Publications by authors named "Christian R Wick"

9 Publications

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Structural characterization of an ionic liquid in bulk and in nano-confined environment using data from MD simulations.

Data Brief 2020 Feb 23;28:104794. Epub 2019 Nov 23.

Group for Computational Life Sciences, Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia.

This article contains data on structural characterization of the [C2Mim][NTf2] in bulk and in nano-confined environment obtained using MD simulations. These data supplement those presented in the paper "Insights from Molecular Dynamics Simulations on Structural Organization and Diffusive Dynamics of an Ionic Liquid at Solid and Vacuum Interfaces" [1], where force fields with three different charge methods and three charge scaling factors were used for the analysis of the IL in the bulk, at the interface with the vacuum and the IL film in the contact with a hydroxylated alumina surface. Here, we present details on the construction of the model systems in an extended detailed methods section. Furthermore, for best parametrization, structural and dynamic properties of IL in different environment are studied with certain features presented herein.
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http://dx.doi.org/10.1016/j.dib.2019.104794DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6909096PMC
February 2020

Insights from molecular dynamics simulations on structural organization and diffusive dynamics of an ionic liquid at solid and vacuum interfaces.

J Colloid Interface Sci 2019 Oct 6;553:350-363. Epub 2019 Jun 6.

Group of Computational Life Sciences, Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; PULS Group, Center for Nanostructured Films, Department of Physics, FAU Erlangen-Nürnberg, Cauerstraße 3, 91058, Erlangen, Germany. Electronic address:

Hypothesis: A reliable modelling approach is required for simultaneous characterisation of static and dynamic properties of bulk and interfacial ionic liquids (ILs). This is a prerequisite for a successful investigation of experimentally inaccessible, yet important properties, including those that change significantly with the distance from both vacuum and solid interfaces.

Simulations: We perform molecular dynamics simulations of bulk [CMim][NTf], and thick IL films in contact with vacuum and hydroxylated sapphire surface, using the charge methods CHelpG, RESP-HF and RESP-B3LYP with charge scaling factors 1.0, 0.9 and 0.85.

Findings: By determining and employing appropriate system sizes and simulations lengths, and by benchmarking against self-diffusion coefficients, surface tension, X-ray reflectivity, and structural data, we identify RESP-HF/0.9 as the best non-polarizable force field for this IL. We use this optimal parametrisation to predict novel physical properties of confined IL films. First we fully characterise the internal configurations and orientations of IL molecules relative to, and as a function of the distance from the solid and vacuum interfaces. Second, we evaluate densities together with mobilities in-plane and normal to the interfaces and find that strong correlations between the IL's stratification and diffusive transport in the interfacial layers persist for several nanometres deep into IL films.
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http://dx.doi.org/10.1016/j.jcis.2019.06.017DOI Listing
October 2019

Mechanism of the Water-Gas Shift Reaction Catalyzed by Efficient Ruthenium-Based Catalysts: A Computational and Experimental Study.

Angew Chem Int Ed Engl 2019 Jan 12;58(3):741-745. Epub 2018 Dec 12.

Group of Computational Life Sciences, Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia.

Supported ionic liquid phase (SILP) catalysis enables a highly efficient, Ru-based, homogeneously catalyzed water-gas shift reaction (WGSR) between 100 °C and 150 °C. The active Ru-complexes have been found to exist in imidazolium chloride melts under operating conditions in a dynamic equilibrium, which is dominated by the [Ru(CO) Cl ] complex. Herein we present state-of-the-art theoretical calculations to elucidate the reaction mechanism in more detail. We show that the mechanism includes the intermediate formation and degradation of hydrogen chloride, which effectively reduces the high barrier for the formation of the requisite dihydrogen complex. The hypothesis that the rate-limiting step involves water is supported by using D O in continuous catalytic WGSR experiments. The resulting mechanism constitutes a highly competitive alternative to earlier reported generic routes involving nucleophilic addition of hydroxide in the gas phase and in solution.
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http://dx.doi.org/10.1002/anie.201811627DOI Listing
January 2019

A Fluorescent Benzo[g]isoquinoline-Based HIF Prolyl Hydroxylase Inhibitor for Cellular Imaging.

ChemMedChem 2019 01 21;14(1):94-99. Epub 2018 Dec 21.

Department of Chemistry and Pharmacy, Inorganic and Organometallic Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058, Erlangen, Germany.

Prolyl hydroxylation domain (PHD) enzymes catalyze the hydroxylation of the transcription factor hypoxia-inducible factor (HIF) and serve as cellular oxygen sensors. HIF and the PHD enzymes regulate numerous potentially tissue-protective target genes which can adapt cells to metabolic and ischemic stress. We describe a fluorescent PHD inhibitor (1-chloro-4-hydroxybenzo[g]isoquinoline-3-carbonyl)glycine which is suited to fluorescence-based detection assays and for monitoring PHD inhibitors in biological systems. In cell-based assays, application of the fluorescent PHD inhibitor allowed co-localization with a cellular PHD enzyme and led to live cell imaging of processes involved in cellular oxygen sensing.
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http://dx.doi.org/10.1002/cmdc.201800483DOI Listing
January 2019

On bond-critical points in QTAIM and weak interactions.

J Mol Model 2018 May 31;24(6):142. Epub 2018 May 31.

Computer-Chemistry Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstrasse 25, 91052, Erlangen, Germany.

Bond critical points (BCPs) in the quantum theory of atoms in molecules (QTAIM) are shown to be a consequence of the molecular topology, symmetry, and the Poincaré-Hopf relationship, which defines the numbers of critical points of different types in a scalar field. BCPs can be induced by a polarizing field or by addition of a single non-bonded atom to a molecule. BCPs and their associated bond paths are therefore suggested not to be a suitable means of identifying chemical bonds, or even attractive intermolecular interactions. Graphical abstract Bond-critical points in QTAIM and weak interactionsᅟ.
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http://dx.doi.org/10.1007/s00894-018-3684-xDOI Listing
May 2018

Modeling the Reactions Catalyzed by Coenzyme B Dependent Enzymes: Accuracy and Cost-Quality Balance.

J Phys Chem A 2018 Feb 7;122(6):1747-1755. Epub 2018 Feb 7.

Division of Physical Chemistry, Group for Computational Life Sciences, Ruđer Bošković Institute , Bijenička cesta 54, 10000 Zagreb, Croatia.

The reactions catalyzed by coenzyme B dependent enzymes are formally initiated by the homolytic cleavage of a carbon-cobalt bond and a subsequent or concerted H-atom-transfer reaction. A reasonable model chemistry for describing those reactions should, therefore, account for an accurate description of both reactions. The inherent limitation due to the necessary system size renders the coenzyme B system a suitable candidate for DFT or hybrid QM/MM methods; however, the accurate description of both homolytic Co-C cleavage and H-atom-transfer reactions within this framework is challenging and can lead to controversial results with varying accuracy. We present an assessment study of 16 common density functionals applied to prototypical model systems for both reactions. H-abstraction reactions were modeled on the basis of four reference reactions designed to resemble a broad range of coenzyme B reactions. The Co-C cleavage reaction is treated by an ONIOM(QM/MM) setup that is in excellent agreement with solution-phase experimental data and is as accurate as full DFT calculations on the complete model system. We find that the meta-GGAs TPSS-D3 and M06L-D3 and the meta-hybrid M06-D3 give the best overall performance with MUEs for both types of reactions below 10 kJ mol. Our recommended model chemistry allows for a fast and accurate description of coenzyme B chemistry that is readily applicable to study the reactions in an enzymatic framework.
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http://dx.doi.org/10.1021/acs.jpca.7b11798DOI Listing
February 2018

Multiply bonded metal(II) acetate (rhodium, ruthenium, and molybdenum) complexes with the trans-1,2-bis(N-methylimidazol-2-yl)ethylene ligand.

Inorg Chem 2014 Dec 13;53(23):12305-14. Epub 2014 Nov 13.

Inorganic Chemistry and Interdisciplinary Center for Molecular Materials, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 1, 91058 Erlangen, Germany.

The synthesis and structural characterization of new coordination polymers with the N,N-donor ligand trans-1,2-bis(N-methylimidazol-2-yl)ethylene (trans-bie) are reported. It was found that the acetate-bridged paddlewheel metal(II) complexes [M2(O2CCH3)4(trans-bie)]n with M = Rh, Ru, Mo, and Cr are linked by the trans-bie ligand to give a one-dimensional alternating chain. The metal-metal multiple bonds were analyzed with density functional theory and CASSCF/CASPT2 calculations (bond orders: Rh, 0.8; Ru, 1.7; Mo, 3.3).
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http://dx.doi.org/10.1021/ic501435aDOI Listing
December 2014

Self-consistent field convergence for proteins: a comparison of full and localized-molecular-orbital schemes.

J Mol Model 2014 Mar 28;20(3):2159. Epub 2014 Feb 28.

Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052, Erlangen, Germany.

Proteins in the gas phase present an extreme (and unrealistic) challenge for self-consistent-field iteration schemes because their ionized groups are very strong electron donors or acceptors, depending on their formal charge. This means that gas-phase proteins have a very small band gap but that their frontier orbitals are localized compared to "normal" conjugated semiconductors. The frontier orbitals are thus likely to be separated in space so that they are close to, but not quite, orthogonal during the SCF iterations. We report full SCF calculations using the massively parallel EMPIRE code and linear scaling localized-molecular-orbital (LMO) calculations using Mopac2009. The LMO procedure can lead to artificially over-polarized wavefunctions in gas-phase proteins. The full SCF iteration procedure can be very slow to converge because many cycles are needed to overcome the over-polarization by inductive charge shifts. Example molecules have been constructed to demonstrate this behavior. The two approaches give identical results if solvent effects are included.
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http://dx.doi.org/10.1007/s00894-014-2159-yDOI Listing
March 2014

Predicting the sites and energies of noncovalent intermolecular interactions using local properties.

J Chem Inf Model 2012 Apr 13;52(4):1061-71. Epub 2012 Apr 13.

Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraβe 25, 91052 Erlangen, Germany.

Feed-forward artificial neural nets have been used to recognize H-bond donor and acceptor sites on drug-like molecules based on local properties (electron density, molecular electrostatic potential and local ionization energy, electron affinity, and polarizability) calculated at grid points around the molecule. Interaction energies for training were obtained from B97-D and ωB97X-D/aug-cc-pVDZ density-functional theory calculations on a series of model central molecules and H-bond acceptor and donor probes constrained to the grid points used for training. The resulting models provide maps of both classical and unusual H- and halogen-bonding sites. Note that these reactions result even though only classical H-bond donors and acceptors were used as probes around the central molecules. Some examples demonstrate the ability of the models to take the electronics of the central molecule into consideration and to provide semiquantitative estimates of interaction energies at low computational cost.
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http://dx.doi.org/10.1021/ci300095xDOI Listing
April 2012