Natural bond orbital analysis in the ONETEP code: Applications to large protein systems

First principles electronic structure calculations are typically performed in terms of molecular orbitals (or bands), providing a straightforward theoretical avenue for approximations of increasing sophistication, but do not usually provide any qualitative chemical information about the system. We can derive such information via post‐processing using natural bond orbital (NBO) analysis, which produces a chemical picture of bonding in terms of localized Lewis‐type bond and lone pair orbitals that we can use to understand molecular structure and interactions. We present NBO analysis of large‐scale calculations with the ONETEP linear‐scaling density functional theory package, which we have interfaced with the NBO 5 analysis program. In ONETEP calculations involving thousands of atoms, one is typically interested in particular regions of a nanosystem whilst accounting for long‐range electronic effects from the entire system. We show that by transforming the Non‐orthogonal Generalized Wannier Functions of ONETEP to natural atomic orbitals, NBO analysis can be performed within a localized region in such a way that ensures the results are identical to an analysis on the full system. We demonstrate the capabilities of this approach by performing illustrative studies of large proteins—namely, investigating changes in charge transfer between the heme group of myoglobin and its ligands with increasing system size and between a protein and its explicit solvent, estimating the contribution of electronic delocalization to the stabilization of hydrogen bonds in the binding pocket of a drug‐receptor complex, and observing, in situ, the n → π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones. © 2012 Wiley Periodicals, Inc.     

Improving neutron activation analysis accuracy for the measurement of gold in the characterization of heterogeneous catalysts using a TRIGA reactor

To measure the gold content of a catalyst accurately, neutron activation analysis (NAA) is one of the methods of choice. NAA is preferred for such heterogeneous catalysts because: (1) it requires minimal sample preparation; (2) NAA provides consistent and accurate results; and (3) in most cases results are obtained much quicker than competing methods. NAA is also used as a referee for the other elemental techniques when results do not fall within expected statistical uncertainties. However, at very high gold concentrations, applying NAA to determine the gold in a heterogeneous catalyst is more challenging than a routine NAA procedure. On the one hand, the neutron absorption cross section for gold is very high, resulting in significant self-shielding related errors. On the other hand, gold exhibits low energy resonance neutron absorptions. In this application the self-shielding minimization effort was handled more rigorously than the classic suppression of neutron flux within a specimen. This non-routine approach was used because: (1) for most applications, high accuracy, <3 % relative, is desired, (2) the low energy resonances of gold make its neutron reaction rate complex and (3) the TRIGA reactor flux profile used in this study contains both thermal and significant epithermal neutron fluxes. Accuracy and precision, using this new approach, are expected to improve from 15 % to better than 3 % relative uncertainty. This has been accomplished through a rigorous assessment of the observed effects of low energy resonance on the neutron flux spectral shape within the sample and designing an experiment to minimize the effects.     

Numerical analysis of nematic liquid crystal alignment on asymmetric surface grating structures

The influence of an asymmetric periodic grooved cell surface on the 2D static director configuration of a nematic liquid crystal has been investigated. The minimum in the Frank-Oseen free energy was solved numerically with the Rapini-Papoular form of the surface anchoring energy at the nematic-grating interface. Results are presented for the variation of pretilt angle in the tilted bulk director field as a function of the surface groove depth, pitch and asymmetry and the bulk parameters. The simulations demonstrate the existence of two energetically degenerate high and low pretilted bulk alignment configurations. The pretilt values in these two regimes and also for the low tilt regime with finite surface anchoring are consistent with experimental results. An effective increase in the resolution of the model is obtained by using an irregular grid to describe the surface profile.     

Communication: An Unusual Side Reaction in the Perallylation of a Glucoside Brought About by Sodium Hydride

We are presently working on the combination of carbohydrate and dendrimer chemistry, both to develop the synthesis of multivalent glycomimetics and to prepare novel dendrimers with advantageous properties. In the course of this work we have used saccharides as oligofunctional core molecules for the synthesis of carbohydrate-centered dendrimers¹ and carbohydrate-centered glycoclusters.²     

Evaluation of sphingomyelin,cholester, and phosphatidylcholine-based immobilized artificial membrane liquid chromatography to predict drug penetration across the blood-brain barrier

Over the past decades, several in vitro methods have been tested for their ability to predict drug penetration across the blood-brain barrier. So far, in high-performance liquid chromatography, most attention has been paid to micellar liquid chromatography and immobilized artificial membrane (IAM) LC. IAMLC has been described as a viable approach, since the stationary phase emulates the lipid environment of a cell membrane. However, research in IAMLC has almost exclusively been limited to phosphatidylcholine (PC)-based stationary phases, even though PC is only one of the lipids present in cell membranes. In this article, sphingomyelin and cholester stationary phases have been tested for the first time towards their ability to predict drug penetration across the blood-brain barrier. Upon comparison with the PC stationary phase, the sphingomyelin- and cholester-based columns depict similar predictive performance. Combining data from the different stationary phases did not lead to improvements of the models. Figure

Schematic representation of how IAM-LC is used to predict drug penetration across the blood-brain barrier.     

Light-Sensitive Phenacyl Crosslinked Dextran Hydrogels for Controlled Delivery**

Stimuli-responsive soft materials enable controlled release of loaded drug molecules and biomolecules. Controlled release of potent chemotherapeutic or immunotherapeutic agents is crucial to reduce unwanted side effects. In an effort to develop controlled release strategies that can be triggered by using Cerenkov luminescence, we have developed polymer hydrogels that can release bovine serum albumin and immunoglobulin G by using light (254 nm–375 nm) as a trigger. We describe the synthesis and photochemical characterization of two light sensitive phenacyl bis-azide crosslinkers that are used to prepare transparent self-supporting hydrogel patches. One crosslinker was designed to optimize the overlap with the Cerenkov luminescence emission window, bearing an π-extended phenacyl core, resulting in a high quantum yield (14 %) of photocleavage when irradiated with 375 nm light. We used the extended phenacyl crosslinker for the preparation of protein-loaded dextran hydrogel patches, which showed efficient and selective dosed release of bovine serum albumin or immunoglobulin G after irradiation with 375 nm light. Cerenkov-triggered release is as yet inconclusive due to unexpected side-reactivity. Based on the high quantum yield, efficient release and large overlap with the Cerenkov window, we envision application of these photosensitive soft materials in radiation targeted drug release.     

Characterization of a highly stable zwitterionic hydrophilic interaction chromatography stationary phase based on hybrid organic–inorganic particles

We have characterized a sulfobetaine stationary phase based on 1.7 μm ethylene-bridged hybrid organic–inorganic particles, which is intended for use in hydrophilic interaction chromatography. The efficiency of a column packed with this material was determined as a function of flow rate, demonstrating a minimum reduced plate height of 2.4. The batch-to-batch reproducibility was assessed using the separation of a mixture of acids, bases, and neutrals. We compared the retention and selectivity of the hybrid sulfobetaine stationary phase to that of several benchmark materials. The hybrid sulfobetaine material gave strong retention for polar neutrals and high selectivity for methyl groups, hydroxy groups, and configurational isomers. Large differences in cation and anion retention were observed among the columns. We characterized the acid and base stability of the hybrid sulfobetaine stationary phase, using accelerated tests at pH 1.3 and 11.0, both at 70°C. The results support a recommended pH range of 2–10. We also investigated the performance of columns packed with this material for metal-sensitive analytes, comparing conventional stainless steel column hardware to hardware that incorporates hybrid surface technology to mitigate interactions with metal surfaces. Compared to the conventional columns, the hybrid surface technology columns showed a greatly improved peak shape.     

Irradiation of Fe–Mn@SiO2 with microwave energy enhanced its Fenton-like catalytic activity for the degradation of methylene blue

Research on Chemical Intermediates - The application of microwave energy in the synthesis of catalytic materials has been indicated to induce desirable effects that lead to improved activity....