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.     

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.     

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.     

A decanuclear oxomolybdenum(V,VI) cluster with 4-isopropylpyridine

The title centrosymmetric cluster octakis(4-iso­propyl­pyridine-N)-di-μ₄-oxo-hexa-μ₃-oxo-octa-μ₂-oxo-deca­oxo­octa­molyb­denum(V)­dimolybdenum(VI), [Mo₁₀O₂₆(C₈H₁₁N)₈], consists of ten Mo atoms connected together by bridging oxo groups. Pentavalent Mo atoms are linked into four Mo₂^V pairs by metal–metal single bonds with lengths of 2.5637 (6) and 2.6132 (6) Å.     

Synthesis of 3‐(4‐Oxo‐4H‐quinolizinyl‐3) and 3‐(4‐Oxo‐4H‐pyridino[1,2‐a]pyrimidinyl‐3) substituted lactic acid derivatives

A one‐step ‘ring switching’ transformation of (S)‐3‐[(dimethylamino)methylidene]‐5‐(methoxycarbonyl)tetrahydrofuran‐2‐one ( 4 ) with 2‐pyridineacetic acid derivatives ( 5–7 ) and 2‐aminopyridines ( 8, 9 ) afforded the corresponding 3‐(4‐oxo‐4H‐quinolizinyl‐3)‐ (15–17) and 3‐(4‐oxo‐4H‐pyridino[1,2‐a]pyrimidinyl‐3)‐2‐hydroxypropanoates ( 18, 19 ), respectively.     

Enaminone‐Based Synthesis of Dipodazine Derivatives

A series of racemic dipodazine analogues 9 were prepared in 22–80% yield from (3Z,6RS)‐3‐[(dimethylamino)methylidene]‐6‐methyl‐1‐(phenylmethyl)piperazine‐2,5‐dione ( 7 ) (Scheme 1), which was prepared in four steps from (RS)‐alanine methyl ester hydrochloride. The preparation of nonracemic 7 from (S)‐alanine methyl ester hydrochloride failed, since the introduction of the enamino functionality at position 3 of the precursor 6 was accompanied by almost complete racemization.     

Synthesis and transformations of methyl (E)-2-(acetylamino)-3-cyanoprop-2-enoate und methyl (E)-2-(benzoylamino)-3-cyanoprop-2-enoate,versatile reagents for the preparation of polyfunctional heterocyclic systems

Methyl (E)-2-(acetylamino)-3-cyanoprop-2-enoate ( 2a ), and its 2-benzoyl analog 2b ere prepared from the corresponding methyl (Z)-2-(acylamino)-3-(dimethylamino)propenoates 1 Multifunctional compounds 2 are versatile synthons for preparation of polysubstituted heterocyclic systems such as pyrroles 4 , pyrimidines 5 and 6 , pyridazines 7 , pyrazoles 8 , 9 , and 11 , and isoxazoles 10 .     

Fluorine containing coordination compounds of Cr(III)

Trans-[Cr(NH₃)₄F₂]I·H₂O (A) has monoclinic P2_l/m (No. 11) space group witha=5.033 (3),b=16.333 (10),c=5.539 (3) Å and =98.47 (3)°,Z=2.Cis-[Cr(NH₃)₄F₂]ClO₄ (B) has tetragonal space group I4_lmd (No. 109) witha=7.417 (1),c=16.610 (2) Å,Z=4. Cr–F and Cr–N bonding distances are 1.894 (3); 2.087 and 2.083 (5) Å for A and 1.887 (6); 2.062 (5) and 2.051 (7) Å for B. Octahedral angles within the cations are close to 90° for both compounds. Cr–N bondtrans to Cr–F bond in thecis compound is shorter. Structures were refined toR ₂ values of 0.072 (A) and 0.058 (B).Trans-[Cr(NH₃)₄F₂]I·H₂O has weak N–H–F hydrogen bonds between the cations. None such interactions were found incis-[Cr(NH₃)₄F₂]ClO₄.

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Fluorhältige Komplexe des Cr(III), 2. Mitt.: Kristall- und Molekülstruktur von trans-[Cr(NH₃)₄F₂]I·H₂O und cis-[Cr(NH₃)₄F₂]ClO₄

Zusammenfassung Trans-[Cr(NH₃)₄F₂]I·H₂O (A) kristallisiert in der Raumgruppe P2_l/m (No. 11) mitZ=2 unda=5,033 (3),b=16,333 (10),c=5,539 (3) Å und =98,47 (3)°.Cis-[Cr(NH₃)₄F₂]ClO₄ (B) kristallisiert in der Raumgruppe I4_lmd (No. 109) mitZ=4,a=7,417 (1) undc=16,610 (2) Å. Die Cr–F- und Cr–N-Abstände sind 1,894 (3); 2,087 (6), 2,083 (5) Å für A und 1,887 (6); 2,062 (5), 2,051 (7) Å für B. Die octaedrischen Bindungswinkel innerhalb der Kationen weichen nicht viel von 90° ab. Der Cr–N-Abstand intrans-Position der Cr–F-Bindung ist kürzer. Die Strukturen wurden bis zu GütefaktorenR ₂ 0,072 (A) und 0,058 (B) verfeinert. Bei der Verbindung A wurden schwache N–H ... F-Wasserstoff-Bindungen zwischen verschiedenen Kationen beobachtet, während bei der Verbindung B keine Wasserstoff-Bindungen vorhanden sind.