Equilibrium structure of the hydrogen bonded dimer H2O ⋯ HF

The equilibrium structure of the hydrogen bonded complex H2O HF has been calculated ab initio using the CCSD(T) method with basis sets up to sextuple- quality with diffuse functions and taking into account the basis set superposition error correction. The calculations carried out confirm the importance of diffuse functions and of counterpoise correction to obtain an accurate geometry. The most important point is that the basis set convergence is extremely slow and, for this reason an accurate ab initio structure requires a very large basis set. Nevertheless, the ab initio structure is significantly different from the experimental r0 and rm structures. Analysis of the basis set convergence and of the approximations used for the determination of the experimental structures indicates that the ab initio structure is expected to be more reliable.

Towards more accurate and reliable predictions for nuclear applications

The need for nuclear data far from the valley of stability, for applications such as nuclear as- trophysics or future nuclear facilities, challenges the robustness as well as the predictive power of present nuclear models. Most of the nuclear data evaluation and prediction are still performed on the basis of phenomenological nuclear models. For the last decades, important progress has been achieved in funda- mental nuclear physics, making it now feasible to use more reliable, but also more complex microscopic or semi-microscopic models in the evaluation and prediction of nuclear data for practical applications. In the present contribution, the reliability and accuracy of recent nuclear theories are discussed for most of the relevant quantities needed to estimate reaction cross sections and beta-decay rates, namely nuclear masses, nuclear level densities, gamma-ray strength, fission properties and beta-strength functions. It is shown that nowadays, mean-field models can be tuned at the same level of accuracy as the phenomenological mod- els, renormalized on experimental data if needed, and therefore can replace the phenomenogical inputs in the prediction of nuclear data. While fundamental nuclear physicists keep on improving state-of-the-art models, e.g. within the shell model or ab initio models, nuclear applications could make use of their most recent results as quantitative constraints or guides to improve the predictions in energy or mass domain that will remain inaccessible experimentally.

Vibrational spectroscopy and DFT calculations of di-amino acid cyclic peptides. Part I: cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) in the solid state and in aqueous solution

Investigations of the vibrational spectra of cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(t-Ala-Gly) are reported. Raman scattering and Fourier transform infrared (FTIR) spectra of solid-state and aqueous protonated samples, as well as their corresponding N-deuterated isotopomers, have been examined. In addition, density functional theory (DFT) (B3-LYP/cc-pVDZ) calculations of molecular structures and their associated vibrational modes were carried out. In each case, the calculated structures of lowest energy for the isolated gas-phase molecules have boat conformations. Assignments have been made for the observed Raman and FTIR vibrational bands of the cyclic di-amino acid peptides (CDAPs) examined. Raman polarization studies of aqueous phase samples are consistent with C-2 and C-1 symmetries for the six-membered rings of cyclo(L-Ala-L-Ala) and cydo(L-Ala-Gly), respectively. There is a good correlation between experimental and calculated vibrational bands for the three CDAPs. These data are in keeping with boat conformations for cydo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) molecules, predicted by the ab initio calculations, in both the solid and aqueous solution states. However, Raman spectroscopic results might infer that cyclo(L-AlaGly) deviates only slightly from planarity in the solid state. The potential energy distributions of the amide I and II modes of a cis-peptide linkage are shown to be significantly different from those of the trans-peptides. For example, deuterium shifts have shown that the cis-amide I vibrations found in cyclo(Gly-Gly), cyclo(L-Ala-L-Ala), and cyclo(L-Ala-Gly) have larger N-H contributions compared to their trans-amide counterparts. Compared to trans-amide II vibrations, cis-amide II vibrations show a considerable decrease in N-H character.

Synthesis and enzymatic evaluation of the guanosine analogue 2-amino-6-mercapto-7-methylpurine ribonucleoside (MESG): insights into the phosphorolysis reaction mechanism based on the blueprint transition state: SN1 or SN2?

A modified experimental procedure for the synthesis of MESG (2-amino-6-mercapto-7-methylpurine ribonucleoside) 1 has been successfully performed and its full characterization is presented. High resolution ESI(+)-MSMS indicates both the nucleoside bond cleavage as the main fragmentation in the gas phase and a possible SN1 mechanism. Ab initio transition state calculations based on the blue print transition state support this mechanistic rationale and discard an alternative SN2 mechanism. Assays using purine nucleoside phosphorylase (PNP) enzyme (human and M. tuberculosis sources) indicate its efficiency in the phosphorolysis of MESG and allow the quantitative determination of inorganic phosphate in real time assay.

Multiple proton translocation in biomolecular systems: concerted to stepwise transition in a simple model

In this paper we study a simple model potential energy surface (PES) useful for describing multiple proton translocation mechanisms. The approach presented is relevant to the study of more complex biomolecular systems like enzymes. In this model, at low temperatures, proton tunnelling favours a concerted proton transport mechanism, while at higher temperatures there is a crossover from concerted to stepwise mechanisms; the crossover temperature depends on the energetic features of the PES. We illustrate these ideas by calculating the crossover temperature using energies taken from ab initio calculations on specific systems. Interestingly, typical crossover temperatures lie around room temperature; thus both concerted and stepwise reaction mechanisms should play an important role in biological systems, and one can be easily turned into another by external means such as modifying the temperature or the pH, thus establishing a general mechanism for modulation of the biomolecular function by external effectors.

Correlation Effects in the Compton Profile of Silicon

Ab initio nonlocal pseudopotential variational quantum Monte Carlo techniques are used to compute the correlation effects on the valence momentum density and Compton profile of silicon. Our results for this case are in excellent agreement with the Lam-Platzman correction computed within the local density approximation. Within the approximations used, we rule out valence electron correlations as the dominant source of discrepancies between calculated and measured Compton profiles of silicon.

Compton profiles of Si: Pseudopotential calculation and reconstruction effects

Using an ab initio pseudopotential calculation, we compute Compton profiles of silicon along the (100), (110), and (111) directions, and then reconstruct the pseudo-wave-functions to regain the oscillatory behavior of the all-electron valence wave functions near the atomic cores. We study the effect that this reconstruction has on the Compton profiles and their anisotropies. We find a decrease in the magnitude of the profiles at small wave vectors and in their anisotropies. These changes bring the theoretical predictions closer to experimental results.

Solvation Structure and Transport of Acidic Protons in Ionic Liquids: A First-principles Simulation Study

Ab initio simulations of a single molecule of HCl in liquid dimethyl imidazolium chloride [dmim][Cl] show that the acidic proton exists as a symmetric, linear ClHCl- species. Details of the solvation structure around this molecule are given. The proton-transfer process was investigated by applying a force along the antisymmetric stretch coordinate until the molecule broke. Changes in the free energy and local solvation structure during this process were investigated. In the reaction mechanism identified, a free chloride approaches the proton from the side. As the original ClHCl- distorts and the incoming chloride forms a new bond to the proton, one of the original chlorine atoms is expelled and a new linear molecule is formed.

Molecular electrostatic properties of ions in an ionic liquid

We have analysed the electronic wave functions from an ab initio simulation of the ionic liquid (room temperature molten salt) dimethyl imidazolium chloride ([dmim][Cl] or [C1mim][Cl]) using localized Wannier orbitals. This allows us to assign electron density to individual ions. The probability distributions of the ionic dipole moments for an isolated ion and for ions in solution are compared. The liquid environment is found to polarize the cation by about 0.7 D and to increase the amplitude of the fluctuations in the dipole moments of both cation and anion. The relative changes in nuclear and electronic contributions are shown. The implications for classical force fields are discussed.

R-matrix theory of electron molecule scattering

This paper presents an overview of R-matrix theory of electron scattering by diatomic and polyatomic molecules. The paper commences with a detailed discussion of the fixed-nuclei approximation which in recent years has been used as the basis of the most accurate ab initio calculations. This discussion includes an overview of the computer codes which enable electron collisions with both diatomic and polyatomic molecules to be calculated. Nuclear motion including rotational and vibrational excitation and dissociation is then discussed. In non-resonant energy regions, or when the scattered electron energy is not close to thresholds, the adiabatic-nuclei approximation can be successfully used. However, when these conditions are not applicable, non-adiabatic R-matrix theory must be used and a detailed discussion of this theory is given. Finally, recent applications of the theory to treat electron scattering by polyatomic molecules are reviewed and a detailed comparison of R-matrix calculations and experimental measurements for water is presented.

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.

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.

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.