Hadronic structure from the lattice

In recent years the investigation of hadron structure using lattice techniques has attracted growing attention. The computation of several important quantities has become feasible. Furthermore, theoretical developments as well as progress in algorithms and an increase in computing resources have contributed to a significantly improved control of systematic errors. In this article we give an overview on the work that has been carried out in the framework of the Hadron Physics I3 (I3HP) network “Computational (lattice) hadron physics”. Here we will not restrict ourselves to spin physics but focus on results for nucleon spectrum and structure from the QCDSF collaboration. For a broader overview of developments in this field see, e.g., [1].     

How to Separate Kinase Inhibition from Undesired Monoamine Oxidase A Inhibition—The Development of the DYRK1A Inhibitor AnnH75 from the Alkaloid Harmine

The β-carboline alkaloid harmine is a potent DYRK1A inhibitor, but suffers from undesired potent inhibition of MAO-A, which strongly limits its application. We synthesized more than 60 analogues of harmine, either by direct modification of the alkaloid or by de novo synthesis of β-carboline and related scaffolds aimed at learning about structure–activity relationships for inhibition of both DYRK1A and MAO-A, with the ultimate goal of separating desired DYRK1A inhibition from undesired MAO-A inhibition. Based on evidence from published crystal structures of harmine bound to each of these enzymes, we performed systematic structure modifications of harmine yielding DYRK1A-selective inhibitors characterized by small polar substituents at N-9 (which preserve DYRK1A inhibition and eliminate MAO-A inhibition) and beneficial residues at C-1 (methyl or chlorine). The top compound AnnH75 remains a potent DYRK1A inhibitor, and it is devoid of MAO-A inhibition. Its binding mode to DYRK1A was elucidated by crystal structure analysis, and docking experiments provided additional insights for this attractive series of DYRK1A and MAO-A inhibitors.     

Novel synthesis of pyran,thiophene, and pyridine derivatives incorporating thiazole ring and their antitumor evaluation

This study aims to design and synthesize a number of novel pyran, thiophene, and pyridine derivatives incorporating thiazole ring and evaluate their antitumor inhibition (μM) as significant anticancer agents. The reactivity of compound 1 [2-(4-oxo-4,5-dihydrothiazol-2-yl)acetonitrile] towards different chemical reagents was described. Furthermore, the reactivity of all the newly synthesized products was evaluated. The most active compounds towards all the three tumor cancer cell lines used such as MCF-7 (breast adenocarcinoma), NCI-H460 (non-small cell lung cancer) and SF-268 (CNS cancer), and normal fibroblasts human cell line (WI-38) were compounds 6d , 8 , and 10b , which compared with the antiproliferative effects of the reference control doxorubicin. Also, some of the novel compounds indicate higher inhibition than doxorubicin against some of the cancer cell lines used such as 6c (especially towards MCF-7) and 2b , 6b (especially towards SF-268).     

A Silica Bilayer Supported on Ru(0001): Following the Crystalline-to Vitreous Transformation in Real Time with Spectro-microscopy

The crystalline-to-vitreous phase transformation of a SiO₂ bilayer supported on Ru(0001) was studied by time-dependent LEED, local XPS, and DFT calculations. The silica bilayer system has parallels to 3D silica glass and can be used to understand the mechanism of the disorder transition. DFT simulations show that the formation of a Stone–Wales-type of defect follows a complex mechanism, where the two layers show decoupled behavior in terms of chemical bond rearrangements. The calculated activation energy of the rate-determining step for the formation of a Stone—Wales-type of defect (4.3 eV) agrees with the experimental value. Charge transfer between SiO₂ bilayer and Ru(0001) support lowers the activation energy for breaking the Si−O bond compared to the unsupported film. Pre-exponential factors obtained in UHV and in O₂ atmospheres differ significantly, suggesting that the interfacial ORu underneath the SiO₂ bilayer plays a role on how the disordering propagates within the film.     

Ac conductivity study of lithium and potassium diphosphate LiK3P2O7 using impedance spectroscopy

In this work, a LiK₃P₂O₇ ceramic material was prepared by the solid-state reaction method and identified by X-ray diffractometry. The dielectric properties, impedance characteristics, and modulus were studied over a range of frequency (200 Hz to 5 MHz) and temperature (615–708 K). The frequency and temperature dependence of dielectric permittivity, dielectric loss, and electric modulus is studied. The frequency analysis of modulus properties showed a distribution of relaxation times. Conductivity plots against frequency at a higher frequency suggested the response obeying the universal power law. The temperature behavior of the frequency exponents shows that the correlated barrier hopping CBH model is well adapted to this material. The activation energy associated with the impedance relaxation and the electric modulus spectra is close to the activation energy for dc conductivity indicating the similar nature of relaxation and conductivity. Thermodynamic parameters such as free energy of activation, enthalpy, and entropy have been calculated.     

Sensitive and selective fluorescence detection of guanosine nucleotides by nanoparticles conjugated with a naphthyridine receptor

Novel fluorescent nanosensors, based on a naphthyridine receptor, have been developed for the detection of guanosine nucleotides, and both their sensitivity and selectivity to various nucleotides were evaluated. The nanosensors were constructed from polystyrene nanoparticles functionalized by (N-(7-((3-aminophenyl)ethynyl)-1,8-naphthyridin-2-yl)acetamide) via carbodiimide ester activation. We show that this naphthyridine nanosensor binds guanosine nucleotides preferentially over adenine, cytosine, and thymidine nucleotides. Upon interaction with nucleotides, the fluorescence of the nanosensor is gradually quenched yielding Stern–Volmer constants in the range of 2.1 to 35.9 mM⁻¹. For all the studied quenchers, limits of detection (LOD) and tolerance levels for the nanosensors were also determined. The lowest (3σ) LOD was found for guanosine 3’,5’-cyclic monophosphate (cGMP) and it was as low as 150 ng/ml. In addition, we demonstrated that the spatial arrangement of bound analytes on the nanosensors’ surfaces is what is responsible for their selectivity to different guanosine nucleotides. We found a correlation between the changes of the fluorescence signal and the number of phosphate groups of a nucleotide. Results of molecular modeling and ζ-potential measurements confirm that the arrangement of analytes on the surface provides for the selectivity of the nanosensors. These fluorescent nanosensors have the potential to be applied in multi-analyte, array-based detection platforms, as well as in multiplexed microfluidic systems.     

Synthesis of some nucleosides derivatives from L- rhamnose with expected biological activity

Practical procedures for production of variously blocked compounds from L-rhamnose have been developed. These compounds are highly useful as indirect β-L-rhamnosyl donors. This approach represents a new method for the synthesis of aromatic nucleoside analogues and the synthesis of ( 3S, 4S, 5S, 6R) 3, 4, 5-triacetoxy-2-methyl-7,9-diaza-1-oxa-spiro [4,5]decane-10-one-8-thione (7).     

Novel synthesis and antitumor evaluation of polyfunctionally substituted heterocyclic compounds derived from 2-cyano-N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-acetamide

The reaction of 2-amino-3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophene with ethyl cyanoacetate gave 2-cyano-N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-acetamide. The latter was used to synthesize different heterocyclic derivatives comprising thiophene, thiazole, pyrazole, pyridine, pyrimidine, and coumarin rings. The mechanistic and synthetic pathways depended on regioselective attack and/or cyclization by the cyanoacetamido moiety in the key precursor on various chemical reagents. The competition of the reaction pathways including dipolar cyclization, dinucleophilic-bielectrophilic attack, β-attack, Gewald-type attack, and condensation reactions led to the diversity of the synthesized products. The antitumor activities of the synthesized products were studied and evaluated. Most of the compounds revealed high inhibitory effects when screened in vitro for their antiproliferative activity. Three human cancer cell lines, namely, breast adenocarcinoma (MCF-7), non-small cell lung cancer (NCI-H460) and CNS cancer (SF-268) were used in the screening tests. The simplicity of the synthetic procedures which mainly involved one-pot reactions under mild reaction conditions, the convenience of yield production and the diversity of the reactive sites in the produced systems play a valuable role for further heterocyclic transformations and further biological investigations.     

Initial excited-state structural dynamics of 2'-deoxyguanosine determined via UV resonance Raman spectroscopy

The resonance Raman spectra of 2'-deoxyguanosine, a DNA nucleoside, were measured in aqueous solution at wavelengths throughout its 260 nm absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism with two electronic states yielded the initial excited-state structural dynamics in both states. The vibrational modes containing the N(7)═C(8) stretching and C(8)-H bending internal coordinates were found to exhibit significant initial structural dynamics upon photoexcitation to either state and are coincident with the photochemical reaction coordinate involving the formation of the 2'-deoxyguanosine cation radical.     

Synthesis,X-ray analysis and photophysical properties of a new N-containing pentacyclic helicene

A new helically chiral pentacyclic system containing one pyrrole ring was prepared in a good yield and purity via a three-step sequence involving Heck coupling and classical oxidative photocyclization. X-ray crystal structure analysis indicated that the conformation resembled that of unsubstituted pentahelicene, the idealized symmetry of which is C₂. The optical properties of the pentacyclic helicene were investigated and show interesting behaviour.