Spin-orbit configuration interaction study of the electronic structure of the 5f (2) manifold of U(4+) and the 5f manifold of U(5+)

The energy levels of the 5f configuration of U(5+) and 5f(2) configuration of U(4+) have been calculated in a dressed effective Hamiltonian relativistic spin-orbit configuration interaction framework. Electron correlation is treated in the scalar relativistic scheme with either the multistate multireference second-order multiconfigurational perturbation theory (MS-CASPT2) or with the multireference single and double configuration interaction (MRCI) and its size-extensive Davidson corrected variant. The CASPT2 method yields relative energies which are lower than those obtained with the MRCI method, the differences being the largest for the highest state (1)S(0) of the 5f(2) manifold. Both valence correlation effects and spin-orbit polarization of the outer-core orbitals are shown to be important. The satisfactory agreement of the results with experiments and four-component correlated calculations illustrates the relevance of dressed spin-orbit configuration interaction methods for spectroscopy studies of heavy elements.     

QM/MM-PBSA method to estimate free energies for reactions in proteins

We have developed a method to estimate free energies of reactions in proteins, called QM/MM-PBSA. It estimates the internal energy of the reactive site by quantum mechanical (QM) calculations, whereas bonded, electrostatic, and van der Waals interactions with the surrounding protein are calculated at the molecular mechanics (MM) level. The electrostatic part of the solvation energy of the reactant and the product is estimated by solving the Poisson-Boltzmann (PB) equation, and the nonpolar part of the solvation energy is estimated from the change in solvent-accessible surface area (SA). Finally, the change in entropy is estimated from the vibrational frequencies. We test this method for five proton-transfer reactions in the active sites of [Ni,Fe] hydrogenase and copper nitrite reductase. We show that QM/MM-PBSA reproduces the results of a strict QM/MM free-energy perturbation method with a mean absolute deviation (MAD) of 8-10 kJ/mol if snapshots from molecular dynamics simulations are used and 4-14 kJ/mol if a single QM/MM structure is used. This is appreciably better than the original QM/MM results or if the QM energies are supplemented with a point-charge model, a self-consistent reaction field, or a PB model of the protein and the solvent, which give MADs of 22-36 kJ/mol for the same test set.     

Proteome profiling of human cerebrospinal fluid: exploring the potential of capillary electrophoresis with surface modified capillaries for analysis of complex biological samples

A bottom-up proteomic approach, based on capillary electrophoresis (CE) in combination with matrix- assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-ToF/ToF MS), was used to analyze immunoaffinity depleted human cerebrospinal fluid (CSF) and compare it with a non-depleted sample. After enzymatic digestion and desalting, the tryptic peptides were separated by CE using PolyE-323 modified capillaries and fractionated off-line onto MALDI target plates for further analysis by MALDI-MS and MS/MS. The protein profile of the depleted sample was compared with non depleted CSF. Overall, 85 proteins were identified with 95% significance in both samples. The significance scores for proposed biomarkers, such as amyloid-like protein 1 precursor, could be increased up to 12 times after the depletion. Other proteins, often suggested to be related to neurodegenerative diseases, like amyloid beta A4 protein precursor, superoxide dismutase and apolipoprotein E precursor could only be found in the depleted CSF samples. The effect of a derivatization of tryptic peptides with 2- methoxy-4,5-dihydro-1H-imidazole reagent for protein identification with MS was also employed to increase the number of identified proteins and the sequence coverages. The results presented in this study illustrate the benefit of combining a sample pre-fractionation step and a label's ability to enhance the ionization efficiency with the potential of CE using PolyE-323 modified capillaries in the analysis of complex samples. The straight-forward approach that provides speed and simplicity resulting in high-resolution separations and low sample consumption represents an easily applicable separation technique that can serve as a complement to other currently existing analytical approaches needed in modern proteomic analysis of clinically relevant samples.     

Lamellar miscibility gap in a binary catanionic surfactant-water system

The coexistence of two lamellar liquid-crystalline phases in equilibrium for binary surfactant-water systems is a rare and still puzzling phenomenon. In the few binary systems where it has been demonstrated experimentally, the surfactant is invariably ionic and the miscibility gap is thought to stem from a subtle balance between attractive and repulsive interbilayer forces. In this paper, we report for the first time a miscibility gap for a catanionic lamellar phase formed by the surfactant hexadecyltrimethylammonium octylsulfonate (TASo) in water. Synchrotron small-angle X-ray scattering, polarizing light microscopy, and 2H NMR unequivocally show the coexistence of a dilute (or swollen) lamellar phase, Lalpha', and a concentrated (or collapsed) lamellar phase, Lalpha' '. Furthermore, linear swelling is observed for each of the phases, with the immiscibility region occurring for 15-54 wt % surfactant. In the dilute region, the swollen lamellar phase is in equilibrium with an isotropic micellar region. Vesicles can be observed in this two-phase region as a dispersion of Lalpha' in the solution phase. A theoretical cell model based on combined DLVO and short-range repulsive potentials is presented in order to provide physical insight into the miscibility gap. The surfactant TASo is net uncharged, but it undergoes partial dissociation owing to the higher aqueous solubility of the short octylsulfonate chain. Thus, a residual positive charge in the bilayer is originated and, consequently, an electrostatic repulsive force, whose magnitude is dependent on surfactant concentration. For physically reasonable values of the solubility of the octyl chain, assumed to be constant with surfactant volume fraction, a fairly good agreement is observed between the experimental miscibility gap and the theoretical one.     

Synthesis and DNA incorporation of an ethynyl-bridged cytosine C-nucleoside as guanosine surrogate

As a guanosine mimic that lacks the preference for syn or anti conformation a cytosine C-nucleoside was synthesized connecting the nucleobase at the anomeric center by an ethynyl linker. The key step was a Sonogashira cross coupling of 5-iodocytosine with 1'-ethynyl-2'-deoxyribose. The new C-nucleoside incorporated into G/C-alternating oligonucleotides emerged as guanosine substitute, however, with reduced duplex stability. B-Form DNA was strongly stabilized by the new surrogate even in typically Z-DNA forming sequences and in Z-form inducing environment.     

Experiments on sound generation in corrugated pipes with flow

The article reports acoustic measurements on short corrugated pipes with flow. Such pipes might generate high sound levels associated with length resonances. One of the main objectives of the study was to estimate the location of the effective sources by studying the energy flow through the pipes. It was found that a short section of corrugations will only produce sound effectively when placed at the inflow end, while for fully corrugated pipes, the sound-producing regions are located around the pressure maxima of the observed standing waves. It was further found that the net energy flow is in the upstream direction for nearly the complete length of pipe.     

Portable, low-cost NMR with laser-lathe lithography produced microcoils

Nuclear Magnetic Resonance (NMR) is unsurpassed in its ability to non-destructively probe chemical identity. Portable, low-cost NMR sensors would enable on-site identification of potentially hazardous substances, as well as the study of samples in a variety of industrial applications. Recent developments in RF microcoil construction (i.e. coils much smaller than the standard 5mm NMR RF coils), have dramatically increased NMR sensitivity and decreased the limits-of-detection (LOD). We are using advances in laser pantographic microfabrication techniques, unique to LLNL, to produce RF microcoils for field deployable, high sensitivity NMR-based detectors. This same fabrication technique can be used to produce imaging coils for MRI as well as for standard hardware shimming or "ex-situ" shimming of field inhomogeneities typically associated with inexpensive magnets. This paper describes a portable NMR system based on the use of a 2 kg hand-held permanent magnet, laser-fabricated microcoils, and a compact spectrometer. The main limitations for such a system are the low resolution and sensitivity associated with the low field values and quality of small permanent magnets, as well as the lack of large amounts of sample of interest in most cases. The focus of the paper is on the setting up of this system, initial results, sensitivity measurements, discussion of the limitations and future plans. The results, even though preliminary, are promising and provide the foundation for developing a portable, inexpensive NMR system for chemical analysis. Such a system will be ideal for chemical identification of trace substances on site.     

Copper(I) mediated oligomerisation of a phosphaalkyne

The oligomerisation of tert-butylphosphaalkyne, tBuC[triple bond, length as m-dash]P, mediated by Cu(I) complexes yields an unprecedented C4P5 cage compound, which is stabilised in a matrix of copper(I) iodide.