Formation and bonding of alane clusters on Al(111) surfaces studied by infrared absorption spectroscopy and theoretical modeling

Alanes are believed to be the mass transport intermediate in many hydrogen storage reactions and thus important for understanding rehydrogenation kinetics for alanates and AlH3. Combining density functional theory (DFT) and surface infrared (IR) spectroscopy, we provide atomistic details about the formation of alanes on the Al(111) surface, a model environment for the rehydrogenation reactions. At low coverage, DFT predicts a 2-fold bridge site adsorption for atomic hydrogen at 1150 cm(-1), which is too weak to be detected by IR but was previously observed in electron energy loss spectroscopy. At higher coverage, steps are the most favorable adsorption sites for atomic H adsorption, and it is likely that the AlH3 molecules form (initially strongly bound to steps) at saturation. With increasing exposures AlH3 is extracted from the step edge and becomes highly mobile on the terraces in a weakly bound state, accounting for step etching observed in previous STM studies. The mobility of these weakly bound AlH3 molecules is the key factor leading to the growth of larger alanes through AlH3 oligomerization. The subsequent decomposition and desorption of alanes is also investigated and compared to previous temperature programmed desorption studies.     

Cluster analysis application identifies muscle characteristics of importance for beef tenderness

Background

Unsaturated fatty acids are susceptible to oxidation and damaged chains are removed from glycerophospholipids by phospholipase A₂. De-acylated lipids are then re-acylated by lysophospholipid acyltransferase enzymes such as LPCAT1 which catalyses the formation of phosphatidylcholine (PC) from lysoPC and long-chain acyl-CoA.

Results

Activity of LPCAT1 is inhibited by Ca²⁺, and a Ca²⁺-binding motif of the EF-hand type, EFh-1, was identified in the carboxyl-terminal domain of the protein. The residues Asp-392 and Glu-403 define the loop of the hairpin structure formed by EFh-1. Substitution of D³⁹² and E⁴⁰³ to alanine rendered an enzyme insensitive to Ca²⁺, which established that Ca²⁺ binding to that region negatively regulates the activity of the acyltransferase amino-terminal domain. Residue Cys-211 of the conserved motif III is not essential for catalysis and not sufficient for sensitivity to treatment by sulfhydryl-modifier agents. Among the several active cysteine-substitution mutants of LPCAT1 generated, we identified one to be resistant to treatment by sulfhydryl-alkylating and sulfhydryl-oxidizer agents.

Conclusion

Mutant forms of LPCAT1 that are not inhibited by Ca²⁺ and sulfhydryl-alkylating and ?Coxidizing agents will provide a better understanding of the physiological function of a mechanism that places the formation of PC, and the disposal of the bioactive species lysoPC, under the control of the redox status and Ca²⁺ concentration of the cell.     

Near-infrared chiro-optical effects in metallogels

A series of novel metallogelators containing near-IR nickel-bis(dithiolene) absorbers were rationally designed and synthesized. Robust gel networks are formed by right handed helical 1D-nanofibers which generate strong and remarkable chiro-optical effects in the near-infrared region.     

Comparative molecular surface analysis (CoMSA) for virtual combinatorial library screening of styrylquinoline HIV-1 blocking agents

We used comparative molecular surface analysis to design molecules for the synthesis as part of the search for new HIV-1 integrase inhibitors. We analyzed the virtual combinatorial library (VCL) constituted from various moieties of styrylquinoline and styrylquinazoline inhibitors. Since imines can be applied in a strategy of dynamic combinatorial chemistry (DCC), we also tested similar compounds in which the -C=N- or -N=C- linker connected the heteroaromatic and aromatic moieties. We then used principal component analysis (PCA) or self-organizing maps (SOM), namely, the Kohonen neural networks to obtain a clustering plot analyzing the diversity of the VCL formed. Previously synthesized compounds of known activity, used as molecular probes, were projected onto this plot, which provided a set of promising virtual drugs. Moreover, we further modified the above mentioned VCL to include the single bond linker -C-N- or -N-C-. This allowed increasing compound stability but expanded also the diversity between the available molecular probes and virtual targets. The application of the CoMSA with SOM indicated important differences between such compounds and active molecular probes. We synthesized such compounds to verify the computational predictions.     

Hopf fibrations and frustrated matter

Frustrated order appear in different scientific contexts like complex crystals, amorphous materials, liquid crystals, foams and even biological organizations, with scales ranging from the atomic level up to macroscopic scales. In this article, we shall first review several cases where it is possible to release frustration and allows for an unfrustrated structural model by curving the underlying Euclidean space into a positively curved space, the hypersphere S ³. The real Euclidean structure is then analyzed in terms ordered regions interrupted by topological defects, whose presence and density is directly related to the change of curvature from S ³ to R ³. We then focus on a rather fascinating geometrical structure, the Hopf fibration, which can be defined on the hypersphere, and show how this tool is very well suited to describe the defect geometries (both linear, helicoidal and bidimensional) which arises from the decurving procedure.     

Selectivity over coverage in de novo sequencing of IgGs

Although incredibly diverse in specificity, millions of unique Immunoglobulin G (IgG) molecules in the human antibody repertoire share most of their amino acid sequence. These constant parts of IgG do not yield any useful information in attempts to sequence antibodies de novo. Therefore, methods focusing solely on the variable regions and providing unambiguous sequence reads are strongly advantageous. We report a mass spectrometry-based method that uses electron capture dissociation (ECD) to provide straightforward-to-read sequence ladders for the variable parts of both the light and heavy chains, with a preference for the functionally important CDR3. We optimized this method on the therapeutic antibody Trastuzumab and demonstrate its applicability on two monoclonal quartets of the four IgG subclasses, IgG1, IgG2, IgG3 and IgG4. The method is based on proteolytically separating the variable F(ab′)₂ part from the conserved Fc part, whereafter the F(ab′)₂ portions are mass-analyzed and fragmented by ECD. Pure ECD, without additional collisional activation, leads to straightforward-to-read sequence tags covering the CDR3 of both the light and heavy chains. Using molecular modelling and structural analysis, we discuss and explain this selective fragmentation behavior and describe how structural features of the different IgG subclasses lead to distinct fragmentation patterns. Overall, we foresee that pure ECD on F(ab′)₂ or Fab molecules can become a valuable tool for the de novo sequencing of serum antibodies.     

Qualitative analysis of excess dielectric properties of binary mixtures, ternary mixtures and mixing dynamics measurement using surface plasmon resonance

The analysis of the excess dielectric properties for various binary mixtures and a ternary mixture is demonstrated using a surface plasmon resonance (SPR) sensor. Strong deviations from ideality are seen using SPR to monitor deviations in the dielectric properties following mixing. Binary mixtures with similar refractive index were measured: hexanes/isopropanol, n-heptanes/propanol, 1-acetoxy-2-methoxyethane/2-methoxyethanol, butanol/dipropylamine, hexanes/ethylacetate, and ethylacetate/isopropanol binary mixtures. The ternary mixture was composed of 60 different proportions of hexanes, isopropanol, and ethylacetate. Using SPR, mixing dynamics is easily accessible. The mixing of hexanes and isopropanol in static solution was monitored.     

Capture of Gaseous Iodine in Isoreticular Zirconium-Based UiO-n Metal-Organic Frameworks: Influence of Amino Functionalization,DFT Calculations,Raman and EPR Spectroscopic Investigation

A series of Zr-based UiO-n MOF materials (n=66, 67, 68) have been studied for iodine capture. Gaseous iodine adsorption was collected kinetically from a home-made set-up allowing the continuous measurement of iodine content trapped within UiO-n compounds, with organic functionalities (−H, −CH₃, −Cl, −Br, −(OH)₂, −NO₂, −NH₂, (−NH₂)₂, −CH₂ NH₂) by in-situ UV-Vis spectroscopy. This study emphasizes the role of the amino groups attached to the aromatic rings of the ligands connecting the {Zr₆O₄(OH)₄} brick. In particular, the preferential interaction of iodine with lone-pair groups, such as amino functions, has been experimentally observed and is also based on DFT calculations. Indeed, higher iodine contents were systematically measured for amino-functionalized UiO-66 or UiO-67, compared to the pristine material (up to 1211 mg/g for UiO-67-(NH₂)₂). However, DFT calculations revealed the highest computed interaction energies for alkylamine groups (−CH₂NH₂) in UiO-67 (−128.5 kJ/mol for the octahedral cavity), and pointed out the influence of this specific functionality compared with that of an aromatic amine. The encapsulation of iodine within the pore system of UiO-n materials and their amino-derivatives has been analyzed by UV-Vis and Raman spectroscopy. We showed that a systematic conversion of molecular iodine (I₂) species into anionic I⁻ ones, stabilized as I⁻⋅⋅⋅I₂ or I₃⁻ complexes within the MOF cavities, occurs when I₂@UiO-n samples are left in ambient light.     

Strong Jordan Separation and Applications to Rigidity

We prove that simple, thick hyperbolic P-manifolds of dimensionat least three exhibit Mostow rigidity. We also prove a quasi-isometryrigidity result for the fundamental groups of simple, thickhyperbolic P-manifolds of dimension at least three. The keytool in the proof of these rigidity results is a strong formof the Jordan separation theorem, for maps from Sⁿ Sⁿ⁺¹ whichare not necessarily injective.