MOLSIM: A modular molecular simulation software

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Regioselective synthesis of 1- and 4-substituted 7-oxopyrazolo[1,5-a]pyrimidine-3-carboxamides

The synthesis of 7-substituted pyrazolo[1,5-a]pyrimidine-3-carboxamides was studied. First, methyl 7-hydroxypyrazolo[1,5-a]pyrimidine-3-carboxylate (5) was prepared in three steps from methyl 5-amino-1H-pyrazole-4-carboxylate (3). Treatment of 5 with POCl₃ gave the highly reactive 7-chloro derivative 10, which was reacted with amines, benzyl alcohol, and phenylboronic acid in the presence of Pd-catalyst to give the corresponding 7-substituted derivatives 11. Hydrolysis of the esters 5 and 11 followed by amidation gave the corresponding carboxamides 16a–h and 15. Regioselectivity of N-alkylation of 7-hydroxypyrazolo[1,5-a]pyrimidine-3-carboxylic acid derivatives 5 and 16 was tunable by the carboxy function. Alkylation of the secondary amides 16a–f furnished the 1-alkyl derivatives 17a–f, whereas the ester 5 and the tertiary amides 16g,h gave the 4-alkyl derivatives 14a–d and 16m,n, selectively.     

Synthesis of (S)‐3‐heteroaryl‐2‐hydroxy‐l‐propyl benzoates by ‘ring switching’ methodology

(S)‐5‐Benzoyloxymethyl‐3‐[(E)‐(dimethylamino)methylidene]tetrahydrofuran‐2‐one (6), prepared in 5 steps from L‐glutamic acid (1), was used as precursor in a one step ‘ring switching’ synthesis of (S)‐2‐hydroxy‐3‐heteroaryl‐l‐propyl benzoates 13‐18, 23, 24. In the reaction of 6 with 2‐aminopyridine (21) and 2‐amino‐4,6‐dimethylpyrimidine (22) the corresponding dimethylamine substitution products (25, 26) were obtained.     

Reactions of enaminones and related compounds with N,N-dimethylacetamide dimethyl acetal. A simple one-pot metal-free synthesis of polysubstituted benzene derivatives

Herein a simple one-pot metal-free synthesis of alkyl-, aryl-, heteroaryl- and alkoxycarbonyl substituted 1,3-bis(dimethylamino)benzene derivatives is described. The products were prepared from the corresponding methyl ketones or compounds with an α-methylene group in regard to the carbonyl group, using N,N-dimethylacetamide dimethyl acetal (DMADMA) as the reagent.     

Synthesis and antimycobacterial activity of alkyl 1‐heteroaryl‐1H‐1,2,3‐triazole‐4‐carboxylates

A series of alkyl l‐heteroaryl‐1H‐1,2,3‐triazole‐4‐carboxylates 6a‐u were synthesised in four steps from methyl (Z)‐2‐benzyloxycarbonylarmino‐3‐(dimethylamino)prop‐2‐enoate ( 1 ) and heterocyclic amines 2a‐s. Triazoles 6a‐o were tested against antimycobacterial activity. For the most active compound, n‐pentyl 1‐(6‐phenylpyridazin‐3‐yl)‐1H‐1,2,3‐triazole‐4‐carboxylate ( 6n ), minimum inhibitory concentration 3.13 μg/ml was determined.     

Ex-Chiral Pool Enaminones in the Synthesis of Functionalised Heterocycles

Various chiral enaminones and hydrazones, derived from chiral pool starting materials, such as L-aspartic acid, L-3-phenylalanine, (+)-camphor, and D-aldoses were employed as key-intermediates in the synthesis of functionalised heterocycles, such as aminomethylidene substituted tetramic acids, heteroaryl substituted phenethylamines and terpenes, and C-nucleosides.     

Application of X-ray fluorescence analytical techniques in phytoremediation and plant biology studies

Phytoremediation is an emerging technology that employs the use of higher plants for the clean-up of contaminated environments. Progress in the field is however handicapped by limited knowledge of the biological processes involved in plant metal uptake, translocation, tolerance and plant–microbe–soil interactions; therefore a better understanding of the basic biological mechanisms involved in plant/microbe/soil/contaminant interactions would allow further optimization of phytoremediation technologies. In view of the needs of global environmental protection, it is important that in phytoremediation and plant biology studies the analytical procedures for elemental determination in plant tissues and soil should be fast and cheap, with simple sample preparation, and of adequate accuracy and reproducibility. The aim of this study was therefore to present the main characteristics, sample preparation protocols and applications of X-ray fluorescence-based analytical techniques (energy dispersive X-ray fluorescence spectrometry—EDXRF, total reflection X-ray fluorescence spectrometry—TXRF and micro-proton induced X-ray emission—micro-PIXE). Element concentrations in plant leaves from metal polluted and non-polluted sites, as well as standard reference materials, were analyzed by the mentioned techniques, and additionally by instrumental neutron activation analysis (INAA) and atomic absorption spectrometry (AAS). The results were compared and critically evaluated in order to assess the performance and capability of X-ray fluorescence-based techniques in phytoremediation and plant biology studies. It is the EDXRF, which is recommended as suitable to be used in the analyses of a large number of samples, because it is multi-elemental, requires only simple preparation of sample material, and it is analytically comparable to the most frequently used instrumental chemical techniques. The TXRF is compatible to FAAS in sample preparation, but relative to AAS it is fast, sensitive and multi-elemental. The micro-PIXE technique requires rather expensive instrumentation, but offers multi-elemental analysis on the tissue and cellular level.     

Oka's principle for holomorphic submersions with sprays

We classify, up to a local isometry, all non-K?hler almost K?hler 4-manifolds for which the fundamental 2-form is an eigenform of the Weyl tensor, and whose Ricci tensor is invariant with respect to the almost complex structure. Equivalently, such almost K?hler 4-manifolds satisfy the third curvature condition of A. Gray. We use our local classification to show that, in the compact case, the third curvature condition of Gray is equivalent to the integrability of the corresponding almost complex structure. Received: 1 October 2001 / Published online: 17 June 2002