Energies of ions in water and nanopores within density functional theory

Accurate calculations of electrostatic potentials and treatment of substrate polarizability are critical for predicting the permeation of ions inside water-filled nanopores. The ab initio molecular dynamics method, based on density functional theory (DFT), accounts for the polarizability of materials, water, and solutes, and it should be the method of choice for predicting accurate electrostatic energies of ions. In practice, DFT coupled with the use of periodic boundary conditions in a charged system leads to large energy shifts. Results obtained using different DFT packages may vary because of the way pseudopotentials and long-range electrostatics are implemented. Using maximally localized Wannier functions, we apply robust corrections that yield relatively unambiguous ion energies in select molecular and aqueous systems and inside carbon nanotubes. Large binding energies are predicted for ions in metallic carbon nanotube arrays, while Na+ and Cl- energies are found to exhibit asymmetry in water that is smaller than but comparable with those computed using nonpolarizable water force fields.     

Ferroelectric switching and electrochemistry of pyrrole substituted trialkylbenzene‐1,3,5‐tricarboxamides

We explore a new approach to organic ferroelectric diodes using a benzene‐tricarboxamide (BTA) core connected with C10 alkyl chains to pyrrole groups, which can be polymerized to provide a semiconducting ferroelectric material. The compound possesses a columnar hexagonal liquid crystalline (LC) phase and exhibits ferroelectric switching. At low switching frequencies, an additional process occurs, which leads to a high hysteretic charge density of up to ～1000 mC/m². Based on its slow rate, the formation of gas bubbles, and the emergence of characteristic polypyrrole absorption bands in the UV–Vis–NIR, the additional process is identified as the oxidative polymerization of pyrrole groups, enabled by the presence of amide groups. Polymerization of the pyrrole groups, which is essential to obtain semiconductivity, is limited to thin layers at the electrodes, amounting to ～17 nm after cycling for 21 h. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 673–683     

High-Q cavities in photosensitive photonic crystals

We propose a novel concept for creating high-Q cavities in photonic crystal slabs (PCSs) composed of photosensitive material. To date, high-Q cavities have been realized through the use of double heterostructures where the lattice geometry is altered via nanolithography. Here, we show that selective postexposure to light of a uniform PCS composed of photosensitive material, altering the refractive index permanently, can also yield high-Q microcavities. We show theoretically that high-Q cavities (up to Q = 1 x 10(6)) can be achieved with photoinduced index changes that are well within what can be achieved in chalcogenide glasses.     

Enforcement of the ban on aristolochic acids in Chinese traditional herbal preparations on the Dutch market

In traditional chinese medicine several Aristolochia species are used. Aristolochia spp. contain a mixture of aristolochic acids (AAs), mainly AA I and AA II which are nephrotoxicants and carcinogens. After AA-related nephropathy (AAN) and urothelial cancer were described in female patients in Belgium following intake of AA-contaminated herbal preparations, herbs with AAs were prohibited worldwide. Confusing nomenclature can cause AA contamination of certain Chinese traditional herbal preparations (THPs). Here we report the results of investigations by the Dutch Food and Consumer Product Safety Authority (VWA) into the presence of AAs in THPs sampled on the Dutch market using a liquid-chromatography–-mass spectrometry method. Between 2002 and 2006 we sampled 190 Chinese THPs using recent information on Chinese THPs potentially containing AAs. AA I was found in 25 samples up to a concentration of 1,676 mg/kg. AA II was also found in 13 of these samples up to 444 mg/kg. All 25 positive samples including Mu Tong, Fang Ji, Tian Xian Teng and Xi Xin were part of a group of 68 THPs identified as possibly containing AAs. In a worst-case scenario, use of a sample of Mu Tong with the highest AA content over a 7-day period would result in the same intake levels of AAs which significantly raised the cancer risk in the Belgian AAN cases. Our results show that contaminated THPs still can be found on the market following worldwide publicity. Therefore, it can be concluded that testing of possibly AA-contaminated THPs is still essential. Figure Various Chinese Herbs     

Real time quantitative amplification detection on a microarray: towards high multiplex quantitative PCR

Quantitative real-time polymerase chain reaction (qrtPCR) is widely used as a research and diagnostic tool. Notwithstanding its many powerful features, the method is limited in the degree of multiplexing to about 6 due to spectral overlap of the available fluorophores. A new method is presented that allows quantitative amplification detection at higher multiplexing by the integration of amplification in solution and monitoring via hybridization to a microarray in real-time. This method does not require any manipulation of the PCR product and runs in a single closed chamber. Employing labeled primers, one of the main challenges is to measure surface signals against a high fluorescence background from solution. A compact, confocal scanner is employed, based on miniaturized optics from DVD technology and combined with a flat thermocycler for simultaneous scanning and heating. The feasibility of this method is demonstrated in singleplex with an analytical sensitivity comparable to routine qrtPCR.     

Hydrogen Bonding Directed Supramolecular Polymerisation of Oligo(Phenylene-Ethynylene)s: Cooperative Mechanism, Core Symmetry Effect and Chiral Amplification

The design of supramolecular motifs with tuneable stability and adjustable supramolecular polymerisation mechanisms is of crucial importance to precisely control the properties of supramolecular assemblies. This report focuses on constructing π-conjugated oligo(phenylene ethynylene) (OPE)-based one-dimensional helical supramolecular polymers that show a cooperative growth mechanism. Thus, a novel set of discotic molecules comprising a rigid OPE core, three amide groups, and peripheral solubilising wedge groups featuring C(3) and C(2) core symmetry was designed and synthesised. All of the discotic molecules are crystalline compounds and lack a columnar mesophase in the solid state. In dilute methylcyclohexane solution, one-dimensional supramolecular polymers are formed stabilised by threefold intermolecular hydrogen bonding and π-π interactions, as evidenced by (1) H?NMR measurements. Small-angle X-ray and light scattering measurements reveal significant size differences between the columnar aggregates of C(3) - and C(2) -symmetrical discotics, that is, the core symmetry strongly influences the nature of the supramolecular polymerisation process. Temperature-dependent CD measurements show a highly cooperative polymerisation process for the C(3) -symmetrical discotics. In contrast, the self-assembly of C(2) -symmetrical discotics shows a smaller enthalpy release upon aggregation and decreased cooperativity. In all cases, the peripheral stereogenic centres induce a preferred handedness in the columnar helical aggregates. Moreover, one stereogenic centre suffices to fully bias the helicity in the C(2) -symmetrical discotics. Finally, chiral amplification studies with the C(3) -symmetrical discotics were performed by mixing chiral and achiral discotics (sergeants-and-soldiers experiment) and discotics of opposite chirality (majority-rules experiment). The results demonstrate a very strong sergeants-and-soldiers effect and a rather weak majority-rules effect.     

Probing noncovalent protein—Ligand interactions of the cGMP-dependent protein kinase using electrospray ionization time of flight mass spectrometry

Nanoflow electrospray ionization time of flight mass spectrometry (ESI-TOF-MS) was used to study activation properties of the cGMP-dependent protein kinase (PKG). Our nanoflow ESI-TOF-MS analysis confirms that PKG mainly occurs as a 153 kDa homodimer and is able to bind four cGMP molecules, which is in agreement with the known stoichiometry. Binding order and stoichiometry of cGMP, the non-hydrolysable ATP analog beta,gamma-imidoadenosine 5'-triphosphate (AMPPNP) and Mn2+ for PKG were characterized as model for the active PKG-cGMP-ATP/Mg2+ complex. Already in the absence of cGMP, a noncovalent complex between PKG and two molecules of AMPPNP could be observed by ESI-TOF-MS. Binding of AMPPNP to PKG was strongly enhanced by the addition of MnCl2 to the spray solution. This is in agreement with binding of AMPPNP/Mn2+ in the ATP binding pocket of PKG since all protein kinases require a metal ion to accompany ATP in the ATP-binding pocket for proper positioning of the beta and gamma phosphates. Additionally, this finding could imply that within the inactive conformation of PKG, the autoinhibition-domain, when in contact with the substrate-docking domain, does not block the entrance to the ATP-binding site. In the presence of cGMP, less of the fully saturated PKG-(cGMP)4(AMPPNP/Mn2+)2 complex was observed, suggesting that the PKG-ATP interaction is weakened in the active conformation of PKG. Additionally, limited proteolysis in combination with native-ESI MS showed to be a useful tool to study the contact regions on the PKG-dimer and also allowed the rapid determination of the overall autophosphorylation status of the protein. These measurements indicated that autophosphorylation mainly occurs within the first 80 aminoterminal residues and involves in total 3-4 phosphates per subunit.     

Implementation of at‐line capillary zone electrophoresis for fast and reliable determination of adenovirus concentrations in vaccine manufacturing

A CZE method was validated and implemented for fast and accurate in‐process determination of adenovirus concentrations of downstream process samples obtained during manufacturing of adenovirus vector‐based vaccines. An analytical‐quality‐by‐design approach was embraced for method development, method implementation, and method maintenance. CZE provided separation of adenovirus particles from sample matrix components, such as cell debris, residual DNA and proteins. The intermediate precision of the virus particle concentration was 6.9% RSD and the relative bias was 2.3%. In comparison, the CZE method is intended to replace a quantitative polymerase chain reaction method which requires three replicates in three analytical runs to achieve an intermediate precision of 8.1% RSD. Given that, in addition, the time from sampling till reporting results of the CZE method was less than 2 h, whereas quantitative polymerase chain reaction requires 3 days, it follows that the CZE method enables faster processing times in downstream processing.     

Large-amplitude, spatially correlated fluctuations in BOLD fMRI signals during extended rest and early sleep stages

A number of recent studies of human brain activity using blood-oxygen-level-dependent (BOLD) fMRI and EEG have reported the presence of spatiotemporal patterns of correlated activity in the absence of external stimuli. Although these patterns have been hypothesized to contain important information about brain architecture, little is known about their origin or about their relationship to active cognitive processes such as conscious awareness and monitoring of the environment. In this study, we have investigated the amplitude and spatiotemporal characteristics of resting-state activity patterns and their dependence on the subjects' alertness. For this purpose, BOLD fMRI was performed at 3.0 T on 12 normal subjects using a visual stimulation protocol, followed by a 27 min rest period, during which subjects were allowed to fall asleep. In subjects who were asleep at the end of the scan, we found (a) a higher amplitude of BOLD signal fluctuation during rest compared with subjects who were awake at the end of the scan; (b) spatially independent patterns of correlated activity that involve all of gray matter, including deep brain nuclei; (c) many patterns that were consistent across subjects; (d) that average percentage levels of fluctuation in visual cortex (VC) and whole brain were higher in subjects who were asleep (up to 1.71% and 1.16%, respectively) than in those who were awake (up to 1.15% and 0.96%) at the end of the scan and were comparable with those levels evoked by intense visual stimulation (up to 1.85% and 0.76% for two subject groups); (e) no confirmation of correlation, positive or negative, between thalamus and VC found in earlier studies. These findings suggest that resting-state activity continues during sleep and does not require active cognitive processes or conscious awareness.