Institute of Organic Chemistry

It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a standard "zero-damping" formula and rational damping to finite values for small interatomic distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coefficients is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interatomic forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramolecular dispersion in four representative molecular structures are found. For the noncovalently-bonded structures in the S22 set, both schemes lead to very similar intermolecular distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of corrected GGAs for non-covalent interactions. According to the thermodynamic benchmarks BJ-damping is more accurate especially for medium-range electron correlation problems and only small and practically insignificant double-counting effects are observed. It seems to provide a physically correct short-range behavior of correlation/dispersion even with unmodified standard functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying density functional.

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green's functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.

Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are members of the Bacillus cereus group of bacteria, demonstrating widely different phenotypes and pathological effects. B. anthracis causes the acute fatal disease anthrax and is a potential biological weapon due to its high toxicity. B. thuringiensis produces intracellular protein crystals toxic to a wide number of insect larvae and is the most commonly used biological pesticide worldwide. B. cereus is a probably ubiquitous soil bacterium and an opportunistic pathogen that is a common cause of food poisoning. In contrast to the differences in phenotypes, we show by multilocus enzyme electrophoresis and by sequence analysis of nine chromosomal genes that B. anthracis should be considered a lineage of B. cereus. This determination is not only a formal matter of taxonomy but may also have consequences with respect to virulence and the potential of horizontal gene transfer within the B. cereus group.

The efficient and selective conversion of CO₂as a sustainable C₁resource into valuable chemicals and energy-related products through catalysis is reviewed.

The use of NHCs for generating homoenolate species has gained widespread popularity in recent years. A number of highly stereoselective processes of NHC-homoenolates have emerged. Homoenolate reactions have also been employed as key steps in the total synthesis of a number of natural products. The use of compatible co-catalysts, improved NHC-catalyst design and the use of novel precursors for homoenolate generation are among the major developments in this area that were disclosed recently. This tutorial review organises and presents the advancements in this rapidly growing area of catalysis and in the process updates a previous account published in 2011 in this journal.

The integration of several responsive moieties within one polymer yields smart polymers exhibiting a multifaceted responsive behaviour.

<ns4:p>GoodVibes is an open-source Python toolkit for processing the results of quantum chemical calculations. Thermochemical data are not simply parsed, but evaluated by evaluation of translational, rotational, vibrational and electronic partition functions. Changes in concentration, pressure, and temperature can be applied, and deficiencies in the rigid rotor harmonic oscillator treatment can be corrected. Vibrational scaling factors can also be applied by automatic detection of the level of theory and basis set. Absolute and relative thermochemical values are output to text and graphical plots in seconds. GoodVibes provides a transparent and reproducible way to process raw computational data into publication-quality tables and figures without the use of spreadsheets.</ns4:p>

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

Fluoroquinolones are an important class of wide-spectrum antibacterial agents. The first quinolone described was nalidixic acid, which showed a narrow spectrum of activity. The evolution of quinolones to more potent molecules was based on changes at positions 1, 6, 7 and 8 of the chemical structure of nalidixic acid. Quinolones inhibit DNA gyrase and topoisomerase IV activities, two enzymes essential for bacteria viability. The acquisition of quinolone resistance is frequently related to (i) chromosomal mutations such as those in the genes encoding the A and B subunits of the protein targets (gyrA, gyrB, parC and parE), or mutations causing reduced drug accumulation, either by a decreased uptake or by an increased efflux, and (ii) quinolone resistance genes associated with plasmids have been also described, i.e. the qnr gene that encodes a pentapeptide, which blocks the action of quinolones on the DNA gyrase and topoisomerase IV; the aac(6')-Ib-cr gene that encodes an acetylase that modifies the amino group of the piperazin ring of the fluoroquinolones and efflux pump encoded by the qepA gene that decreases intracellular drug levels. These plasmid-mediated mechanisms of resistance confer low levels of resistance but provide a favourable background in which selection of additional chromosomally encoded quinolone resistance mechanisms can occur.

Abstract Als mechanistische Kriterien für die zu fünfgliedrigen Ringen führende 1.3‐Dipolare Cycloaddition dienen die Stereoselektivität bei Verwendung cis‐trans‐isomerer Dipolarophile, die Einflüsse von Lösungsmittel und Substituenten auf die Reaktionsgeschwindigkeitskonstanten, die Aktivierungsparameter und die Orientierungsphänomene. Eine auch in Molecular Orbitals beschriebene Mehrzentren‐Addition, bei der die beiden neuen σ‐Bindungen gleichzeitig, wenn auch nicht unbedingt gleich rasch, entstehen, wird dem experimentellen Material am besten gerecht.

The plant alkaloids castanospermine, dihydroxymethyldihydroxypyrrolidine and deoxynojirimycin have recently been shown to have potential anti-HIV activity [(1987) Proc. Natl. Acad. Sci. USA 84, 8120-8124; (1987) Nature 330, 74-77; (1987) Lancet i, 1025-1026]. They are thought to act by inhibiting alpha-glucosidase I, an enzyme involved in the processing of N-linked oligosaccharides on glycoproteins. We report here the relative efficacy of a spectrum of amino-sugar derivatives as inhibition of HIV cytopathicity. Several alpha-glucosidase inhibitors and alpha-fucosidase inhibitors were found to be active at concentrations which were non-cytotoxic.

Gold [Au(0)] nanoparticles immobilized into a stable covalent organic framework (COF) have been synthesized via the solution infiltration method. The as-synthesized Au(0)@TpPa-1 catalyst shows high recyclability and superior reactivity for nitrophenol reduction reaction than HAuCl4·3H2O.

A new algorithm, called convex constraint analysis, has been developed to deduce the chiral contribution of the common secondary structures directly from experimental CD curves of a large number of proteins. The analysis is based on CD data reported by Yang, J.T., Wu, C.-S.C. and Martinez, H.M. [Methods Enzymol., 130, 208-269 (1986)]. Application of the decomposition algorithm for simulated protein data sets resulted in component spectra [B (lambda, i)] identical to the originals and weights [C (i, k)] with excellent Pearson correlation coefficients (R) [Chang, C.T., Wu, C.-S.C. and Yang, J.T. (1978) Anal. Biochem., 91, 12-31]. Test runs were performed on sets of simulated protein spectra created by the Monte Carlo technique using poly-L-lysine-based pure component spectra. The significant correlational coefficients (R greater than 0.9) demonstrated the high power of the algorithm. The algorithm, applied to globular protein data, independent of X-ray data, revealed that the CD spectrum of a given protein is composed of at least four independent sources of chirality. Three of the computed component curves show remarkable resemblance to the CD spectra of known protein secondary structures. This approach yields a significant improvement in secondary structural evaluations when compared with previous methods, as compared with X-ray data, and yields a realistic set of pure component spectra. The new method is a useful tool not only in analyzing CD spectra of globular proteins but also has the potential for the analysis of integral membrane proteins.

A photoredox-mediated Minisci C–H alkylation of <italic>N</italic>-heteroarenes with easily accessible primary and secondary alkyl boronic acids has been developed.

Covering: July 2012 to June 2015. Previous review: Nat. Prod. Rep., 2013, 30, 869-915The structurally diverse imidazole-, oxazole-, and thiazole-containing secondary metabolites are widely distributed in terrestrial and marine environments, and exhibit extensive pharmacological activities. In this review the latest progress involving the isolation, biological activities, and chemical and biogenetic synthesis studies on these natural products has been summarized.

Each major step leading to the classical yellow, orange and red constituents of <italic>Monascus</italic> azaphilone pigments was defined.

Come in! The use of internal oxidants, embedded in the directing group, in CH activation reactions can lead to higher levels of selectivity and reactivity under milder conditions (see examples). An internal oxidant can be defined as a covalent bond within one of the coupling substrates which oxidizes the metal catalyst. This should open up new avenues in the field of CH activation.

The endocytotic mechanisms involved in the uptake of charged polystyrene nanoparticles into HeLa cells were investigated. Uptake experiments were done in the presence or absence of drugs known to inhibit various factors in endocytosis. Independent of the particle charge, endocytosis is highly dependent on dynamin, F-actin, and tyrosine-specific protein kinases, which suggests a dynamin-dependent and lipid raft-dependent mechanism. However, cholesterol depletion did not hinder particle uptake. Regarding positively charged particles, macropinocytosis, the microtubule network, and cyclooxygenases are also involved. The clathrin-dependent pathway plays a minor role.

This paper reviews the present state of the Reformatsky reaction, the advancement of which has recently led to a considerable extension of its scope. 1. Introduction 2. Reagent Structure and Reaction Mechanism 3. The Role of Metal Activation 4. Substitution of Zinc by Other Metals 5. Reactive Halogen Compounds: Precursors of Reformatsky Donor Reagents 5.1. α-Halo Carbonyl Compounds 5.2. Stereoselectivity in Reformatsky Reactions 5.3. Alkyl 2-Bromomethyl-2-alkenoates and Heteroanalogues 5.4. Alkyl 4-Bromo-2-alkenoates 5.5. Zinc Homocnolates 6. Electrophiles in Reformatsky Reactions 6.1. Carbonyl Compounds and Derivatives, Intermolecular Reactions 6.2. Intramolecular Reformatsky Reactions 6.3. Uncommon Electrophiles in Reformatsky Reactions 7. Conclusions and Outlook

Planar chiral [2.2]paracyclophane-based ligands and employment of such enantiopure representative ligands to facilitate selective transformation of prochiral or racemic substances into enantiopure products are rarely explored compared to the complex chiral scaffolds such as ferrocenes. This tutorial discusses recent findings and inspiring progress in design, synthetic tunability and applications of planar chiral [2.2]paracyclophane systems as a practical class of catalysts for asymmetric synthesis. Here, we summarize a series of planar chiral [2.2]paracyclophanes that are becoming an important new tool-box in asymmetric synthesis, employed in a variety of synthetic venues such as new chiral ligands and catalysts for stereo-controlled and enantioselective addition of alkyl, alkenyl, alkynyl and aryl zinc reagents to aliphatic and aromatic aldehydes, ketones, imines and many more. Besides, planar chiral [2.2]paracyclophanes are useful synthons, from a material perspective, can be incorporated into conjugated polymeric systems for chiroptical and optoelectronic properties, find broad applications in bio- and materials science, for instance, gold-based cytostatics, surface-mounted chiral MOF thin films for selective adsorption or in functionalized parylene polymer coatings, to name a few. This is an up-to-date tutorial review, written exclusively on planar chiral [2.2]paracyclophane chemistry, covering key aspects of synthesis, structures, properties, applications and future directions of chiral polymeric assemblies and novel biomaterials built with [2.2]paracyclophanes.