GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.     

The impact of the natural sciences on archaeology

This article reviews some of the applications of physics to the solution of archaeological problems. The use of magnetic, resistivity and electromagnetic surveying techniques for the location of buried features is described. Various methods of age determination are outlined while the problems associated with radiocarbon dating of organic material and thermoluminescent dating of pottery are discussed in detail. The techniques, including petrological examination, chemical analysis and isotopic analysis, employed in the physical examination of archaeological artefacts are described. Examples of the application of these techniques in establishing the source of the raw materials used in pottery, metal and stone implements and in elucidating the techniques of manufacture of pottery and metal objects are also given.     

Alkane hydroxylation by peroxy acids: a comparison with the cytochrome P450 hydroxylation

Alkane hydroxylation by peroxy acids proceeds by a synchronous nonconcerted peroxy oxygen insertion into the C-H bond according to density functional theory. A comparable reaction sequence, initiated by homolytic peroxy bond cleavage, can be formulated for the alkane hydroxylation by the cytochrome P450 hydroperoxo-heme Compound 0. This hydroxylation reaction proceeds by a two-step process because the formed reactive intermediate, Compound II, is significantly stabilized.     

Proton assisted oxygen-oxygen bond splitting in cytochrome p450

Proton assisted O-O bond splitting of cytochromes' P450 hydroperoxo Compound 0 has been investigated by density functional theory, showing a barrier for the slightly endothermic formation of the iron-oxo Compound I. The barrier and the endothermicity increase with decreasing acidity of the distal proton source. Protonation of the proximal iron heme ligand favors the O-O bond scission and provides an important regulatory component in the catalytic cycle. The Compound 0 --> I conversion is slightly exothermic for the peroxidase and catalase models. Implications of the energetic relationship between the two reactive intermediates are discussed in terms of possible oxidative pathways.     

Phenolic compounds,essential oil composition,and antioxidant activity of Angelica purpurascens (Avé-Lall.) Gill

In this study, methanol extracts (MEs) and essential oil (EO) of Angelica purpurascens (Avé-Lall.) Gill obtained from different parts (root, stem, leaf, and seed) were evaluated in terms of antioxidant activity, total phenolics, compositions of phenolic compound, and essential oil with the methods of 2,2-azino-bis(3ethylbenzo-thiazoline-6-sulfonic acid (ABTS•⁺), 2,2-diphenyl-1-picrylhydrazil (DPPH•) radical scavenging activities, and ferric reducing/antioxidant power (FRAP), the Folin–Ciocalteu, liquid chromatography−tandem mass spectrometry (LC−MS/MS), and gas chromatography-mass spectrometry (GC−MS), respectively. The root extract of A. purpurascens exhibited the highest ABTS•⁺, DPPH•, and FRAP activities (IC₅₀: 0.05 ± 0.0001 mg/mL, IC₅₀: 0.06 ± 0.002 mg/mL, 821.04 ± 15.96 µM TEAC (Trolox equivalent antioxidant capacity), respectively). Moreover, EO of A. purpurascens root displayed DPPH• scavenging activity (IC₅₀: 2.95 ± 0.084 mg/mL). The root extract had the highest total phenolic content (438.75 ± 16.39 GAE (gallic acid equivalent), µg/mL)). Twenty compounds were identified by LC−MS/MS. The most abundant phenolics were ferulic acid (244.39 ± 15.64 μg/g extract), benzoic acid (138.18 ± 8.84 μg/g extract), oleuropein (78.04 ± 4.99 μg/g extract), and rutin (31.21 ± 2.00 μg/g extract) in seed, stem, root, and leaf extracts, respectively. According to the GC−MS analysis, the major components were determined as α-bisabolol (22.93%), cubebol (14.39%), α-pinene (11.63%), and α-limonene (9.41%) among 29 compounds. Consequently, the MEs and EO of A. purpurascens can be used as a natural antioxidant source.     

Auger spectrum of a water molecule after single and double core ionization

The high intensity of free electron lasers opens up the possibility to perform single-shot molecule scattering experiments. However, even for small molecules, radiation damage induced by absorption of high intense x-ray radiation is not yet fully understood. One of the striking effects which occurs under intense x-ray illumination is the creation of double core ionized molecules in considerable quantity. To provide insight into this process, we have studied the dynamics of water molecules in single and double core ionized states by means of electronic transition rate calculations and ab initio molecular dynamics (MD) simulations. From the MD trajectories, photoionization and Auger transition rates were computed based on electronic continuum wavefunctions obtained by explicit integration of the coupled radial Schro?dinger equations. These rates served to solve the master equations for the populations of the relevant electronic states. To account for the nuclear dynamics during the core hole lifetime, the calculated electron emission spectra for different molecular geometries were incoherently accumulated according to the obtained time-dependent populations, thus neglecting possible interference effects between different decay pathways. We find that, in contrast to the single core ionized water molecule, the nuclear dynamics for the double core ionized water molecule during the core hole lifetime leaves a clear fingerprint in the resulting electron emission spectra. The lifetime of the double core ionized water was found to be significantly shorter than half of the single core hole lifetime.     

Transition Metal Ion-binding Properties of a 14-Membered N2O2S2- Macrobicyclic Ligand

The selective liquid–liquid extraction of various transition metal cations from the aqueous phase to the organic phase was carried out using a 14-membered N₂O₂S₂-macrobicycle. Metal picrates such as Pb²⁺, Co²⁺, Zn²⁺, Ni²⁺,Cu²⁺ and Cd²⁺ were used in this extraction studies. It was found that the ligand showed moderate selectivity towards Pb²⁺ only among the other metals. The extraction constant (log K _ex) was determined to be 13.8 for Pb²⁺ complex.