Block Chemistry for Accurate Modeling of Epoxy Resins.

Accurate molecular modeling of the physical and chemical behavior of highly cross-linked epoxy resins at the atomistic scale is important for the design of new property-optimized materials. However, a systematic approach to parametrizing and characterizing these systems in molecular dynamics is missing. We therefore present a unified scheme to derive atomic charges for amine-based epoxy resins, in agreement with the AMBER force field, based on defining reactive fragments─blocks─building the network. The approach is applicable to all stages of curing from pure liquid to gelation to fully cured glass. We utilize this approach to study DGEBA/DDS epoxy systems, incorporating dynamic topology changes into atomistic molecular dynamics simulations of the curing reaction with 127,000 atoms. We study size effects in our simulations and predict the gel point utilizing a rigorous percolation theory to recover accurately the experimental data. Furthermore, we observe excellent agreement between the estimated and the experimentally determined glass transition temperatures as a function of curing rate. Finally, we demonstrate the quality of our model by the prediction of the elastic modulus based on uniaxial tensile tests. The presented scheme paves the way for a broadly consistent approach for modeling and characterizing all amine-based epoxy resins.

Improving the Performance of Supported Ionic Liquid Phase Catalysts for the Ultra-Low-Temperature Water Gas Shift Reaction Using Organic Salt Additives.

The water gas shift reaction (WGSR) is catalyzed by supported ionic liquid phase (SILP) systems containing homogeneous Ru complexes dissolved in ionic liquids (ILs). These systems work at very low temperatures, that is, between 120 and 160 °C, as compared to >200 °C in the conventional process. To improve the performance of this ultra-low-temperature catalysis, we investigated the influence of various additives on the catalytic activity of these SILP systems. In particular, the application of methylene blue (MB) as an additive doubled the activity. Infrared spectroscopy measurements combined with density functional theory (DFT) calculations excluded a coordinative interaction of MB with the Ru complex. In contrast, state-of-the-art theoretical calculations elucidated the catalytic effect of the additives by non-covalent interactions. In particular, the additives can significantly lower the barrier of the rate-determining step of the reaction mechanism via formation of hydrogen bonds. The theoretical predictions, thereby, showed excellent agreement with the increase of experimental activity upon variation of the hydrogen bonding moieties in the additives investigated.

An Exact Algorithm to Detect the Percolation Transition in Molecular Dynamics Simulations of Cross-Linking Polymer Networks.

Periodic molecular dynamics simulations are developing to a routine tool for the investigation of complex, polymeric materials. A typical application is the simulation of the curing reaction of covalently cross-linked polymers, which provides detailed understanding of network formation at the molecular scale, with examples including gelation and glass transitions. In this article, we delineate the connection between percolation theory and gel-point detection in periodic polymeric networks. Specifically, we present an algorithm that can detect the onset of percolation during cross-linking of polymers in periodic molecular dynamic simulations. A sample implementation is provided at https://github.com/puls-group/percolation-analyzer. As an example, we apply the algorithm to simulations of an epoxy resin undergoing curing with an amine hardener. We also compare results with indirect gel point measurements obtained from monitoring the growth of the largest mass and the onset of secondary cycles.

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

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.

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

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 [C2Mim][NTf2], 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.

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

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.

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

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)3 Cl3 ]- 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 D2 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.

On bond-critical points in QTAIM and weak interactions.

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.

Modeling the Reactions Catalyzed by Coenzyme B12 Dependent Enzymes: Accuracy and Cost-Quality Balance.

The reactions catalyzed by coenzyme B12 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 B12 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 B12 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-1. Our recommended model chemistry allows for a fast and accurate description of coenzyme B12 chemistry that is readily applicable to study the reactions in an enzymatic framework.

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

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).

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

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.

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

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.