Molecular dynamics simulations of ordered alkane chains physisorbed on graphite

Hentschke, Reinhard; Schürmann, Britta L.; Rabe, Jürgen P.

doi:10.1063/1.462612

Cited by 216 publications

(93 citation statements)

References 29 publications

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“…nearly parallel to the HOPG substrate h1120i lattice vector, as has been observed for the SAMs of pure alkanes (65)(66)(67)(68). These calculations and all measurements also indicate that the SAMs are incommensurate with the substrate lattice (49,51), and Table 1 shows good agreement between the observed and calculated SAM lattice parameters.…”

Section: Identification Of Sam Atomic Structures By Comparison Of Obssupporting

confidence: 68%

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.

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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Section: Identification Of Sam Atomic Structures By Comparison Of Obssupporting

confidence: 68%

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.

110

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“…ref. 33 ), detailed studies started to appear more recently in the context of molecular association in solutions, 34 molecular adsorption from solutions, 35 formation of ordered monolayers at surfaces, 15 and understanding temperature programmed desorption (TPD) experiments. 36 The experimentally measured enthalpies and entropies of adsorption of relatively small molecules on oxide surfaces have been summarized in ref.…”

Section: 32mentioning

confidence: 99%

Calculating the Entropy Loss on Adsorption of Organic Molecules at Insulating Surfaces

et al. 2016

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Although it is recognized that dynamic behavior of adsorbing molecules strongly affects the entropic contribution to adsorption free energy, detailed studies of the adsorption entropy of large organic molecules at insulating surfaces are still rare. We compared adsorption of two different functionalized organic molecules, 1,3,5-tri-(4-cyano-4,4 biphenyl)-benzene (TCB) and 1,4-bis(cyanophenyl)-2,5-bis(decyloxy)benzene (CDB), on the KCl (001) surface using density functional theory (DFT) and molecular dynamics (MD) simulations. The accuracy of the van der Waals corrected DFT-D3 was benchmarked using Møller-Plesset perturbation theory calculations. Classical force fields were then parameterized for both the TCB and CDB molecules on the KCl (001) surface. These force fields were used to perform potential of mean force (PMF) calculations of adsorption of individual molecules and extract information on the entropic contributions to adsorption energy. The results demonstrate that entropy losses upon adsorption are significant for flexible molecules, such as considered here, and even at relatively low temperatures (e.g. 400 K) can match the enthalpy contribution to adsorption energy.

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“…The formation of these microcrystallite assemblies along the characteristic directions of the HOPG basal surface arises from the initial interplay between alkane-alkane interactions (crystallization energy) and alkane-graphite interactions (adsorption energy), forming primary multilayered lamellae in a physically adsorbed state signifying epitaxial growth. The formation of orientated alkane mono-and multilayered lamellae has been studied extensively by both experimental (STM, AFM) (Hentschke et al 1992;Godovsky & Magonov 2000;Yin et al 2001;Magonov & Yerina 2003;Nečas & Klapetek 2012) and theoretical (MD, DFT) (Yang et al 2008) techniques. Hydrocarbon molecules have been shown to order themselves parallel to the graphitic basal plane, with the zigzag alkane chain lying either flat or vertical with the -CH 2 -hydrogens above the graphitic hexagon ( Figure 1c).…”

Section: Resultsmentioning

confidence: 99%

Bacterial patterning at the three-phase line of contact with microtextured alkanes

et al. 2015

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Aliphatic crystallites, characteristic of the eicosane and docosane components of naturally occurring lipids, were found to form microtextures that were structured by specific interactions with ordered graphite (HOPG) used as the underlying substratum, as confirmed by scanning electron microscopy (SEM) and fast Fourier transform (FFT) analysis. Confocal scanning laser microscopy (CLSM) showed highly directed bacterial alignment for two bacterial species (spherical and rod-shaped), reflecting the preferential orientation of the crystallite-air-water interfaces to give linear and triangular bacterial patterning. The mechanisms of bacterial attachment are demonstrated in terms of the balance between effective radial adhesional forces and the capillary forces resulting from the water contact angle of the bacteria at the three-phase line (TPL) of the lipid surface. It is suggested that these microtextured surfaces, which exhibit the ability to limit bacterial adhesion to a precise patterning at the lipid TPL, could be used as a means of controlling bacterial colonization.

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Molecular dynamics simulations of ordered alkane chains physisorbed on graphite

Cited by 216 publications

References 29 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

Calculating the Entropy Loss on Adsorption of Organic Molecules at Insulating Surfaces

Bacterial patterning at the three-phase line of contact with microtextured alkanes

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