Effects of extending the computational model on DNA-protein T-shaped interactions: the case of adenine-histidine dimers

The MP2/6-31G*(0.25) π-π or π(+)-π T-shaped (edge-to-face) interactions between neutral or protonated histidine and adenine were considered using computational models of varying size to determine the effects of the protein and DNA backbones on the preferred dimer structure and binding strength. The overall consequences of the backbones are reasonably subtle for the neutral adenine-histidine T-shaped dimers. Furthermore, the minor changes in the binding strengths of these dimers upon model extension arise from additional (attractive) backbone-π (bb-π) contacts and changes in the preferred π-π orientations, which is verified by the quantum theory of atoms in molecules (QTAIM). Since the binding strength of the extended dimer equals the sum of the individual backbone-π and π-π contributions, the π-π component is not appreciably affected by polarization of the ring upon inclusion of the biological backbone. In contrast, the larger effect of the backbone on the protonated histidine dimers cannot simply be predicted as the sum of changes in the π-π and bb-π components regardless of the dimer type or model. This suggests, and QTAIM qualitatively supports, that the magnitude of the π(+)-π contribution changes, which is likely due to alterations in the electrostatic landscape of the monomer rings upon inclusion of the biological backbone that largely affect T-shaped dimers. These findings differ from those previously reported for (neutral) π-π stacked and (metallic) cation-π interactions, which highlights the distinct properties of each (π-π, π(+)-π, and cation-π) classification of noncovalent interaction. Furthermore, these results emphasize the importance of considering backbone-π interactions when analyzing contacts that appear in experimental crystal structures and cautions the use of truncated models when evaluating the magnitude of the π(+)-π contribution present in large biological complexes.     

Toward a new elastic-decohesive model of Arctic sea ice

This paper argues for a new constitutive model, an elastic-decohesive model for sea ice. The model is motivated by examining satellite observations of the Arctic processed to show ice deformation in the form of divergence, shear and vorticity. The model is implemented numerically in the material-point method and used to predict motion and deformation of sea ice by simulating a region of the Beaufort Sea. The model is able to capture the qualitative and statistical behavior of localized deformation seen in the observations.     

Using high-resolution in situ radon measurements to determine groundwater discharge at a remote location: Tonle Sap Lake, Cambodia

Tonle Sap Lake (Cambodia) is the largest freshwater lake in SE Asia, and is reported to have one of the highest freshwater fish productions anywhere. During the dry season (November–April) the lake drains through a tributary to the Mekong River. The flow in the connecting tributary completely reverses during the wet monsoon (May–October), adding huge volumes of water back to the lake, increasing its area about fourfold. We hypothesize that nutrients are at least partially delivered via groundwater discharge, especially during the draining portion of the annual flood cycle. We surveyed over 200 km in the northern section of the lake using a customized system that measures natural ²²²Rn (radon), temperature, conductivity, GPS coordinates and water depth while underway. Results showed that there were portions of the lake with significant enrichments in radon, indicating likely groundwater inputs. These same areas were generally characterized by lower electrical conductivities. Samples collected from nearby wells also showed a general inverse relationship between radon and conductivity. Our data suggest that groundwater pathways are important, accounting for roughly 10–20 % of the freshwater flow of the Tonle Sap tributary (connection to the Mekong River), the largest single source of fresh water to the lake. Nutrient inputs from these inputs, because of higher concentrations in groundwater, will be correspondingly higher.     

Development and validation of LC-MS/MS method for determination of very long acyl chain (C22:0 and C24:0) ceramides in human plasma

Ceramide is a key metabolite in both anabolic and catabolic pathways of sphingolipids. The very long fatty acyl chain ceramides N-(docosanoyl)-sphing-4-enine (Cer(22:0)) and N-(tetracosanoyl)-sphing-4-enine (Cer(24:0)) are associated with multiple biological functions. Elevated levels of these sphingolipids in tissues and in the circulation have been associated with insulin resistance and diabetes. To facilitate quantification of these very long chain ceramides in clinical samples from human subjects, we have developed a sensitive, accurate, and high-throughput assay for determination of Cer(22:0) and Cer(24:0) in human plasma. Cer(22:0) and Cer(24:0) and their deuterated internal standards were extracted by protein precipitation and chromatographically separated by HPLC. The analytes and their internal standards were ionized using positive-ion electrospray mass spectrometry, then detected by multiple-reaction monitoring with a tandem mass spectrometer. Total liquid chromatography–tandem mass spectrometry (LC-MS/MS) runtime was 5 min. The assay exhibited a linear dynamic range of 0.02–4 and 0.08–16 μg/ml for Cer(22:0) and Cer(24:0), respectively, in human plasma with corresponding absolute recoveries from plasma at 109 and 114 %, respectively. The lower limit of quantifications were 0.02 and 0.08 μg/ml for Cer(22:0) and Cer(24:0), respectively. Acceptable precision and accuracy were obtained for concentrations over the calibration curve ranges. With the semi-automated format and short LC runtime for the assay, a throughput of ～200 samples/day can easily be achieved.

Degradable Hybrid Materials Based on Cationic Acylhydrazone Dynamic Covalent Polymers Promote DNA Complexation through Multivalent Interactions

The design of smart nonviral vectors for gene delivery is of prime importance for the successful implementation of gene therapies. In particular, degradable analogues of macromolecules represent promising targets as they would combine the multivalent presentation of multiple binding units that is necessary for achieving effective complexation of therapeutic oligonucleotides with the controlled degradation of the vector that would in turn trigger drug release. Toward this end, we have designed and synthesized hybrid polyacylhydrazone‐based dynamic materials that combine bis‐functionalized cationic monomers with ethylene oxide containing monomers. Polymer formation was characterized by ¹H and DOSY NMR spectroscopy and was found to take place at high concentration, whereas macrocycles were predominantly formed at low concentration. HPLC monitoring of solutions of these materials in aqueous buffers at pH values ranging from 5.0 to 7.0 revealed their acid‐catalyzed degradation. An ethidium bromide displacement assay and gel electrophoresis clearly demonstrated that, despite being dynamic, these materials are capable of effectively complexing dsDNA in aqueous buffer and biological serum at N/P ratios comparable to polyethyleneimine polymers. The self‐assembly of dynamic covalent polymers through the incorporation of a reversible covalent bond within their main chain is therefore a promising strategy for generating degradable materials that are capable of establishing multivalent interactions and effectively complexing dsDNA in biological media.     

Correlation consistent, Douglas–Kroll–Hess relativistic basis sets for the 5p and 6p elements

The diatomic carbon molecule has a complex electronic structure with a large number of low-lying electronic excited states. In this work, the potential energy curves (PECs) of the four lowest lying singlet states ( $X^{1} \Sigma^{ + }_{g}$ , $A^{1} \Pi_{u}$ , $B^{1} \Delta_{g}$ , and $B^{\prime1} \Sigma^{ + }_{g}$ ) were obtained by high-level ab initio calculations. Valence electron correlation was accounted for by the correlation energy extrapolation by intrinsic scaling (CEEIS) method. Additional corrections to the PECs included core–valence correlation and relativistic effects. Spin–orbit corrections were found to be insignificant. The impact of using dynamically weighted reference wave functions in conjunction with CEEIS was examined and found to give indistinguishable results from the even weighted method. The PECs showed multiple curve crossings due to the $B^{1} \Delta_{g}$ state as well as an avoided crossing between the two $^{1} \Sigma^{ + }_{g}$ states. Vibrational energy levels were computed for each of the four electronic states, as well as rotational constants and spectroscopic parameters. Comparison between the theoretical and experimental results showed excellent agreement overall. Equilibrium bond distances are reproduced to within 0.05 %. The dissociation energies of the states agree with experiment to within ~0.5 kcal/mol, achieving “chemical accuracy.” Vibrational energy levels show average deviations of ~20 cm^?1 or less. The $B^{1} \Delta_{g}$ state shows the best agreement with a mean absolute deviation of 2.41 cm^?1. Calculated rotational constants exhibit very good agreement with experiment, as do the spectroscopic constants.     

Interpenetration as a Mechanism for Negative Thermal Expansion in the Metal–Organic Framework Cu3(btb)2 (MOF‐14)

Metal–organic framework materials (MOFs) have recently been shown in some cases to exhibit strong negative thermal expansion (NTE) behavior, while framework interpenetration has been found to reduce NTE in many materials. Using powder and single‐crystal diffraction methods we investigate the thermal expansion behavior of interpenetrated Cu₃(btb)₂ (MOF‐14) and find that it exhibits an anomalously large NTE effect. Temperature‐dependent structural analysis shows that, contrary to other interpenetrated materials, in MOF‐14 the large positive thermal expansion of weak interactions that hold the interpenetrating networks together results in a low‐energy contractive distortion of the overall framework structure, demonstrating a new mechanism for NTE.     

Metal–Organic Frameworks for Oxygen Storage

We present a systematic study of metal–organic frameworks (MOFs) for the storage of oxygen. The study starts with grand canonical Monte Carlo simulations on a suite of 10 000 MOFs for the adsorption of oxygen. From these data, the MOFs were down selected to the prime candidates of HKUST‐1 (Cu‐BTC) and NU‐125, both with coordinatively unsaturated Cu sites. Oxygen isotherms up to 30 bar were measured at multiple temperatures to determine the isosteric heat of adsorption for oxygen on each MOF by fitting to a Toth isotherm model. High pressure (up to 140 bar) oxygen isotherms were measured for HKUST‐1 and NU‐125 to determine the working capacity of each MOF. Compared to the zeolite NaX and Norit activated carbon, NU‐125 has an increased excess capacity for oxygen of 237 % and 98 %, respectively. These materials could ultimately prove useful for oxygen storage in medical, military, and aerospace applications.     

Multifunctional silane polymers for persistent surface derivatization and their antimicrobial properties

We demonstrate a versatile methodology combining both covalent surface anchoring and polymer cross-linking that is capable of forming long-lasting coatings on reactive and nonreactive surfaces. Polymers containing reactive methoxysilane groups form strong Si-O-Si links to oxide surfaces, thereby anchoring the polymer chains at multiple points. The interchain cross-linking of the methoxysilane groups provides additional durability to the coating and makes the coatings highly resistant to solvents. By tailoring the chemical structure of the polymer, we were able to control the surface energy (wetting) of a variety of surfaces over a wide range of water contact angles of 30-140 degrees . In addition, we synthesized covalently linked layer-by-layer polymeric assemblies from these novel methoxysilane polymers. Finally, antibacterial agents, such as silver bromide nanoparticles and triiodide ions, were introduced into these functional polymers to generate long-lasting and renewable antiseptic coatings on glass, metals, and textiles.     

Neonatal auditory activation detected by functional magnetic resonance imaging

The objective of this study was to detect auditory cortical activation in non-sedated neonates employing functional magnetic resonance imaging (fMRI). Using echo-planar functional brain imaging, subjects were presented with a frequency-modulated pure tone; the BOLD signal response was mapped in 5 mm-thick slices running parallel to the superior temporal gyrus. Twenty healthy neonates (13 term, 7 preterm) at term and 4 adult control subjects. Blood oxygen level-dependent (BOLD) signal in response to auditory stimulus was detected in all 4 adults and in 14 of the 20 neonates. FMRI studies of adult subjects demonstrated increased signal in the superior temporal regions during auditory stimulation. In contrast, signal decreases were detected during auditory stimulation in 9 of 14 newborns with BOLD response. fMRI can be used to detect brain activation with auditory stimulation in human infants.