Efficient protocol for quantum Monte Carlo calculations of hydrogen abstraction barriers: Application to methanol

Accurate calculation of hydrogen abstraction reaction barriers is a challenging problem, often requiring high level quantum chemistry methods that scale poorly with system size. Quantum Monte Carlo (QMC) methods provide an alternative approach that exhibit much better scaling, but these methods are still computationally expensive. We describe approaches that can significantly reduce the cost of QMC calculations of barrier heights, using the hydrogen abstraction of methanol by a hydrogen atom as an illustrative example. By analysing the combined influence of trial wavefunctions and pseudopotential quadrature settings on the barrier heights, variance, and time‐step errors, we devise a simple protocol that minimizes the cost of the QMC calculations while retaining accuracy comparable to large‐basis coupled cluster theory. We demonstrate that this protocol is transferable to other hydrogen abstraction reactions.     

Adsorption, desorption, and surface-promoted hydrolysis of glucose-1-phosphate in aqueous goethite (α-FeOOH) suspensions

Adsorption, desorption, and precipitation reactions at environmental interfaces govern the fate of phosphorus in terrestrial and aquatic environments. Typically, a substantial part of the total pool of phosphorus consists of organophosphate, and in this study we have focused on the interactions between glucose-1-phosphate (G1P) and goethite (α-FeOOH) particles. The adsorption and surface-promoted hydrolysis reactions have been studied at room temperature as a function of pH, time, and total concentration of G1P by means of quantitative batch experiments in combination with infrared spectroscopy. A novel simultaneous infrared and potentiometric titration (SIPT) technique has also been used to study the rates and mechanisms of desorption of the surface complexes. The results have shown that G1P adsorption occurs over a wide pH interval and at pH values above the isoelectric point of goethite (IEP(goethite) = 9.4), indicating a comparatively strong interaction with the particle surfaces. As evidenced by IR spectroscopy, G1P formed pH-dependent surface complexes on goethite, and investigations of both adsorption and desorption processes were consistent with a model including three types of surface complexes. These complexes interact monodentately with surface Fe but differ in hydrogen bonding interactions via the auxiliary oxygens of the phosphate group. The apparent desorption rates were shown to be influenced by reaction pathways that include interconversion of surface species, which highlights the difficulty in determining the intrinsic desorption rates of individual surface complexes. Desorption results have also indicated that the molecular structures of surface complexes and the surface charge are two important determinants of G1P desorption rates. Finally, this study has shown that surface-promoted hydrolysis of G1P by goethite is base-catalyzed but that the extent of hydrolysis was small.     

AT‐Specific DNA Binding of Binuclear Ruthenium Complexes at the Border of Threading Intercalation

The binuclear ruthenium complex [μ‐bidppz(phen)₄Ru₂]⁴⁺ has been extensively studied since the discovery of its unusual threading intercalation interaction with DNA, a binding mode with extremely slow binding and dissociation kinetics. The complex has been shown to be selective towards long stretches of alternating AT base pairs, which makes it interesting, for example, as a model compound for anti‐malaria drugs due to the high AT content of the genome of the malaria parasite P. falciparum. We have investigated the effect of bridging ligand structure on threading intercalation ability and found that length and rigidity as well as the size of the intercalated ring system are all factors that affect the rate and selectivity of the threading intercalation. In particular, we discovered a new DNA‐threading compound, [μ‐dppzip(phen)₄Ru₂]⁴⁺, which appears to be just at the border of being capable of threading intercalation and displays even greater selectivity for AT‐DNA than the parent compound, [μ‐bidppz(phen)₄Ru₂]⁴⁺.     

Strategies to set global analytical quality specifications in laboratory medicine: 10 years on from the Stockholm consensus conference

The setting of analytical quality specifications in laboratory medicine has attracted attention for many years. Over time, many strategies were advocated and all had advantages and disadvantages. In the final decade of the last millennium, considerable confusion existed on how to define analytical quality specifications correctly and how to apply them in everyday practice. This led to wide professional interest. In 1999, a consensus conference sponsored by IUPAC, IFCC and WHO was held in Stockholm on “Strategies to Set Global Analytical Quality Specifications in Laboratory Medicine”. The consensus set useful and well-documented strategies for the setting of analytical quality specifications into a hierarchy with the best strategy at the highest level, namely, (1) Evaluation of the effect of analytical performance on clinical outcomes in specific clinical situations, (2) Evaluation of the effect of analytical performance on clinical decisions in general, (3) Published professional recommendations, (4) Performance goals set by regulatory bodies and EQAS organisers, and (5) Goals based on the current state of the art. Much success has been achieved since the promulgation of the statement with the approach being adopted by many in laboratory medicine for a very wide variety of purposes, particularly in quality management. However, there is a requirement for additional investigation of, inter alia, quality specifications for examinations done on measurements performed on ordinal and nominal scales, pre-analytical factors and matrix effects, examinations done as POCT, target values of control materials, and ways in which analytical quality specifications can be used both to set what is the optimum performance and as a tool for assessment of everyday practice.     

Electronic and optical properties of defect chalcopyrite HgAl2Se4

The structural, electronic and optical properties of HgAl₂Se₄ are investigated using the full potential linear augmented plane wave method based on density functional theory. The calculated structural parameters using LDA are in excellent agreement with the available experimental result. The obtained energy band gap (2.24 eV) using EV-GGA approximation is in excellent agreement with experimental data (2.20 eV). Variation in the energy band gap as a function of the unit cell lattice parameter has been studied. The optical properties show a considerable anisotropy, which makes this compound very useful for various linear–nonlinear optical devices.     

Dipolar Order in Molecular Fluids: I. Toward an Understanding

The origin behind the dipolar order in molecular fluids is investigated by using a simple dipolar fluid and Monte Carlo simulation technique. A penalty function is employed to separately manipulate the positional and orientational structure of the fluid. By considering the distance-dependent Kirkwood function G _k, which in turn is related to the dielectric permittivity of the fluid, it is observed that both positional and orientational ordering are involved to establish dipolar order.     

Dipolar Order in Molecular Fluids: II. Molecular Influence

The influence on the short-range packing in dipolar fluids by molecular shape and by additional higher order electrostatic moments has been investigated by molecular dynamic simulations. The dipole polarization was found to decrease as the particles were elongated parallel to the dipole and to increase for elongation perpendicular to the dipole, eventually forming a nematic order. The addition of a quadrupole lead to a reduction of the polarization, and the influence of an axial octupole was weaker and more complex. Both a decrease and an increase of the polarization is possible depending on the relative dipole–dipole and octupole–octupole interaction strengths and the relative direction of the symmetry axes of the moments. These observations were attributed to the different parity of a dipole and a quadrupole and the same parity of a dipole and an axial octupole under reflection. In addition, further insights into the formation of dipole polarization were obtained. Short polar and long equatorial radii and strong dipole–dipole interaction are particle properties that promote a fluid with a high dipole polarization.     

Laserlike vibrational instability in rectifying molecular conductors

We study the damping of molecular vibrations due to electron-hole pair excitations in donor-acceptor (D-A) type molecular rectifiers. At finite voltage additional nonequilibrium electron-hole pair excitations involving both electrodes become possible, and contribute to the stimulated emission and absorption of phonons. We point out a generic mechanism for D-A molecules, where the stimulated emission can dominate beyond a certain voltage due to the inverted position of the D and A quantum resonances. This leads to current-driven amplification (negative damping) of the phonons similar to laser action. We investigate the effect in realistic molecular rectifier structures using first-principles calculations.     

Are "pinholes" the cause of excess current in superconducting tunnel junctions? A study of Andreev current in highly resistive junctions

In highly resistive superconducting tunnel junctions, excess subgap current is usually observed and is often attributed to microscopic pinholes in the tunnel barrier. We have studied the subgap current in superconductor-insulator-superconductor (SIS) and superconductor-insulator-normal-metal (SIN) junctions. In Al/AlO(x)/Al junctions, we observed a decrease of 2 orders of magnitude in the current upon the transition from the SIS to the SIN regime, where it then matched theory. In Al/AlO(x)/Cu junctions, we also observed generic features of coherent diffusive Andreev transport in a junction with a homogenous barrier. We use the quasiclassical Keldysh-Green function theory to quantify single- and two-particle tunneling and find good agreement with experiment over 2 orders of magnitude in transparency. We argue that our observations rule out pinholes as the origin of the excess current.