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.

Probing warm dense lithium by inelastic X-ray scattering

One of the grand challenges of contemporary physics is understanding strongly interacting quantum systems comprising such diverse examples as ultracold atoms in traps, electrons in high-temperature superconductors and nuclear matter. Warm dense matter, defined by temperatures of a few electron volts and densities comparable with solids, is a complex state of such interacting matter. Moreover, the study of warm dense matter states has practical applications for controlled thermonuclear fusion, where it is encountered during the implosion phase, and it also represents laboratory analogues of astrophysical environments found in the core of planets and the crusts of old stars, Here we demonstrate how warm dense matter states can be diagnosed and structural properties can be obtained by inelastic X-ray scattering measurements on a compressed lithium sample. Combining experiments and ab initio simulations enables us to determine its microscopic state and to evaluate more approximate theoretical models for the ionic structure.

Time-dependent R -matrix theory for ultrafast atomic processes

We describe an ab initio nonperturbative time-dependent R-matrix theory for ultrafast atomic processes. This theory enables investigations of the interaction of few-femtosecond and -attosecond pulse lasers with complex multielectron atoms and atomic ions. A derivation and analysis of the basic equations are given, which propagate the atomic wave function in the presence of the laser field forward in time in the internal and external R-matrix regions. To verify the accuracy of the approach, we investigate two-photon ionization of Ne irradiated by an intense laser pulse and compare current results with those obtained using the R-matrix Floquet method and an alternative time-dependent method. We also verify the capability of the current approach by applying it to the study of two-dimensional momentum distributions of electrons ejected from Ne due to irradiation by a sequence of 2 as light pulses in the presence of a 780 nm laser field.

Thermochemistry of Ionic Liquid-Catalyzed Reactions. Experimental and Theoretical Study of Chemical Equilibria of Isomerization and Transalkylation of tert-Butylbenzenes

The chemical equilibrium of mutual interconversions of tert-butylbenzenes was studied in the temperature range 286 to 423 K using chloroaluminate ionic liquids as a catalyst. Enthalpies of five reactions of isomerization and transalkylation of tert-butylbenzenes were obtained from temperature dependences of the corresponding equilibrium constants in the liquid phase. Molar enthalpies of vaporization of methyl-tert-butylbenzenes and 1,4-ditert-butylbenzene were obtained by the transpiration method and were used for a recalculation of enthalpies of reactions and equilibrium constants into the gaseous phase. Using these experimental results, ab initio methods (B3LYP and G3MP2) have been tested for prediction thermodynamic functions of the five reactions under study successfully. Thermochemical investigations of tert-butyl benzenes available in the literature combined with experimental results have helped to resolve contradictions in the available thermochemical data for tert-butylbenzene and to recommend consistent and reliable enthalpies of formation for this compound in the liquid and the gaseous state.

Geometric bonding effects in the X2A1, A2∑+u, and B2IIg states of Li2F

Published ab-initio and pseudopotential calculations for the dialkali halide systems suggest that the preferred co-linear geometry is for the metal to approach the metal end of the alkali halide. Here, ab-initio calculations on the Li2F system reveal that the well depth on the halide side in this radical is much deeper and is a local saddle-point associated with the ionic non-linear global minima. Although many features of the pseudopotential surfaces are confirmed, significant differences are apparent including the existence of a linear excited state instead of a triangular one, a considerably deeper global minimum some 50% lower in energy and a close approach between the X2A1 and the states, with the minimum 87 kJ mol-1 below the ground state asymptote. All the results can be rationalised as the avoided crossings between a long range, covalent potential dominant within the LiLiF geometry and an ionic state that forms the global minimum. Calculations on the 3rd 2A' potential indicate that even for Li + LiF collisions at ultracold temperatures the collision dynamics could involve as many as three electronic states.

Multiple Evidence for Gold(I)center dot center dot center dot Silver(I) Interactions in Solution

[AuAg3(C6F5)(CF3CO2)(3)(CH2PPh3)](n) (2) was prepared by reaction of [Au(C6F5)(CH2PPh3)] (1) and [Ag(CF3CO2)] (1:3). The crystal structures of complexes I and 2 were determined by X-ray diffraction, and the latter shows a polymeric 2D arrangement built by Au - Ag, Ag - Ag, and Ag - O contacts. The metallophilic interactions observed in 2 in the solid state seem to be preserved in concentrated THF solutions, as suggested by EXAFS, pulsed-gradient spin-echo NMR, and photophysical studies, which showed that the structural motif [AuAg3(C6F5)(CF3CO2)(3)(CH2PPh3)] is maintained under such conditions. Time-dependent DFT calculations agree with the experimental photophysical energies and suggest a metal-to-ligand charge-transfer phosphorescence process. Ab initio calculations give an estimated interaction energy of around 60 kJ mol(-1) for each Au - Ag interaction.

Ring currents in azulene

We propose a self consistent polarisable ion tight binding theory for the study of push-pull processes in aromatic molecules. We find that the method quantitatively reproduces ab initio calculations of dipole moments and polarisability. We apply the scheme in a simulation which solves the time dependent Schroedinger equation to follow the relaxation of azulene from the second excited to the ground states. We observe rather spectacular oscillating ring currents which we explain in terms of interference between the HOMO and LUMO states.

Solid-state analysis of low-melting 1,3-dialkylimidazolium hexafluorophosphate salts (ionic liquids) by combined x-ray crystallographic and computational analyses

The interactions of ions in the solid state for a series of representative 1,3-dialkylimidazolium hexafluorophosphate salts (either ionic liquids or closely related) have been examined by crystallographic analysis, combined with the theoretical estimation of crystal-packing densities and lattice-interaction energies. Efficient close-packing of the ions in the crystalline states is observed, but there was no compelling evidence for specific directional hydrogen-bonding to the hexafluorophosphate anions or the formation of interstitial voids. The close-packing efficiency is supported by the theoretical calculation of ion volumes, crystal lattice energies, and packing densities, which correlated well with experimental data. The crystal density of the salts can be predicted accurately from the summation of free ion volumes and lattice energies calculated. Of even more importance for future work, on these and related salts, the solid-state density of 1,3-dialkylimidazolium hexafluorophosphate salts can be predicted with reasonable accuracy purely on the basis of on ab initio free ion volumes, and this allows prediction of lattice energies without necessarily requiring the crystal structures.

Suggested Binding Mechanism of the HIV-gp120 to its CD4 Receptor

The molecular recognition and attachment of the CD4 molecule and the HIV envelope glycoprotein (gp120) might be described as a consecutive three-step molecular recognition process. 1. (a) Long range interaction: electrostatic pre-orientation, 2. (b) short range interaction: electronic attachment followed by a ‘Locking-in’ (via aromatic ring orientation) and 3. (c) internal interaction (induced fit): conformational readjustment of the protein molecules. On the basis of the preliminary investigations (X-ray structures of CD4 and biological studies of CD4 and gp120 point mutants) we described a computational model. This approach consists of empirical calculations as well as ab initio level of quantum chemistry. The conformational analysis of the wild type and mutant CD4 molecules was supported by molecular mechanics and dynamics (Amber force field). The latter analysis involves the application of a novel method, the Amino Acid Conformation Assignment of Proteins (ACAP) software, developed for the notation of secondary protein structures. According to the cardinal role of the electrostatic factors during this interaction, several ab initio investigations were performed for better understanding of the recognition process on submolecular level. Using the above mentioned computational model, we could interpret the basic behaviours and predict some additional features of CD4-gp120 interaction, in spite of the missing gp120 X-ray structure.

Lowest energy potentials of Li2 + F accessible at ultracold temperatures

Ab initio calculations for the strongly exoergic Li2+F harpoon reaction are presented using density-functional theory, complete active space self-consistent field, and multireference configuration interaction methods to argue that this reaction would be an ideal candidate for investigation with ultracold molecules. The lowest six states are calculated with the aug-correlation-consistent polarized valence triple-zeta basis set and at least two can be accessed by a ground rovibronic Li2 molecule with zero collision energy at all reaction geometries. The large reactive cross section (characteristic of harpoon reactions) and chemiluminescent products are additional attractive features of these reactions.

The negatively charged nitrogen-vacancy centre in diamond: the electronic solution

The negatively charged nitrogen-vacancy centre in diamond is a unique defect centre in diamond that possesses properties highly suited to many applications, including quantum information processing, quantum metrology, and biolabelling. Although the unique properties of the centre have been extensively documented and utilised, a detailed understanding of the physics of the centre has not yet been achieved. Indeed there persists a number of points of contention regarding the electronic structure of the centre, such as the ordering of the dark intermediate singlet states. Without a sound model of the centre’s electronic structure, the understanding of the system’s unique dynamical properties can not effectively progress. In this work, the molecular model of the defect centre is fully developed to provide a self consistent model of the complete electronic structure of the centre. The application of the model to describe the effects of electric, magnetic and strain interactions, as well as the variation of the centre’s fine structure with temperature, provides an invaluable tool to those studying the centre and a means to design future experiments and ab initio studies of this important defect centre.

Melting of a tetrahedral network model of silica

Thermal properties of an idealised tetrahedral network model of silica are investigated by Monte Carlo simulations. The interatomic potential consists of anharmonic stretching and bending terms, plus a short range repulsion. The model includes a bond interchange rule similar to the well known Wooten, Winer and Weaire (WWW) algorithm (see Phys. Rev. Lett., 1985, 54, 1392). Simulations reveal an apparent first order melting transition at T = 2200 K. The computed changes in the local coordination upon melting are consistent with experimental and ab initio data.

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.

Runx2, p53, and pRB Status as Diagnostic Parameters for Deregulation of Osteoblast Growth and Differentiation in a New Pre-Chemotherapeutic Osteosarcoma Cell Line (OS1)

Osteosarcomas are the most prevalent primary bone tumors found in pediatric patients. To understand their molecular etiology, cell culture models are used to define disease mechanisms under controlled conditions. Many osteosarcoma cell lines (e.g., SAOS-2, U2OS, MG63) are derived from Caucasian patients. However, patients exhibit individual and ethnic differences in their responsiveness to irradiation and chemotherapy. This motivated the establishment of osteosarcoma cell lines (OS1, OS2, OS3) from three ethnically Chinese patients. OS1 cells, derived from a pre-chemotherapeutic tumor in the femur of a 6-year-old female, were examined for molecular markers characteristic for osteoblasts, stem cells, and cell cycle control by immunohistochemistry, reverse transcriptase-PCR, Western blotting and flow cytometry. OS I have aberrant G-banded karyotypes, possibly reflecting chromosomal abnormalities related to p53 deficiency. OS I had ossification profiles similar to human fetal osteoblasts rather than SAOS-2 which ossifies ab initio, (P

Electronic states and spin-forbidden cooling transitions of AlH and AlF

The feasibility of laser cooling AlH and AlF is investigated using ab initio quantum chemistry. All the electronic states corresponding to the ground and lowest two excited states of the Al atom are calculated using multi-reference configuration interaction (MRCI) and the large AV6Z basis set for AlH. The smaller AVQZ basis set is used to calculate the valence electronic states of AlF. Theoretical Franck-Condon factors are determined for the A(1)Pi -> X(1)Sigma(+) transitions in both radicals and found to agree with the highly diagonal factors found experimentally, suggesting computational chemistry is an effective method for screening suitable laser cooling candidates. AlH does not appear to have a transition quite as diagonal as that in SrF (which has been laser cooled) but the A(1)Pi -> X(1)Sigma(+) transition transition of AlF is a strong candidate for cooling with just a single laser, though the cooling frequency is deep in the UV. Furthermore, the a (3)Pi -> X(1)Sigma(+) transitions are also strongly diagonal and in AlF is a practical method for obtaining very low final temperatures around 3 mu K.