Residual dipolar coupling investigation of a heparin tetrasaccharide confirms the limited effect of flexibility of the iduronic acid on the molecular shape of heparin

The solution conformation of a fully sulfated heparin-derived tetrasaccharide, I, was studied in the presence of a 4-fold excess of Ca2+. Proton–proton and proton–carbon residual dipolar couplings (RDCs) were measured in a neutral aligning medium. The order parameters of two rigid hexosamine rings of I were determined separately using singular value decomposition and ab initio structures of disaccharide fragments of I. The order parameters were very similar implying that a common order tensor can be used to analyze the structure of I. Using one order tensor, RDCs of both hexosamine rings were used as restraints in molecular dynamics simulations. RDCs of the inner iduronic acid were calculated for every point of the molecular dynamics trajectory. The fitting of the calculated RDCs of the two forms of the iduronic acid to the experimental values yielded a population of 1C4 and 2So conformers of iduronic acid that agreed well with the analysis based on proton–proton scalar coupling constants. The glycosidic linkage torsion angles in RDC-restrained molecular dynamics (MD) structures of I are consistent with the interglycosidic three-bond proton–carbon coupling constants. These structures also show that the shape of heparin is not affected dramatically by the conformational flexibility of the iduronic acid ring. This is in line with conclusions of previous studies based on MD simulations and the analysis of 1H-1H NOEs. Our work therefore demonstrates the effectiveness of RDCs in the conformational analysis of glycosaminoglycans

The electronic structure of La1−x_{1-x}Srx_{x}MnO3_{3} thin films and its TcT_c dependence as studied by angle-resolved photoemission

We present angle-resolved photoemission spectroscopy results for thin films of the three-dimensional manganese perovskite La$_{1-x}$Sr$_{x}$MnO$_{3}$. We show that the transition temperature ($T_c$) from the paramagnetic insulating to ferromagnetic metallic state is closely related to details of the electronic structure, particularly to the spectral weight at the ${\bf k}$-point, where the sharpest step at the Fermi level was observed. We found that this ${\bf k}$-point is the same for all the samples, despite their different $T_c$. The change of $T_c$ is discussed in terms of kinetic energy optimization. Our ARPES results suggest that the change of the electronic structure for the samples having different transition temperatures is different from the rigid band shift.Comment: Accepted by Journal of Physics: Condensed Matte

Momentum resolved spin dynamics of bulk and surface excited states in the topological insulator Bi2Se3\mathrm{Bi_{2}Se_{3}}

The prospective of optically inducing a spin polarized current for spintronic devices has generated a vast interest in the out-of-equilibrium electronic and spin structure of topological insulators (TIs). In this Letter we prove that only by measuring the spin intensity signal over several order of magnitude in spin, time and angle resolved photoemission spectroscopy (STAR-PES) experiments is it possible to comprehensively describe the optically excited electronic states in TIs materials. The experiments performed on $\mathrm{Bi_{2}Se_{3}}$ reveal the existence of a Surface-Resonance-State in the 2nd bulk band gap interpreted on the basis of fully relativistic ab-initio spin resolved photoemission calculations. Remarkably, the spin dependent relaxation of the hot carriers is well reproduced by a spin dynamics model considering two non-interacting electronic systems, derived from the excited surface and bulk states, with different electronic temperatures.Comment: 5 pages and 4 figure

First-Principles Studies of Hydrogenated Si(111)--7×\times7

The relaxed geometries and electronic properties of the hydrogenated phases of the Si(111)-7$\times$7 surface are studied using first-principles molecular dynamics. A monohydride phase, with one H per dangling bond adsorbed on the bare surface is found to be energetically favorable. Another phase where 43 hydrogens saturate the dangling bonds created by the removal of the adatoms from the clean surface is found to be nearly equivalent energetically. Experimental STM and differential reflectance characteristics of the hydrogenated surfaces agree well with the calculated features.Comment: REVTEX manuscript with 3 postscript figures, all included in uu file. Also available at http://www.phy.ohiou.edu/~ulloa/ulloa.htm

Glycosaminoglycans: What Remains To Be Deciphered?

Glycosaminoglycans (GAGs) are complex polysaccharides exhibiting a vast structural diversity and fulfilling various functions mediated by thousands of interactions in the extracellular matrix, at the cell surface, and within the cells where they have been detected in the nucleus. It is known that the chemical groups attached to GAGs and GAG conformations comprise “glycocodes” that are not yet fully deciphered. The molecular context also matters for GAG structures and functions, and the influence of the structure and functions of the proteoglycan core proteins on sulfated GAGs and vice versa warrants further investigation. The lack of dedicated bioinformatic tools for mining GAG data sets contributes to a partial characterization of the structural and functional landscape and interactions of GAGs. These pending issues will benefit from the development of new approaches reviewed here, namely (i) the synthesis of GAG oligosaccharides to build large and diverse GAG libraries, (ii) GAG analysis and sequencing by mass spectrometry (e.g., ion mobility-mass spectrometry), gas-phase infrared spectroscopy, recognition tunnelling nanopores, and molecular modeling to identify bioactive GAG sequences, biophysical methods to investigate binding interfaces, and to expand our knowledge and understanding of glycocodes governing GAG molecular recognition, and (iii) artificial intelligence for in-depth investigation of GAGomic data sets and their integration with proteomics