Jan P. J. M. van der Eerden

Radboud University Nijmegen

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Margot M. E. Snel

Utrecht University

Thijs J. H. Vlugt

Delft University of Technology

Ben de Kruijff

Utrecht University

Hilde A. Rinia

University of Amsterdam

Aneliya N. Zdravkova

Utrecht University

J. Makkinje

Utrecht University

R.A. Demel

Utrecht University

Leonardus W. Jenneskens

Utrecht University

Richard A. Kik

Wageningen University & Research

Dragomir N. Ganchev

Utrecht University

Cooperative Institutions

Utrecht University

Radboud University Nijmegen

University of Amsterdam

Delft University of Technology

Wageningen University & Research

Radboud University Medical Center

Leiden University

Institute for Atomic and Molecular Physics

Heidelberg University

University of Groningen

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Breaking the Intermolecular Hydrogen Bonds in Organic Dimers with Atomic Force Microscopy

Crystal Growth & Design (2001)

Liesbeth I. de Jong − van Steensel Margot M. E. Snel G.J.K. van den Berg Leonardus W. Jenneskens Jan P. J. M. van der Eerden

Microcrystals of 1,1'-bicyclohexyliden-4-one oxime (oxime) were prepared with the spin-coating technique. In these crystals, the oxime molecules form dimers through intermolecular hydrogen bonding. In this orientation, the crystals have a hydrophobic surface. The crystals were imaged with atomic force microscopy (AFM) at three different temperatures, i.e., 16, 20, and 30 °C. We show that it is possible to break the dimeric hydrogen bond with the AFM tip. The force necessary to accomplish this is temperature dependent and increases with decreasing temperature; its magnitude is on the order of the strength of the dimer bond. Breaking of the dimeric hydrogen bonds only occurs near the step edges. In these regions, a clear contrast in friction imaging was observed with lateral force microscopy together with a reduction of the step height to half the original value. We interpreted this as the removal of one layer of oxime molecules resulting in an (oxime-terminated) hydrophilic surface with a higher friction contrast as compared to the normal hydrophobic surface. In this way, the surface properties of the crystals can be tuned. This concept may be applicable to other systems.

10.1021/cg015525x

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Citations (1)

Quantum cutting by cooperative energy transfer inYbxY1−xPO4:

Physical Review B (2005)

Peter Vergeer Thijs J. H. Vlugt Marianne H. F. Kox Martien I. den Hertog Jan P. J. M. van der Eerden

We present experimental evidence for cooperative energy transfer from ${\mathrm{Tb}}^{3+}$ to two ${\mathrm{Yb}}^{3+}$ ions and a determination of the energy-transfer rate. Energy transfer from ${\mathrm{Tb}}^{3+}$ to ${\mathrm{Yb}}^{3+}$ was investigated by luminescence measurements on $({\mathrm{Yb}}_{x}{\mathrm{Y}}_{1\ensuremath{-}x})\mathrm{P}{\mathrm{O}}_{4}$ doped with 1% ${\mathrm{Tb}}^{3+}$. Time-resolved luminescence experiments were analyzed using Monte Carlo simulations based on theories for phonon-assisted, cooperative, and accretive energy transfer. The luminescence decay curves of the $^{5}D_{4}$ emission from ${\mathrm{Tb}}^{3+}$ show an excellent agreement with simulations based on cooperative energy transfer via dipole-dipole interaction, while a phonon-assisted or an accretive energy-transfer mechanism cannot explain the experimental results. The energy-transfer rate to two nearest-neighbor ${\mathrm{Yb}}^{3+}$ ions is $0.26\phantom{\rule{0.3em}{0ex}}{\mathrm{ms}}^{\ensuremath{-}1}$. This corresponds to an upper limit of the energy-transfer efficiency of 88% in $\mathrm{Yb}\mathrm{P}{\mathrm{O}}_{4}$. Application of cooperative energy transfer has prospects for increasing the energy efficiency of crystalline Si solar cells by photon doubling of the high energy part of the solar spectrum.

10.1103/physrevb.71.014119

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COSMO-3D: Incorporating Three-Dimensional Contact Information into the COSMO-SAC Model

Industrial & Engineering Chemistry Research (2015)

Juan José Gutiérrez‐Sevillano Kai Leonhard Jan P. J. M. van der Eerden Thijs J. H. Vlugt Gerard Krooshof

The COSMO-SAC model for the calculation of activity coefficients has been improved by incorporating three-dimensional geometric information on molecules. This information is added to the model by means of the effective contact area of the molecules. We define a procedure to compute this contact area by using a probing sphere. The probing sphere rolls around the COSMO surfaces of two contacting atoms to define a spherical cap on each atom. The segments of the COSMO surfaces within the spherical caps are marked, and the summation of their areas defines the contact area for a pair of contacting molecules. The effective contact areas are used to compute the σ-profiles and the Onsager screening energies in the calculation of the surface activity coefficients, allowing us to remove one parameter from the COSMO-SAC model. The σ-profiles and effective areas need to be calculated only once and can be stored in a database. We show that the new model, named COSMO-3D because some three-dimensional information (the position of surface segments and atom centers in 3D-space) is taken from the COSMO-output files, agrees better with experimental data than the COSMO-SAC implementation for nonpolar and polar mixtures, even though it uses one parameter less. We feel that the new concept of system-dependent effective contact area is a suitable starting point for the further improvement of COSMO-SAC.

Position (finance)

Chemical polarity

Centroid

COSMO-RS

10.1021/ie504285x

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Citations (5)

Contributions to the theory of crystal growth

Jan P. J. M. van der Eerden

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Laminar signal extraction over extended cortical areas by means of a spatial GLM

PLoS ONE (2019)

Tim van Mourik Jan P. J. M. van der Eerden Pierre‐Louis Bazin David G. Norris

There is converging evidence that distinct neuronal processes leave distinguishable footprints in the laminar BOLD response. However, even though the achievable spatial resolution in functional MRI has much improved over the years, it is still challenging to separate signals arising from different cortical layers. In this work, we propose a new method to extract laminar signals. We use a spatial General Linear Model in combination with the equivolume principle of cortical layers to unmix laminar signals instead of interpolating through and integrating over a cortical area: thus reducing partial volume effects. Not only do we provide a mathematical framework for extracting laminar signals with a spatial GLM, we also illustrate that the best case scenarios of existing methods can be seen as special cases within the same framework. By means of simulation, we show that this approach has a sharper point spread function, providing better signal localisation. We further assess the partial volume contamination in cortical profiles from high resolution human ex vivo and in vivo structural data, and provide a full account of the benefits and potential caveats. We eschew here any attempt to validate the spatial GLM on the basis of fMRI data as a generally accepted ground-truth pattern of laminar activation does not currently exist. This approach is flexible in terms of the number of layers and their respective thickness, and naturally integrates spatial regularisation along the cortex, while preserving laminar specificity. Care must be taken, however, as this procedure of unmixing is susceptible to sources of noise in the data or inaccuracies in the laminar segmentation.

Laminar organization

Partial volume

Ground truth

SIGNAL (programming language)

10.1371/journal.pone.0212493

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Citations (35)

Domain Formation in Phosphatidylcholine Bilayers Containing Transmembrane Peptides: Specific Effects of Flanking Residues

Biochemistry (2002)

Hilde A. Rinia Jan-Willem P. Boots Dirk T. S. Rijkers Richard A. Kik Margot M. E. Snel

Lateral segregation in biological membranes leads to the formation of domains. We have studied the lateral segregation in gel-state model membranes consisting of supported dipalmitoylphosphatidylcholine (DPPC) bilayers with various model peptides, using atomic force microscopy (AFM). The model peptides are derivatives of the Ac-GWWL(AL)(n)WWA-Etn peptides (the so-called WALP peptides) and have instead of tryptophans, other flanking residues. In a previous study, we found that WALP peptides induce the formation of extremely ordered, striated domains in supported DPPC bilayers. In this study, we show that WALP analogues with other uncharged residues (tyrosine, phenylalanine, or histidine at pH 9) can also induce the formation of striated domains, albeit in some cases with a slightly different pattern. The WALP analogues with positively charged residues (lysine or histidine at low pH) cannot induce striated domains and give rise to a completely different morphology: they induce irregularly shaped depressions in DPPC bilayers. The latter morphology is explained by the fact that the positively charged peptides repel each other and hence are not able to form striated domains in which they would have to be in close vicinity. They would reside in disordered, fluidlike lipid areas, appearing below the level of the ordered gel-state lipid domains, which would account for the irregularly shaped depressions.

Dipalmitoylphosphatidylcholine

Morphology

10.1021/bi011796x

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Citations (77)

Polythiophenes Containing Oligo(oxyethylene) Side Chains as a Thin Film on a ZnSe Single Crystal Surface

Macromolecular Chemistry and Physics (2005)

Rick van Beek Leonardus W. Jenneskens Aneliya N. Zdravkova Jan P. J. M. van der Eerden Cornelis A. van Walree

Abstract Summary: Two polythiophenes, containing either one (PTT) or two (PBTT) 2,5,8‐trioxanonyl side chains per repeating unit, were synthesized with the objective of developing hybrid inorganic/organic semiconductor systems. From absorption and fluorescence spectroscopy and cyclic voltammetry it appears that introduction of a second 2,5,8‐trioxanonyl side chain on a repeating unit leads to a very short conjugation length. Atomic Force Microscopy (AFM) performed on composites of the two polythiophenes and a ZnSe single crystal reveals excellent wetting of the crystal by the polymers, leading to the formation of thin films. For the PTT/ZnSe composite, good contact between the constituents is substantiated by a red‐shift of the PTT absorption relative to that of PTT on quartz. Fluorescence measurements indicate the occurrence of energy transfer from ZnSe to PTT, which might imply that there is electronic contact between ZnSe and PTT. Because of its highly distorted backbone, neither a significant red‐shift compared with a film on quartz nor excitation energy transfer was found for the thin film of PBTT deposited on ZnSe. Nevertheless, it is shown that the presence of polar 2,5,8‐trioxanonyl side chains guarantees strong binding of polythiophenes to the ZnSe surface. AFM contact mode topographical image of a PBTT film cast onto a ZnSe single crystal. magnified image AFM contact mode topographical image of a PBTT film cast onto a ZnSe single crystal.

Side chain

Crystal (programming language)

10.1002/macp.200500055

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Adsorption Selectivity of Benzene/Propene Mixtures for Various Zeolites

The Journal of Physical Chemistry C (2007)

Shuai Ban Adri van Laak Petra E. de Jongh Jan P. J. M. van der Eerden Thijs J. H. Vlugt

The nine-site benzene model of Zhao et al. (J. Phys. Chem. B 2005, 109, 5368−5374) has been used to systematically study the adsorption of benzene, propene, and benzene−propene mixtures in zeolites mordenite, Y, β, silicalite, and MCM22. Interaction parameters for the benzene−zeolite interactions have been fitted to available adsorption experiments from literature. As an independent check of our force field, we have performed additional adsorption experiments using the TEOM technique and excellent agreement between simulations and TEOM experiments was found. High adsorption selectivities for benzene in benzene−propene mixtures were found in all zeolites, except for silicalite.

Propene

Mordenite

10.1021/jp074918p

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Citations (39)

Introduction to Molecular Simulation and Statistical Thermodynamics

Thijs J. H. Vlugt Jan P. J. M. van der Eerden Marjolein Dijkstra Bram de Smit Daan Frenkel

Statistical Thermodynamics and Molecular Simulation aim at describing the properties of systems that consist of many individual particles (atoms, molecules). Although the properties of the complete system follow directly from the properties and interactions of the individual particles, usually these properties cannot be calculated directly by using pen and paper only. Computer simulations are a convenient and modern tool to actually calculate these properties. These so-called molecular simulations are widely used in the field of chemistry and physics to (1) predict properties of existing or new materials, (2) predict new phenomena, which may lead to new experiments and the development of new theories (3) test approximate theories for these systems. Our book is organized into two parts. In Part I, the concepts of statistical thermodynamics are illustrated with simple computer simulations. These concepts (for example the second law of thermodynamics) can be quite abstract for beginning students. Our teaching experience is that computer simulations are an excellent tool for understanding these concepts. This part of the book is specifically aimed at the bachelor level. In Part II, the basics of molecular simulations are explained based on the concepts that were introduced in Part I. It is shown how these simulations can be used to calculate properties of systems of interacting molecules. This part of the book is specifically aimed at the master level. A beginning master student with some basic knowledge of classical thermodynamics will be able to start with Part II of the book.

Statistical Mechanics

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Peptide Aggregation in Lipid Bilayers — Is the Peptide Really in the Striated Domains?

Single Molecules (2002)

Dragomir N. Ganchev Margot M. E. Snel Jan P. J. M. van der Eerden Ben de Kruijff

In order to elucidate the structure and function of biomembranes, it is useful to investigate interactions between lipids and proteins, which are the main building blocks of all biological membranes. Supported lipid/peptide bilayers, which can be prepared, using established protocols, are a widely used model system to perform these investigations. Atomic Force Microscopy (AFM) offers a unique possibility to investigate these supported bilayers under physiological conditions (in water environment). We (H. Rinia et al., Biochemistry, 2000, 39, 5852-5858) previously found that synthetic transmembrane peptides self organize in highly characteristic striated domains in supported gel state bilayer. The precise morphology of the domains depends on the type of peptide and lipid. In the present study we attempt to localize the peptide in these domains by AFM using Au particles (app. 10 nm.) and thiol containing peptides. These peptides were also found to form striated domains. We also showed by Dynamic Light Scattering experiments that thiol group of a peptide, incorporated in a bilayer is available for reaction with gold. After addition of the gold particles over the supported bilayer we observe with contact mode AFM the presence of gold particles predominantly over domains and cracks, connecting them.

10.1002/1438-5171(200206)3:2/3<163::aid-simo163>3.0.co;2-k

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