Emergence of Band Structure in a Two-Dimensional Metal-Organic Framework upon Hierarchical Self-Assembly.

Two-dimensional metal-organic frameworks (2D-MOFs) represent a category of atomically thin materials that combine the structural tunability of molecular systems with the crystalline structure characteristic of solids. The strong bonding between the organic linkers and transition metal centers is expected to result in delocalized electronic states. However, it remains largely unknown how the band structure in 2D-MOFs emerges through the coupling of electronic states in the building blocks. Here, we demonstrate the on-surface synthesis of a 2D-MOF exhibiting prominent π-conjugation. Through a combined experimental and theoretical approach, we provide direct evidence of band structure formation upon hierarchical self-assembly, going from metal-organic complexes to a conjugated two-dimensional framework. Additionally, we identify the robustly dispersive nature of the emerging hybrid states, irrespective of the metallic support type, highlighting the tunability of the band structure through charge transfer from the substrate. Our findings encourage the exploration of band-structure engineering in 2D-MOFs for potential applications in electronics and photonics.

Bias-Free Access to Orbital Angular Momentum in Two-Dimensional Quantum Materials.

The demonstration of a topological band inversion constitutes the most elementary proof of a quantum spin Hall insulator (QSHI). On a fundamental level, such an inverted band gap is intrinsically related to the bulk Berry curvature, a gauge-invariant fingerprint of the wave function's quantum geometric properties in Hilbert space. Intimately tied to orbital angular momentum (OAM), the Berry curvature can be, in principle, extracted from circular dichroism in angle-resolved photoemission spectroscopy (CD-ARPES), were it not for interfering final state photoelectron emission channels that obscure the initial state OAM signature. Here, we outline a full-experimental strategy to avoid such interference artifacts and isolate the clean OAM from the CD-ARPES response. Bench-marking this strategy for the recently discovered atomic monolayer system indenene, we demonstrate its distinct QSHI character and establish CD-ARPES as a scalable bulk probe to experimentally classify the topology of two-dimensional quantum materials with time reversal symmetry.

Stripe-Like hBN Monolayer Template for Self-Assembly and Alignment of Pentacene Molecules.

Metallic surfaces with unidirectional anisotropy are often used to guide the self-assembly of organic molecules along a particular direction. Such supports thus offer an avenue for the fabrication of hybrid organic-metal interfaces with tailored morphology and precise elemental composition. Nonetheless, such control often comes at the expense of detrimental interfacial interactions that might quench the pristine properties of molecules. Here, hexagonal boron nitride grown on Ir(100) is introduced as a robust platform with several coexisting 1D stripe-like moiré superstructures that effectively guide unidirectional self-assemblies of pentacene molecules, concomitantly preserving their pristine electronic properties. In particular, highly-aligned longitudinal arrays of equally-oriented molecules are formed along two perpendicular directions, as demonstrated by comprehensive scanning tunneling microscopy and photoemission characterization performed at the local and non-local scale, respectively. The functionality of the template is demonstrated by photoemission tomography, a surface-averaging technique requiring a high degree of orientational order of the probed molecules. The successful identification of pentacene's pristine frontier orbitals underlines that the template induces excellent long-range molecular ordering via weak interactions, preventing charge transfer.

Electronic Band Structure Changes across the Antiferromagnetic Phase Transition of Exfoliated MnPS3 Flakes Probed by µ-ARPES.

Exfoliated magnetic 2D materials enable versatile tuning of magnetization, e.g., by gating or providing proximity-induced exchange interaction. However, their electronic band structure after exfoliation has not been probed, presumably due to their photochemical sensitivity. Here, we provide micrometer-scale angle-resolved photoelectron spectroscopy of the exfoliated intralayer antiferromagnet MnPS3 above and below the Néel temperature down to one monolayer. Favorable comparison with density functional theory calculations enables identifying the orbital character of the observed bands. Consistently, we find pronounced changes across the Néel temperature for bands consisting of Mn 3d and 3p levels of adjacent S atoms. The deduced orbital mixture indicates that the superexchange is relevant for the magnetic interaction. There are only minor changes between monolayer and thicker films, demonstrating the predominant 2D character of MnPS3. The novel access is transferable to other MPX3 materials (M: transition metal, P: phosphorus, X: chalcogenide), providing several antiferromagnetic arrangements.

Soft X-ray Fermi surface tomography of palladium and rhodium via momentum microscopy.

Fermi surfaces of transition metals, which describe all thermodynamical and transport quantities of solids, often fail to be modeled by one-electron mean-field theory due to strong correlations among the valence electrons. In addition, relativistic spin-orbit coupling pronounced in heavier elements lifts the degeneracy of the energy bands and further modifies the Fermi surface. Palladium and rhodium, two 4d metals attributed to show significant spin-orbit coupling and electron correlations, are ideal for a systematic and fundamental study of the two fundamental physical phenomena and their interplay in the electronic structure. In this study, we explored the Fermi surface of the 4d noble metals palladium and rhodium obtained via high-resolution constant initial state momentum microscopy. The complete 3D-Fermi surfaces of palladium and rhodium were tomographically mapped using soft X-ray photon energies from 34 eV up to 660 eV. To fully capture the orbital angular momentum of states across the Fermi surface, the Fermi surface tomography was performed using p- and s- polarized light. Applicability and limitations of the nearly-free electron final state model in photoemission are discussed using a complex band structure model supported by experimental evidence. The significance of spin-orbit coupling and electron correlations across the Fermi surfaces will be discussed within the context of the photoemission results. State-of-the-art fully relativistic Korringa-Kohn-Rostoker (KKR) calculations within the one-step model of photoemission are used to support the experimental results.

Surface-Mediated Spin Locking and Thermal Unlocking in a 2D Molecular Array.

Molecule-based functional devices may take advantage of surface-mediated spin state bistability. Whereas different spin states in conventional spin crossover complexes are only accessible at temperatures well below room temperature, and the lifetimes of the high-spin state are relatively short, a different behavior exhibited by prototypical nickel phthalocyanine is shown here. Direct interaction of the organometallic complex with a copper metal electrode mediates the coexistence of a high spin and a low spin state within the 2D molecular array. The spin state bistability is extremely non-volatile, since no external stimuli are required to preserve it. It originates from the surface-induced axial displacement of the functional nickel cores, which generates two stable local minima. Spin state unlocking and the full conversion to the low spin state are only possible by a high temperature stimulus. This spin state transition is accompanied by distinct changes in the molecular electronic structure that might facilitate the state readout at room temperature, as evidenced by valence spectroscopy. The non-volatility of the high spin state up to elevated temperatures and the controllable spin bistability render the system extremely intriguing for applications in molecule-based information storage devices.

Structural, Thermodynamic and Enzymatic Characterization of N,N-Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus.

Chitin is a major source of energy and macroelements for many organisms. An important step in its degradation is the deacetylation of chitin or its fragments. Deacetylase from the extremophile Pyrococcus chitonophagus has been analyzed by X-ray crystallography, small-angle X-ray scattering, differential scanning calorimetry, isothermal titration calorimetry and NMR to determine its structure, thermodynamics and enzymatic properties. It is a hexameric, zinc-containing metalloenzyme that retains its structural integrity up to temperatures slightly exceeding 100 °C. It removes the acetyl group specifically from the non-reducing end of the sugar substrate. Its main substrate is N,N-diacetylchitobiose but it also active, at a reduced level, toward N-acetyl-d-glucosamine or a trimer of N-acetyl-d-glucosamine units. Crystallographic analysis includes the structure of the enzyme with its main substrate approaching the active site in a monodentate manner, replacing the single water molecule that is bound at the Zn2+ cation when the ligand is absent. The Zn2+ cation remains tetrahedrally coordinated, with three of its ligands provided by the protein's conserved His-Asp-His triad. The crystal structures are consistent with the reaction mechanism proceeding via an anhydride intermediate. Hydrolysis as the first step cannot be ruled out in a hydrated environment but no defined 'hydrolytic water' site can be identified in the analyzed structures.

Conservation of Nickel Ion Single-Active Site Character in a Bottom-Up Constructed π-Conjugated Molecular Network.

On-surface chemistry holds the potential for ultimate miniaturization of functional devices. Porphyrins are promising building-blocks in exploring advanced nanoarchitecture concepts. More stable molecular materials of practical interest with improved charge transfer properties can be achieved by covalently interconnecting molecular units. On-surface synthesis allows to construct extended covalent nanostructures at interfaces not conventionally available. Here, we address the synthesis and properties of covalent molecular network composed of interconnected constituents derived from halogenated nickel tetraphenylporphyrin on Au(111). We report that the π-extended two-dimensional material exhibits dispersive electronic features. Concomitantly, the functional Ni cores retain the same single-active site character of their single-molecule counterparts. This opens new pathways when exploiting the high robustness of transition metal cores provided by bottom-up constructed covalent nanomeshes.

Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex-Duplex Hybrid Formation.

In this paper, a method to discriminate between two target RNA sequences that differ by one nucleotide only is presented. The method relies on the formation of alternative structures, i.e., quadruplex-duplex hybrid (QDH) and duplex with dangling ends (Dss), after hybridization of DNA or RNA G-rich oligonucleotides with target sequences containing 5'-GGGCUGG-3' or 5'-GGGCGGG-3' fragments. Using biophysical methods, we studied the effect of oligonucleotide types (DNA, RNA), non-nucleotide modifications (aliphatic linkers or abasic), and covalently attached G4 ligand on the ability of G-rich oligonucleotides to assemble a G-quadruplex motif. We demonstrated that all examined non-nucleotide modifications could mimic the external loops in the G-quadruplex domain of QDH structures without affecting their stability. Additionally, some modifications, in particular the presence of two abasic residues in the G-rich oligonucleotide, can induce the formation of non-canonical QDH instead of the Dss structure upon hybridization to a target sequence containing the GGGCUGG motif. Our results offer new insight into the sequential requirements for the formation of G-quadruplexes and provide important data on the effects of non-nucleotide modifications on G-quadruplex formation.

RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity.

Guanine (G)-rich single-stranded nucleic acids can adopt G-quadruplex structures. Accumulating evidence indicates that G-quadruplexes serve important regulatory roles in fundamental biological processes such as DNA replication, transcription, and translation, while aberrant G-quadruplex formation is linked to genome instability and cancer. Understanding the biological functions played by G-quadruplexes requires detailed knowledge of their protein interactome. Here, we report that both RNA and DNA G-quadruplexes are bound by human Dicer in vitro. Using in vitro binding assays, mutation studies, and computational modeling we demonstrate that G-quadruplexes can interact with the Platform-PAZ-Connector helix cassette of Dicer, the region responsible for anchoring microRNA precursors (pre-miRNAs). Consequently, we show that G-quadruplexes efficiently and stably inhibit the cleavage of pre-miRNA by Dicer. Our data highlight the potential of human Dicer for binding of G-quadruplexes and allow us to propose a G-quadruplex-driven sequestration mechanism of Dicer regulation.

Formation of an RNA Quadruplex-Duplex Hybrid in Living Cells between mRNA of the Epidermal Growth Factor Receptor (EGFR) and a G-Rich Antisense Oligoribonucleotide.

Antisense DNA oligonucleotides, short interfering RNAs (siRNAs), and CRISPR/Cas9 genetic tools are the most useful therapeutic nucleic acids regulating gene expression based on the antisense specificity towards messenger RNA. Here, we present an effective novel strategy for inhibiting translation based on the antisense-controlled formation of an RNA quadruplex-duplex hybrid (QDH) between a G-rich RNA antisense oligoribonucleotide (Q-ASO) and specific mRNA, comprising two distant G-tracts. We selected epidermal growth factor receptor (EGFR) as a well-established target protein in anticancer therapy. The chemically modified, bi-functional anti-EGFR Q-ASO and a 56-nt long EGFR mRNA fragment, in the presence of potassium ions, were shown to form in vitro very stable parallel G-quadruplex containing a 28-nt long external loop folding to two duplex-stem structure. Besides, the Q-ASOs effectively reduced EGFR mRNA levels compared to the non-modified RNA and DNA antisense oligonucleotides (rASO, dASO). In addition, the hybridization specificity of Q-ASO comprising a covalently attached fluorescent tag was confirmed in living cells by visualization of the G4 green fluorescent species in the presence of other antisense inhibitors under competitive conditions. The results presented here offer novel insights into the potential application of Q-ASOs for the detection and/or alteration of (patho)biological processes through RNA:RNA quadruplex-duplex formation in cellular systems.

Synthesis and Characterization of Low-Cost Cresol-Based Benzoxazine Resins as Potential Binders in Abrasive Composites.

A series of cresol-based benzoxazines were synthesized for potential application as a polymer matrix in abrasive composites. The chemical structures of the obtained benzoxazine resins were investigated in detail using Fourier transform infrared spectroscopy (FTIR) and hydrogen-1 as well as carbon-13 nuclear magnetic resonance spectroscopy (1H NMR, 13C NMR) with an additional analysis using two-dimensional NMR techniques (2D NMR 1H-1H COSY, 1H-13C gHSQC and gHMBC). Structural analysis confirmed the presence of vibrations of -O-C-N- at ~950 cm-1 wavenumber, characteristic for an oxazine ring. The thermal properties of benzoxazine monomers were examined using differential scanning calorimetry (DSC) analysis. The polymerization enthalpy varied from 143.2 J/g to 287.8 J/g. Thermal stability of cresol-based benzoxazines was determined using thermogravimetry (TGA) analysis with additional analysis of the amount of volatile organic compounds (VOC) emitted from the synthesized benzoxazines during their crosslinking by static headspace coupled with gas chromatography technique (HS-GC). The amount of residual mass significantly differed between all synthesized polybenzoxazines in the range from 8.4% to 21.2%. The total VOC emission for benzoxazines decreased by 46-77% in reference to a conventional phenolic binder. The efficiency of abrasive composites with the benzoxazine matrix was evaluated based on abrasion tests. Performed analyses confirmed successful synthesis and proper chemical structure of cresol-based benzoxazines. All the experiments indicated that benzoxazines based on different cresol isomers significantly differ from each other. Good thermal performance and stability of the abrasive composites with the polybenzoxazine matrix and significantly lower VOC emission allow us to state that benzoxazines can be a promising and valuable alternative to the phenolics and a new path for the development of modern, eco-friendly abrasives.

Biodegradation of ritalinic acid by Nocardioides sp. - Novel imidazole-based alkaloid metabolite as a potential marker in sewage epidemiology.

The consumption of methylphenidate, a nootropic drug used to improve mental performance, is becoming increasingly serious. Methylphenidate is metabolized in human liver to ritalinic acid, which has been commonly detected in sewage and surface waters. Additionally, ritalinic acid serves as a biomarker in sewage epidemiology studies. Thus knowledge of the stability and microbial degradation pathways of ritalinic acid is essential for proper estimation of methylphenidate consumption. In the study reported here, we describe the fast formation of a previously unknown, dead-end metabolite of ritalinic acid by Nocardioides sp. strain MW5. HRMS and 2D NMR analyses allowed precisely identification of the compound as an imidazole-based alkaloid cation with chemical formula 11-[3-(formylamino)propyl]-1,2,3,4,6,7,8,9-octahydrodipyrido[1,2-a:1',2'-c]imidazole-5-ium. In experiments, Nocardioides sp. strain MW5 transformed 34% of ritalinic acid into this metabolite, while 52% was mineralized into CO2. Alkaloid was not biodegraded during the OECD 301 F test. This study provides new insight into the environmental fate of methylphenidate and its metabolites. The data collected are essential for assessing nootropic drug consumption by sewage epidemiology and should lead to a better understanding of microbial degradation of ritalinic acid.

Nucleoside dimers analogs containing floxuridine and thymidine with unnatural linker groups: synthesis and cancer line studies. Part III.

Two series of novel fluorinated nucleosides dimers with an unnatural 1,2,3-triazole linkage were synthesized. The obtained molecules were prepared using "click" chemistry approach based on copper(I) catalyzed Huisgen azide-alkyne cycloaddition. It was performed between 3'- and 5'-azido-nucleosides as the azide components, and the 3'-O- and 5'-O-propargyl-nucleosides as the alkyne components. Based on analysis of the 3 JHH, 3 JH1'C2 and 3 JH1'C6 we estimated conformational preferences of sugar part and orientation around glycosidic bond. All described nucleosides dimers analogs were characterized by spectroscopic methods and evaluated for their in vitro cytotoxicity in three human cancer cell lines: cervical (HeLa), oral (KB) and breast (MCF-7).

Nucleoside dimers analogues with a 1,2,3-triazole linkage: conjugation of floxuridine and thymidine provides novel tools for cancer treatment. Part II.

The fluorinated nucleoside dimers with a 1,2,3-triazole linkage are novel compounds within the field of bioorganic chemistry. We report on the synthesis and properties of two groups of nucleoside dimers analogs possessing a different arrangement of the 1,4-disubstituted 1,2,3-triazole linkage. Based on analysis of the 3JHH, 3JH1'C2, and 3JH1'C6 we estimated conformational preferences of sugar part and orientation around glycosidic bond. These compounds show moderate anticancer activity, with cytostatic studies in three different cancer cell lines.

3'-O- and 5'-O-Propargyl Derivatives of 5-Fluoro-2'-Deoxyuridine: Synthesis, Cytotoxic Evaluation and Conformational Analysis.

A series of new 3'-O- and 5'-O-propargyl derivatives of 5-fluoro-2'-deoxyuridine (1-4) was synthesized by means of propargyl reaction of properly blocked nucleosides (2,4), followed by the deprotection reaction with ammonium fluoride. The synthesized propargylated 5-fluoro-2'-deoxyuridine analogues (1-4) were evaluated for their cytotoxic activity in three human cancer cell lines: cervical (HeLa), oral (KB) and breast (MCF-7), using the sulforhodamine B (SRB) assay. The highest activity and the best SI coefficient in all of the investigated cancer cells were displayed by 3'-O-propargyl-5-fluoro-2'-deoxyuridine (1), and its activity was higher than that of the parent nucleoside. The other new compounds exhibited moderate activity in all of the used cell lines.

Fusion of the 1H NMR data of serum, urine and exhaled breath condensate in order to discriminate chronic obstructive pulmonary disease and obstructive sleep apnea syndrome.

Chronic obstructive pulmonary disease, COPD, affects the condition of the entire human organism and causes multiple comorbidities. Pathological lung changes lead to quantitative changes in the composition of the metabolites in different body fluids. The obstructive sleep apnea syndrome, OSAS, occurs in conjunction with chronic obstructive pulmonary disease in about 10-20 % of individuals who have COPD. Both conditions share the same comorbidities and this makes differentiating them difficult. The aim of this study was to investigate whether it is possible to diagnose a patient with either COPD or the OSA syndrome using a set of selected metabolites and to determine whether the metabolites that are present in one type of biofluid (serum, exhaled breath condensate or urine) or whether a combination of metabolites that are present in two biofluids or whether a set of metabolites that are present in all three biofluids are necessary to correctly diagnose a patient. A quantitative analysis of the metabolites in all three biofluid samples was performed using 1H NMR spectroscopy. A multivariate bootstrap approach that combines partial least squares regression with the variable importance in projection score (VIP-score) and selectivity ratio (SR) was adopted in order to construct discriminant diagnostic models for the groups of individuals with COPD and OSAS. A comparison study of all of the discriminant models that were constructed and validated showed that the discriminant partial least squares model using only ten urine metabolites (selected with the SR approach) has a specificity of 100 % and a sensitivity of 86.67 %. This model (AUCtest = 0.95) presented the best prediction performance. The main conclusion of this study is that urine metabolites, among the others, present the highest probability for correctly identifying patents with COPD and the lowest probability for an incorrect identification of the OSA syndrome as developed COPD. Another important conclusion is that the changes in the metabolite levels of exhaled breath condensates do not appear to be specific enough to differentiate between patients with COPD and OSAS.

Hybridization Properties of RNA Containing 8-Methoxyguanosine and 8-Benzyloxyguanosine.

Modified nucleobase analogues can serve as powerful tools for changing physicochemical and biological properties of DNA or RNA. Guanosine derivatives containing bulky substituents at 8 position are known to adopt syn conformation of N-glycoside bond. On the contrary, in RNA the anti conformation is predominant in Watson-Crick base pairing. In this paper two 8-substituted guanosine derivatives, 8-methoxyguanosine and 8-benzyloxyguanosine, were synthesized and incorporated into oligoribonucleotides to investigate their influence on the thermodynamic stability of RNA duplexes. The methoxy and benzyloxy substituents are electron-donating groups, decreasing the rate of depurination in the monomers, as confirmed by N-glycoside bond stability assessments. Thermodynamic stability studies indicated that substitution of guanosine by 8-methoxy- or 8-benzyloxyguanosine significantly decreased the thermodynamic stability of RNA duplexes. Moreover, the presence of 8-substituted guanosine derivatives decreased mismatch discrimination. Circular dichroism spectra of modified RNA duplexes exhibited patterns typical for A-RNA geometry.

2-Methylwyosine, a nucleoside with restricted anti conformation in the east region enforced by nucleobase moiety modification: synthesis and conformational analysis by NMR and molecular dynamics.

We synthesized a new 2-methyl derivative of wyosine using a multistep procedure starting from guanosine. We examined different synthetic paths and optimized the conditions for each step. Based on MD calculations and analysis of the (3) J (HH) and J (C1'H1') of the ribose moiety, we discovered that the sugar part adopted conformation specific for the East region rarely occurring in solution. This unusual conformational preference is probably due to steric repulsions between the methyl group at position 2 and the 5'-CH(2)OH group. We observed that N-glycosidic bond stability weakened 14-fold upon the introduction of the methyl group in position 2 compared with wyosine.

Conformationally restricted 2-substituted wyosine derivatives. 1H, 13C, and 15N NMR study.

It was found by 1H, 13C and 15N NMR study that substitution of 4,9-dihydro-4,6-dimethyl-9-oxo-3-(2',3',5'-tri-O-acetyl-beta-D-ribofuranosyl) imidazo [1,2-a]purine (wyosine triacetate, 1) at C2 position with electronegative groups CH30 and C6H5CH2O results in a noticeable electron distribution disturbance in the "left-hand" imidazole ring and a significant increase in the North conformer population of the sugar moiety.