Electronic structure of the nitrogen-vacancy center in diamond from first-principles theory

The nitrogen-vacancy (NV) center is a paramagnetic defect in diamond with applications as a qubit. Here, we investigate its electronic structure by using ab initio density functional theory for five different NV center models of two different cluster sizes. We describe the symmetry and energetics of the low-lying states and compare the optical frequencies obtained to experimental results. We compute the major transition of the negatively charged NV centers to within 25–100 meV accuracy and find that it is energetically favorable for substitutional nitrogens to donate an electron to NV0. The excited state of the major transition and the NV0 state with a neutral donor nitrogen are found to be close in energy.

Sexual dimorphism in amphipods: the role of male posterior gnathopods revealed in Gammarus pulex

In the mate-guarding amphipod, Gammarus pulex, the enlarged male posterior gnathopods have been variously suggested to function to grasp and subdue the female, to be used as weapons in fights between males, to signal to the female the male presence and stimulate moult accelaration, egg development or egg extrusion. These hypotheses were tested in a series of experiments, the results of which reveal an unexpected function. Ablation of the posterior gnathopods of males showed that they were neither necessary for, nor advantageous in, establishment and/ or maintenance of precopula mate guarding, with or without competition with intact males. Furthermore, these appendages do not function to advance female moult, or stimulate egg development or extrusion. However, only males with intact posterior gnathopods were able to copulate. We also show that females require a full copulation of several bouts to extrude eggs. We conclude that the function of the posterior gnathopods is to facilitate copulation and suggest future studies focus on the selective pressures acting on copulating males.

Size-assortative pairing in Gammarus pulex (Crustacea : Amphipoda): a test of the timing hypothesis

We present the first empirical test of the timing hypothesis regarding the generation of size-assortative pairing in amphipods. The timing hypothesis proposes that, since large males are better able to afford the costs of mate guarding than small males, the former can take larger females into precopula earlier in the female moult cycle than is feasible for the latter. This leaves small males to form pairs with smaller females closer to moult, thus generating size assortment. We presented male Gammarus pulex, collected both in precopula and as singletons, with females that were (1) previously guarded and therefore near to copulatory moult and (2) previously unguarded and therefore far from copulatory moult. This comparison tested the prediction of the timing hypothesis, that size assortment should break down when the opportunity for time-based male decisions is removed, but that size assortment should occur where timing is not disrupted. Counter to the hypothesis, we found that size assortment did not break down upon removal of the time factor. Large males tended to initiate mate guarding earlier than small males in both female moult groups. However, only in the previously unguarded group did large males guard for longer than small males. This result suggests that, although size assortment occurred in all groups, the causative mechanisms that generated this pattern may differ between these groups. We therefore consider the possible importance of mechanisms such as aggression, simultaneous manipulation of females and female resistance in producing size assortment where males encounter numerous females that are close to moult. We also observed that prior recent guarding experience by males had no effect on latency to guard or size-assortative pairing. (C) 2002 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved.

Application of static charge transfer within an ionic-liquid force field and its effect on structure and dynamics

The effects of linear scaling of the atomic charges of a reference potential on the structure, dynamics, and energetics of the ionic liquid 1,3-dimethylimidazolium chloride are investigated. Diffusion coefficients that span over four orders of magnitude are observed between the original model and a scaled model in which the ionic charges are +/- 0.5 e. While the three-dimensional structure of the liquid is less affected, the partial radial distribution functions change markedly-with the positive result that for ionic charges of +/- 0.7 e, an excellent agreement is observed with ab initio molecular dynamics data. Cohesive energy densities calculated from these partial-charge models are also in better agreement with those calculated from the ab initio data. We postulate that ionic-liquid models in which the ionic charges are assumed to be +/- 1 e overestimate the intermolecular attractions between ions, which results in overstructuring, slow dynamics, and increased cohesive energy densities. The use of scaled-charge sets may be of benefit in the simulation of these systems-especially when looking at properties beyond liquid structure-thus providing on alternative to computationally expensive polarisable force fields.

CO oxidation and NO reduction on metal surfaces: density functional theory investigations

This article reviews the accumulated theoretical results, in particular density functional theory calculations, on two catalytic processes, CO oxidation and NO reduction on metal surfaces. Owing to their importance in automotive emission control, these two reactions have generated a lot of interest in the last 20 years. Here the pathways and energetics of the involved elementary reactions under different catalytic conditions are described in detail and the understanding of the reactions is generalized. It is concluded that density functional theory calculations can be applied to catalysis to elucidate mechanisms of complex surface reactions and to understand the electronic structure of chemical processes in general. The achieved molecular knowledge of chemical reactions is certainly beneficial to new catalyst design.

Mechanism of H-2 metabolism on Fe-only hydrogenases

The metabolism of hydrogen (H-2 2H(+) + 2e(-)) constitutes a central process in the global biological energy cycle. Among all the enzymes that can mediate this process, Fe-only hydrogenases are unique in their particular high reactivity. Recently, some important progresses have been achieved. Following our previous paper [Z.-P. Liu and P. Hu, J. Am. Chem. Soc. 124, 5175 (2002)] that characterizes the individual redox state of the active site of Fe-only hydrogenase, in this work we have determined the feasible reaction pathways and energetics for the H-2 metabolism on the active site of Fe-only hydrogenases, using density functional theory. We show that H-2 metabolism possesses very low reaction barriers and a proximal base from a nearby protein plays an important role in H-2 metabolism. (C) 2002 American Institute of Physics.

A density functional theory study of stepwise addition reactions in ammonia synthesis on Ru(0001)

To shed light on stepwise addition reactions in ammonia synthesis, density functional theory calculations are carried out to investigate NHx (x = 1-3) formation on Ru(0001). The reactions on a flat surface are first examined. Transition states and reaction barriers are determined. It is found that the reaction barriers for these stepwise addition reactions are rather high. For example, the barrier for NH hydrogenation is calculated to be 1.28 eV, which is comparable with that of N-2 dissociation. One of the stepwise addition reactions, NH + H --> NH2, on a stepped surface is also considered. Interestingly, the reaction barrier is found to be significantly lower than that on the flat surface, but is considerably higher than that of N-2 dissociation on the same stepped surface. In addition, the coverage effect on the reaction energetics is also addressed. (C) 2001 Published by Elsevier Science B.V.

Let your feet do the walking: constraints on the stability of bipedal coordination

In this paper we consider whether the behaviour of the neural circuitry that controls lower limb movements in humans is shaped primarily by the spatiotemporal characteristics of bipedal gait patterns, or by selective pressures that are sensitive to considerations of balance and energetics. During the course of normal locomotion, the full dynamics of the neural circuitry are masked by the inertial properties of the limbs. In the present study, participants executed bipedal movements in conditions in which their feet were either unloaded or subject to additional inertial loads. Two patterns of rhythmic coordination were examined. In the in-phase mode, participants were required to flex their ankles and extend their ankles in synchrony. In the out-of-phase mode, the participants flexed one ankle while extending the other and vice versa. The frequency of movement was increased systematically throughout each experimental trial. All participants were able to maintain both the in-phase and the out-of-phase mode of coordination, to the point at which they could no longer increase their frequency of movement. Transitions between the two modes were not observed, and the stability of the out-of-phase and in-phase modes of coordination was equivalent at all movement frequencies. These findings indicate that, in humans, the behaviour of the neural circuitry underlying coordinated movements of the lower limbs is not constrained strongly by the spatiotemporal symmetries of bipedal gait patterns.

Choline saccharinate and choline acesulfamate: Ionic liquids with low toxicities

Choline saccharinate and choline acesulfamate are two examples of hydrophilic ionic liquids, which can be prepared from easily available starting materials (choline chloride and a non-nutritive sweetener). The (eco)toxicity of these ionic liquids in aqueous solution is very low in comparison to other types of ionic liquids. A general method for the synthesis and purification of hydrophilic ionic liquids is presented. The method consists of a silver-free metathesis reaction, followed by purification of the ionic liquid by ion-exchange chromatography. The crystal structures show a marked difference in hydrogen bonding between the two ionic liquids, although the saccharinate and the acesulfamate anions show structural similarities. The optimized structures, the energetics, and the charge distribution of cation-anion pairs in the ionic liquids were studied by density functional theory (DFT) and second-order (Moller-Plesset) perturbation theory calculations. The occupation of the non-Lewis orbitals was considered to obtain a qualitative picture of the Lewis structures. The calculated interaction energies and the dipole moments for the ion pairs in the gas phase were discussed.

Task-specific ionic liquid for solubilizing metal oxides

Protonated betaine bis(trifluoromethylsulfonyl) imide is an ionic liquid with the ability to dissolve large quantities of metal oxides. This metal-solubilizing power is selective. Soluble are oxides of the trivalent rare earths, uranium(VI) oxide, zinc(II) oxide, cadmium( II) oxide, mercury( II) oxide, nickel( II) oxide, copper(II) oxide, palladium(II) oxide, lead(II) oxide, manganese( II) oxide, and silver( I) oxide. Insoluble or very poorly soluble are iron(III), manganese(IV), and cobalt oxides, as well as aluminum oxide and silicon dioxide. The metals can be stripped from the ionic liquid by treatment of the ionic liquid with an acidic aqueous solution. After transfer of the metal ions to the aqueous phase, the ionic liquid can be recycled for reuse. Betainium bis( trifluoromethylsulfonyl) imide forms one phase with water at high temperatures, whereas phase separation occurs below 55.5 degrees C ( temperature switch behavior). The mixtures of the ionic liquid with water also show a pH-dependent phase behavior: two phases occur at low pH, whereas one phase is present under neutral or alkaline conditions. The structures, the energetics, and the charge distribution of the betaine cation and the bis( trifluoromethylsulfonyl) imide anion, as well as the cation-anion pairs, were studied by density functional theory calculations.

Atomic ordering in nano-layered FePt: Multiscale Monte Carlo simulation

Nano- and meso-scale simulation of chemical ordering kinetics in nano-layered L1(0)-AB binary intermetallics was performed. In the nano- (atomistic) scale Monte Carlo (MC) technique with vacancy mechanism of atomic migration implemented with diverse models for the system energetics was used. The meso-scale microstructure evolution was, in turn, simulated by means of a MC procedure applied to a system built of meso-scale voxels ordered in particular L1(0) variants. The voxels were free to change the L1(0) variant and interacted with antiphase-boundary energies evaluated within the nano-scale simulations. The study addressed FePt thin layers considered as a material for ultra-high-density magnetic storage media and revealed metastability of the L1(0) c-variant superstructure with monoatomic planes parallel to the (001)-oriented layer surface and off-plane easy magnetization. The layers, originally perfectly ordered in the c-variant, showed discontinuous precipitation of a- and b-L1(0)-variant domains running in parallel with homogeneous disordering (i.e. generation of antisite defects). The domains nucleated heterogeneously on the free monoatomic Fe surface of the layer, grew inwards its volume and relaxed towards an equilibrium microstructure of the system. Two

Shell Model Study of Local and Global Energy Barriers in KDP

We perform a study of the energetics of KH2PO4 (KDP) by using a shell model (SM) which was constructed by adjusting the interaction parameters to ab initio calculations, and was fitted to reproduce phonons, polarization-inversion energies and structural properties. We calculate the energy profiles by performing global displacements and local distortions following the ferroelectric (FE) mode pattern in clusters of different sizes embedded in a paraelectric (PE) phase matrix. These properties are expected to be relevant to the PE-FE phase transition. The obtained SM results are compared to corresponding ab initio (AI) data. The global instabilities are found in good agreement for both KDP and DKDP. We also find qualitative good agreement in the KDP structure and even quantitative agreement in the expanded DKDP structure for the local distortions. The SM results reproduce well different trends like increasing instabilities as the cluster sizes grows, as the heavier atoms are included, and as the volume is increased, in accordance with the corresponding data from AI calculations.

Dispersion interactions in room-temperature ionic liquids: Results from a non-empirical density functional

The role of dispersion or van de Waals (VDW) interactions in imidazolium-based room-temperature ionic liquids is studied within the framework of density functional theory, using a recently developed non-empirical functional [M. Dion, H. Rydberg, E. Schroder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004)], as efficiently implemented in the SIESTA code [G. Roman-Perez and J. M. Soler, Phys. Rev. Lett. 103, 096102 (2009)]. We present results for the equilibrium structure and lattice parameters of several crystalline phases, finding a general improvement with respect to both the local density (LDA) and the generalized gradient approximations (GGA). Similar to other systems characterized by VDW bonding, such as rare gas and benzene dimers as well as solid argon, equilibrium distances and volumes are consistently overestimated by approximate to 7%, compared to -11% within LDA and 11% within GGA. The intramolecular geometries are retained, while the intermolecular distances and orientations are significantly improved relative to LDA and GGA. The quality is superior to that achieved with tailor-made empirical VDW corrections ad hoc [M. G. Del Popolo, C. Pinilla, and P. Ballone, J. Chem. Phys. 126, 144705 (2007)]. We also analyse the performance of an optimized version of this non-empirical functional, where the screening properties of the exchange have been tuned to reproduce high-level quantum chemical calculations [J. Klimes, D. Bowler, and A. Michaelides, J. Phys.: Condens. Matter 22, 074203 (2010)]. The results for solids are even better with volumes and geometries reproduced within 2% of experimental data. We provide some insight into the issue of polymorphism of [bmim][Cl] crystals, and we present results for the geometry and energetics of [bmim][Tf] and [mmim][Cl] neutral and charged clusters, which validate the use of empirical force fields. (C) 2011 American Institute of Physics. [doi:10.1063/1.3652897]

Micro-environmental conditions modulate protein secretion and infectivity of the Trichinella spiralis L1 larva

After digestion of infected meat the free L1 of Trichinella spp. penetrate the intestinal mucosa where they moult to the mature adult stage. We have used proteomics to identify changes in protein secretion during in vitro culture of free T. spiralis muscle larvae under different environmental conditions, and to correlate these changes with their infectivity in mice. Muscle larvae were cultured in different media (RPMI-1640, C-199 and HBSS) under conditions of anaerobiosis, microaerobiosis and in 5% CO(2) at 37 degrees C. Following incubation the larval excretory/secretory proteins were analysed by two-dimensional gel electrophoresis and the larvae were used to orally infect naïve CD1 mice. For all culture media tested, infectivity of the L1 was preserved following incubation in anaerobic conditions. In contrast, the infectivity of worms cultured in nutrient-rich media was almost completely abolished in both microaerobiosis and in the presence of 5% CO(2). Some infectivity was retained in poor or reduced culture media. Comparative analysis of larval infectivity and protein secretion showed that loss of infectivity correlated with the appearance of non-tyvelosylated proteins that in turn may be related to the onset of moulting.

Vibrational state-selected photodissociation of ClO+

We report on the UV photodissociation of specific vibrational states (v = 2–45) of ClO+ using velocity map
ion imaging. The high vibrational states of ClO+ are prepared via a double resonant scheme through the
ClO (A 2P) state and ion-pair states followed by photoionization with a third photon. The absorption of a
fourth photon results in photodissociation of the ClO+ into two dominant asymptotic channels. The Cl+
and O+ fragment ion images reveal information on both the energetics of high-lying cation vibrational
states and the low-lying dissociative electronic states that correlate to Cl+(3P) + O(3P) and Cl(2P) + O+(4S)
asymptotic channels. We also report ab initio potentials for the bound ClO+ and ion-pair states as well as
calculations of the ClO+ excited states relevant to the photodissociation process.