The GROMOS software for biomolecular simulation: GROMOS05

We present the latest version of the Groningen Molecular Simulation program package, GROMOS05. It has been developed for the dynamical modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization. An overview of GROMOS05 is given, highlighting features not present in the last major release, GROMOS96. The organization of the program package is outlined and the included analysis package GROMOS++ is described. Finally, some applications illustrating the various available functionalities are presented.     

Esterification with solid enzymes

Water activation of the enzyme (an esterase of Mucor miehei) is studied during oleic acid/1-decanol esterification with or without solvent. The activation is rapid, but not instantaneous. Reaction water and water added before the beginning of the reaction do not have the same influence. The activation of the enzyme is effected by its swelling with water. When the initial quantity of water is sufficient, the reaction order is zero. But from a certain conversion, the rate decreases very suddenly or very slowly. This observation is attributed to the partitioning of an aqueous phase around the enzyme.

     

Planar-chiral (2E,7Z)- and (2Z,7E)-cyclonona-2,7-dien-1-yl carbamates by asymmetric,bis-allyic,alpha, alpha'-cycloalkylation--studies on their conformational stability

Enantiomerically enriched (>80 % ee) (M,1R,2Z,7E)- and (M,1R,2E,7Z)-cyclonona-2,7-dienyl carbamates have been synthesized by an intramolecular cycloalkylation of the corresponding 1-lithio-9-chloronona-2,7-dienyl carbamates. The enantioenriched precursors were generated by asymmetric deprotonation of the dienyl carbamates by means of n-BuLi/(-)-sparteine. The primarily obtained cyclononadienes, each bearing one element of planar and centre chirality, were formed by an , coupling of both allylic moieties. These are the thermodynamically less favoured epimers, which arise from those allyllithiums bearing the carbamoyloxy residue in a 1-endo position. Both (M,R)-cyclononadienes epimerize slowly (t(1/2) = 209 min and 328 min at 308 K) with inversion of the planar chirality to the corresponding, more stable (P)-epimers (ratios 3:97 and 30:70). The kinetics were measured by 1H NMR spectroscopy, the activation energies EA were found to be 26.4 and 27.5 kcal mol(-1). From quantum-chemical calculations with the B3LYP density functional, the epimerization process was shown to consist of two coupled major conformational changes with high energy barriers. The calculated values match well with the observed ones.     

Comparative study by single crystal X-ray structure determinations of tetramethylaminoborane and tetramethylethene at 110 K

The single crystal structures of the two isoelectronic and isosteric compounds tetramethylaminoborane and tetramethylethene have been determined by an X-ray study at 110 K. The distances of the central bonds are refined to 140.3(1) pm (B=N) and 134.8(1) pm (C=C), the CXXC-torsion angles (XX=CC, BN) are smaller than 1° in both compounds. A bond-length-bond-order correlation for the aminoboranes [(CH₃)₂N] _n B(CH₃)_3–n withn=1, 2, and 3 give a regression coefficient of 0.9977, the same is found for the CNC-angle as a function of the CBNC-torsion angle. Also, the comparison among these aminoboranes show that the variation of CBNC-torsion angles has more influence on bond lengths at small angles.     

The MICE facility – a new tool to study plant–soil C cycling with a holistic approach

Plant–soil interactions are recognized to play a crucial role in the ecosystem response to climate change. We developed a facility to disentangle the complex interactions behind the plant–soil C feedback mechanisms. The MICE (‘Multi-Isotope labelling in a Controlled Environment’) facility consists of two climate chambers with independent control of the atmospheric conditions (light, CO₂, temperature, humidity) and the soil environment (temperature, moisture). Each chamber holds 15 plant–soil systems with hermetical separation of the shared above ground (shoots) from the individual belowground compartments (roots, rhizosphere, soil). Stable isotopes (e.g. ¹³C, ¹⁵N, ²H, ¹⁸O) can be added to either compartment and traced within the whole system. The soil CO₂ efflux rate is monitored, and plant material, leached soil water and gas samples are taken frequently. The facility is a powerful tool to improve our mechanistic understanding of plant–soil interactions that drive the C cycle feedback to climate change.     

Vector algebra and molecular symmetry: a tribute to Professor Josiah Willard Gibbs

Vector algebra, as developed by Josiah Willard Gibbs, is much simpler than matrix or tensor algebra, therefore, it is more suitable to introduce the students of chemistry into the wonderful world of molecular symmetry. A program based on elementary vector algebra has been written to determine all symmetry elements and symmetry operations of rigid molecular structures. The program also contains data for 57 point groups common in chemistry. Therefore, it automatically supplies the particular point group to which the structure belongs. Since the locations of the nuclei related to the symmetry elements are also revealed by the program, even the detailed notation of the framework group of the molecular structure can be deduced. The program can be a great help in determining the symmetries of the normal modes of vibration, too.     

Crystal‐smectic E mesophases in a series of 2‐(4‐n‐alkylphenyl)indenes

A series of 2‐(4‐n‐alkylphenyl)indenes (3) with different alkyl substituents (CH₃ to C₁₀H₂₁) were synthesized and systematically characterized using differential scanning calorimetry, polarizing optical microscopy and X‐ray diffraction compared with 2‐phenylindene (3a). Depending on the alkyl chain length, highly ordered crystal‐smectic E mesophases were observed and confirmed by X‐ray diffraction for the derivatives 3h–3k with heptyl to decyl chains (n = 6?9). For 3f with a pentyl side chain (n = 4), an X‐ray crystal structure analysis was carried out.