. Density functional theory calculations give evidence of an original self-assembly process in which the molecules have to change their conformation to self-assemble on the Ag͑111͒ surface. The intermolecular and molecule-substrate interactions are studied by electron density topology. This reveals the formation of strong O-H¯O hydrogen bonds between adjacent molecules and Ag¯O bonds between molecule and substrate, inducing a large charge transfer from the surface to the lowest unoccupied molecular orbital of THQ.

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First-principle study of the hydrogen bonds in a thin film of phthalocyanine molecules

Cited by 8 publications

References 34 publications

Modeling the Self-Assembly of Nano Objects: Applications to Supramolecular Organic Monolayers Adsorbed on Metal Surfaces

Modeling the Self-Assembly of Nano Objects: Applications to Supramolecular Organic Monolayers Adsorbed on Metal Surfaces

Ab Initio Based conformational study of the crystalline α‐chitin

Conformational change of tetrahydroxyquinone molecules deposited on Ag(111)

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