Polymorphism in porphyrin monolayers: the relation between adsorption configuration and molecular conformation

Coenen, Michiel J. J.; Boer, Duncan den; Bruele, Fieke J. van den; Habets, Thomas; Timmers, Koen A. A. M.; Maas, Minko van der; Khoury, Tony; Panduwinata, Dwi; Crossley, Maxwell J.; Reimers, Jeffrey R.; Enckevort, W.J.P. van; Hendriksen, Bas L. M.; Elemans, Johannes A. A. W.; Speller, S.

doi:10.1039/c3cp50829c

Cited by 20 publications

(41 citation statements)

References 41 publications

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“…Different 2D polymorphs of Cu−C 11 P have been produced by varying the porphyrin concentration in the supernatant solution, with higher-coverage polymorphs forming at higher solution concentrations (51,52). Increasing the porphyrin concentration once a SAM has formed brings about dynamic changes to the SAM only around defects, however, indicating that the SAMs are kinetically trapped, and this trapping takes only seconds to manifest after first application of the solution to the substrate.…”

mentioning

confidence: 99%

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

Reimers

Panduwinata

Visser

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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110

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Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorphdependent dispersion-induced substrate−molecule interactions (e.g., −100 kcal mol −1 to −150 kcal mol −1 for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol −1 ) and entropy effects (25-40 kcal mol −1 at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.self-assembled monolayers | density functional theory | dispersion | free energy | polymorphism A priori calculations of the free energies of chemical reactions using density functional theory (DFT) and/or ab initio methods are now well established for gas-phase processes (1, 2), gas surface reactions (3), and, using continuum self-consistent reaction field (SCRF) methods, for condensed phase processes also (4). Over the last few years, a major advance in computational methods has occurred, however, allowing for rapid and accurate evaluation of intermolecular dispersion interactions. This makes feasible similar SCRF calculations for physisorption, macromolecule structuring, and other self-assembly processes in condensed phases. We present the first application of this type, to our knowledge, considering the free energy of formation of various polymorphs of tetraalkylporphyrin self-assembled monolayers (SAMs) at solid/liquid interfaces on highly ordered pyrolytic graphite (HOPG) surfaces. Calculated structures and free energies are used to interpret new and existing high-resolution scanning tunneling microscopy (STM) images, focusing on the critical roles played by the dispersion interaction in driving SAM formation and by entropy and dispersion-based desolvation effects that oppose it.Calculating a priori free energies for SAM formation from solution is a significant challenge. Accurate representations of the substrate−molecule energies, the intermolecular energies, the solvent interaction energies, and the effects of solvent structure are required, a set of tasks that, with a few exceptions (see e.g., refs. 5 and 6), has remained prohibitive a priori. Alternatively, model calculations have been useful for identifying key qualitative features (7-11), whereas some full molecular dynamics si...

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mentioning

confidence: 99%

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

Reimers

Panduwinata

Visser

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

110

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“…These domain boundaries provide a lot of structural information and their analysis greatly aids the determination of atomic structures representing STM images. Initially, [115] the central L phase of the Cu-C 11 P polymorph shown in Fig. 4 was attributed to a different polymorph then label "B" as its lattice parameters differed appreciably from those of the large domains of L. However, PBE-D3 and QM/MM calculations revealed that the potential-energy surface is very flat in the direction that causes this shift.…”

Section: Rationalizing Interface Structuresmentioning

confidence: 98%

“…[87,88,113,115,116,117,118,119] Relaxing this constraint allows much better fits to be made to the vector lengths, resulting in an overall lower energy penalty for commensurate-lattice production. Table 1 gives the QM/MM optimized lattice parameters defined in Fig.…”

Section: Incommensurate Sam and Substrate Latticesmentioning

confidence: 99%

“…Atomically smooth interface boundaries between regions containing different SAM polymorphs can often be observed in experiments [87,115] The challenge to be able to perform full free-energy calculations and optimize the structure using 1D periodic boundary conditions is an important one as the molecular configurations can be flexible in certain specific ways, facilitating smooth interfaces forming between differently aligned SAM domains. These domain boundaries provide a lot of structural information and their analysis greatly aids the determination of atomic structures representing STM images.…”

Section: Rationalizing Interface Structuresmentioning

confidence: 99%

“…[87,88,113,115,116,117,118,119] This poses a serious technical challenge as electronic-structure computational methods treat surfaces using periodic boundary conditions, therefore demanding that the two lattices (or multiples thereof) be commensurate. The QM/MM calculations overcome this problem as the MM force field only is used for the intermolecular interactions and these are so efficient that a large real-space sum can be performed, including interactions up to very large distances.…”

Section: Introductionmentioning

confidence: 99%

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Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism

Reimers

Ford

Goerigk

2015

Molecular Simulation

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Externally Applied Manipulation of Molecular Assemblies at Solid‐Liquid Interfaces Revealed by Scanning Tunneling Microscopy

Elemans¹

2016

Adv Funct Materials

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A solid-liquid interface is a unique environment for the construction of twodimensional molecular assemblies as a bottom-up approach towards functional surfaces. Scanning tunneling microscopy (STM) has proven itself as an excellent tool to characterize such surfaces at the molecular level, by means of visualization. Many rules of design for surface, solvent and chemical structure of the adsorbants have been established, but methods to externally manipulate surface assemblies after their formation are still under development. This feature article deals with these manipulation methods at the solid-liquid interface and evaluates, at the molecular level, the effects of temperature variation, irradiation with light, applied electric or magnetic fields, mechanical manipulation with the STM tip, and shear flow of the liquid phase.

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Polymorphism in porphyrin monolayers: the relation between adsorption configuration and molecular conformation

Cited by 20 publications

References 41 publications

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism

Externally Applied Manipulation of Molecular Assemblies at Solid‐Liquid Interfaces Revealed by Scanning Tunneling Microscopy

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