Matthias Hennemann

Improving the charge transport in self-assembled monolayer field-effect transistors:from theory to devices

A three-pronged approach has been used to design rational improvements in self-assembled monolayer field-effect transistors: classical molecular dynamics (MD) simulations to investigate atomistic structure, large-scale quantum mechanical (QM) calculations for electronic properties, and device fabrication and characterization as the ultimate goal. The MD simulations reveal the effect of using two-component monolayers to achieve intact dielectric insulating layers and a well-defined semiconductor channel. The QM calculations identify improved conduction paths in the monolayers that consist of an optimum mixing ratio of the components. These results have been used both to confirm the predictions of the calculations and to optimize real devices. Monolayers were characterized with X-ray reflectivity measurements and by electronic characterization of complete devices.

CypScore: Quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory

CypScore predicts the reactivity of competing positions in the same and different molecules to a variety of cytochrome P450 metabolic reactions on a single reactivity scale.

EMPIRE: a highly parallel semiempirical molecular orbital program: 1: self-consistent field calculations

FigureAn adamantane nanocrystal that is easily calculated with EMPIRE

EMPIRE: a highly parallel semiempirical molecular orbital program: 2: periodic boundary conditions

Abstractᅟ Graphical Abstractᅟ

Quantum mechanics-based properties for 3D-QSAR

We have used a set of four local properties based on semiempirical molecular orbital calculations (electron density (ρ), hydrogen bond donor field (HDF), hydrogen bond acceptor field (HAF), and molecular lipophilicity potential (MLP)) for 3D-QSAR studies to overcome the limitations of the current force field-based molecular interaction fields (MIFs). These properties can be calculated rapidly and are thus amenable to high-throughput industrial applications. Their statistical performance was compared with that of conventional 3D-QSAR approaches using nine data sets (angiotensin converting enzyme inhibitors (ACE), acetylcholinesterase inhibitors (AchE), benzodiazepine receptor ligands (BZR), cyclooxygenase-2 inhibitors (COX2), dihydrofolate reductase inhibitors (DHFR), glycogen phosphorylase b inhibitors (GPB), thermolysin inhibitors (THER), thrombin inhibitors (THR), and serine protease factor Xa inhibitors (fXa)). The 3D-QSAR models generated were tested thoroughly for robustness and predictive ability. The average performance of the quantum mechanical molecular interaction field (QM-MIF) models for the nine data sets is better than that of the conventional force field-based MIFs. In the individual data sets, the QM-MIF models always perform better than, or as well as, the conventional approaches. It is particularly encouraging that the relative performance of the QM-MIF models improves in the external validation. In addition, the models generated showed statistical stability with respect to model building procedure variations such as grid spacing size and grid orientation. QM-MIF contour maps reproduce the features important for ligand binding for the example data set (factor Xa inhibitors), demonstrating the intuitive chemical interpretability of QM-MIFs.

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.

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.

Intramolecular reactivity of π-coordinated P-heterocycles: How to form five-membered rings out of phosphaalkynes

Experimental and theoretical evidence is presented for a novel metal-dependent intramolecular reactivity of ~ -bonded, unsaturated P-heterocycles like 1,3-diphosphete and 1,3,5-triphosphinine. The nucleophilic attack of a P lone pair of 1,3-diphosphete toward a neighboring ligand leads to new bicyclic ligands with unique structural features. A metal-initiated intramolecular hydrogen transfer and C--C bond formation are observed for (1,3,5-triphosphinine)(COD)Fe to result in the formation of [(CO) 5 Cr(4,5,6-trihydro-1,3,5-triphosphinine)(trihydropentalene)Fe].

The Effect of a Complexed Lithium Cation on a Norcarane-Based Radical Clock

Density-functional theory (DFT) and ab initio calculations have been used to investigate the effect of a complexed lithium cation on the radical-clock rearrangement of the 2-norcaranyl radical to the 3-cyclohexenylmethyl radical. As found earlier for ring-closing radical clocks, complexation with a metal ion leads to a significant lowering of the barrier to rearrangement. DFT calculations on a model for the norcaranyl clock in cytochrome P450 confirm the two-state reactivity proposal of Shaik et al. and indicate that the porphyrin exerts little or no electrostatic effect on the rearrangement barrier.

Solvatochromic covalent organic frameworks

Covalent organic frameworks (COFs) are an emerging class of highly tuneable crystalline, porous materials. Here we report the first COFs that change their electronic structure reversibly depending on the surrounding atmosphere. These COFs can act as solid-state supramolecular solvatochromic sensors that show a strong colour change when exposed to humidity or solvent vapours, dependent on vapour concentration and solvent polarity. The excellent accessibility of the pores in vertically oriented films results in ultrafast response times below 200 ms, outperforming commercially available humidity sensors by more than an order of magnitude. Employing a solvatochromic COF film as a vapour-sensitive light filter, we demonstrate a fast humidity sensor with full reversibility and stability over at least 4000 cycles. Considering their immense chemical diversity and modular design, COFs with fine-tuned solvatochromic properties could broaden the range of possible applications for these materials in sensing and optoelectronics.Covalent organic frameworks (COFs) find increasing application as sensor material, but fast switching solvatochromism was not realized. Here the authors demonstrate that combination of electron-rich and -deficient building blocks leads to COFs which fast and reversibly change of their electronic structure depending on the surrounding atmosphere.