Friends or relatives? Phylogenetics and species delimitation in the controversial European orchid Genus ophrys

Background and Aims Highly variable, yet possibly convergent, morphology and lack of sequence variation have severely hindered production of a robust phylogenetic framework for the genus Ophrys. The aim of this study is to produce this framework as a basis for more rigorous species delimitation and conservation recommendations. Methods Nuclear and plastid DNA sequencing and amplified fragment length polymorphism (AFLP) were performed on 85 accessions of Ophrys, spanning the full range of species aggregates currently recognized. Data were analysed using a combination of parsimony and Bayesian tree-building techniques and by principal coordinates analysis. Key Results Complementary phylogenetic analyses and ordinations using nuclear, plastid and AFLP datasets identify ten genetically distinct groups (six robust) within the genus that may in turn be grouped into three sections (treated as subgenera by some authors). Additionally, genetic evidence is provided for a close relationship between the O. tenthredinifera, O. bombyliflora and O. speculum groups. The combination of these analytical techniques provides new insights into Ophrys systematics, notably recognition of the novel O. umbilicata group. Conclusions Heterogeneous copies of the nuclear ITS region show that some putative Ophrys species arose through hybridization rather than divergent speciation. The supposedly highly specific pseudocopulatory pollination syndrome of Ophrys is demonstrably 'leaky', suggesting that the genus has been substantially over-divided at the species level.

The calculation of force constants and normal coordinates IV: XH4 and XH3 molecules

Normal coordinate calculations of XH4 and XH3 molecules are reviewed and discussed. It is shown that for most of these molecules the true values of the force constants in the most General Harmonic Force Field can be uniquely determined only by making use of vibration-rotation interaction constants. It is emphasized that without these extra data the GFF is not determined. The results are compared with various model force fields for these molecules.

The calculation of accurate normal coordinates I: general theory, and application to methane

The calculation of accurate and reliable vibrational potential functions and normal co-ordinates is discussed, for such simple polyatomic molecules as it may be possible. Such calculations should be corrected for the effects of anharmonicity and of resonance interactions between the vibrational states, and should be fitted to all the available information on all isotopic species: particularly the vibrational frequencies, Coriolis zeta constants and centrifugal distortion constants. The difficulties of making these corrections, and of making use of the observed data are reviewed. A programme for the Ferranti Mercury Computer is described by means of which harmonic vibration frequencies and normal co-ordinate vectors, zeta factors and centrifugal distortion constants can be calculated, from a given force field and from given G-matrix elements, etc. The programme has been used on up to 5 × 5 secular equations for which a single calculation and output of results takes approximately l min; it can readily be extended to larger determinants. The best methods of using such a programme and the possibility of reversing the direction of calculation are discussed. The methods are applied to calculating the best possible vibrational potential function for the methane molecule, making use of all the observed data.

Normal coordinates for the planar vibrations of benzene

Force constants and normal coordinates have been recalculated for all of the in-plane vibrations of benzene, making use of the recently observed data on one of the Coriolis constants in the E2g species from the work of Callomon et al. The extent to which the force field is uniquely determined by the data is reviewed for each symmetry species in turn, and the results of a force constant refinement calculation are reported in which a modified valency force field was used based on the hybrid orbital model. The results show considerable differences from Whiffen's normal coordinates for benzene, but somewhat smaller differences from Scherer's recent calculations.

Redundant coordinates in harmonic force-field calculations

Redundancy relations between vibrational coordinates may be linear (as for rectilinear coordinates used in deriving a G matrix), or non-linear (as for curvilinear coordinates used in formulating model force fields). It is shown that geometrically defined internal coordinates are necessarily curvilinear. Hence it is shown that linear force constants can occur in model force field calculations involving redundant coordinates, in disagreement with the recent proposal of Gussoni and Zerbi.

Normal coordinates in the methyl halides

The potential‐energy functions found by Chang for the methyl halides have been put into valence‐type form and revised to eliminate inconsistencies and to accord with the true (nontetrahedral) geometry and the normal frequencies (corrected for Fermi resonance and anharmonicity). The resulting valence‐type force constants and normal coordinates are given for light (CH3) and heavy (CD3) chlorides, bromides, and iodides.

The calculation of force constants and normal coordinates III: constrained force fields for the methyl halides

A method is discussed for imposing any desired constraint on the force field obtained in a force constant refinement calculation. The application of this method to force constant refinement calculations for the methyl halide molecules is reported. All available data on the vibration frequencies, Coriolis interaction constants and centrifugal stretching constants of CH3X and CD3X molecules were used in the refinements, but despite this apparent abundance of data it was found that constraints were necessary in order to obtain a unique solution to the force field. The results of unconstrained calculations, and of three different constrained calculations, are reported in this paper. The constrained models reported are a Urey—Bradley force field, a modified valence force field, and a constraint based on orbital-following bond-hybridization arguments developed in the following paper. The results are discussed, and compared with previous results for these molecules. The third of the above models is found to reproduce the observed data better than either of the first two, and additional reasons are given for preferring this solution to the force field for the methyl halide molecules.

Analytical potentials for triatomic molecules from spectroscopic data VI. On choosing internal coordinates to describe triatomic potential energy surfaces with more than one minimum

Orthogonal internal coordinates are defined which have useful properties for constructing the potential energy functions of triatomic molecules with two or three minima on the surface. The coordinates are used to obtain ground state potentials of ClOO and HOF, both of which have three minima.

Antimalarial drugs based on artemisinin: DFT calculations on the principal reactions

Theoretical calculations have been carried out on the interactions of several endoperoxides which are potential antimalarials, including the clinically useful artemisinin, with two possible sources of iron in the parasite, namely the hexa-aquo ferrous ion [Fe(H2O)(6)](2+) and haeme. DFT calculations show that the reactions of all endoperoxides considered, with both sources of iron, initially generate a Fe-O bond followed by cleavage of the O-O bond to oxygen radical species. Subsequently, they can be transformed into carbon-centred radicals of greater stability. However, with [Fe(H2O)(6)](2+) as the iron source, the oxygen-centred radical species are more likely to react further akin to Fenton's reagent, whereby iron salts encourage hydrogen peroxide to act as an oxidizing agent, and that solvent plays a major role. In contrast, when reacting with haeme, the oxygen-centred radicals interconvert to more stable carbon-centred radicals, which can then alkylate haeme. Subsequent cleavage of the Fe-O bond leads to stable and inactive antimalarial products. These results indicate that the reactivity of the endoperoxides as antimalarials is greater with iron hexahydrates for radical-mediated damage as opposed to haeme, which leads to unreactive species. Since only nanomolar quantities of hydrated metal ions could catalyse the reactions leading to damage to the parasites, this could be an alternative or competitive reaction responsible for the antimalarial activity. (c) 2005 Elsevier B.V. All rights reserved.

Coding of visual space during motor preparation: approaching objects rapidly modulate corticospinal excitability in hand-centered coordinates

Defensive behaviors, such as withdrawing your hand to avoid potentially harmful approaching objects, rely on rapid sensorimotor transformations between visual and motor coordinates. We examined the reference frame for coding visual information about objects approaching the hand during motor preparation. Subjects performed a simple visuomanual task while a task-irrelevant distractor ball rapidly approached a location either near to or far from their hand. After the distractor ball appearance, single pulses of transcranial magnetic stimulation were delivered over the subject's primary motor cortex, eliciting motor evoked potentials (MEPs) in their responding hand. MEP amplitude was reduced when the ball approached near the responding hand, both when the hand was on the left and the right of the midline. Strikingly, this suppression occurred very early, at 70-80ms after ball appearance, and was not modified by visual fixation location. Furthermore, it was selective for approaching balls, since static visual distractors did not modulate MEP amplitude. Together with additional behavioral measurements, we provide converging evidence for automatic hand-centered coding of visual space in the human brain.