Preparation and characterization of non-aromatic ether self-assemblies on a HOPG surface.

On-surface self-assemblies of aromatic organic molecules have been widely investigated, but the characterization of analogous self-assemblies consisting of fully sp3-hybridized molecules remains challenging. The possible on-surface orientations of alkyl molecules not exclusively comprised of long alkyl chains are difficult to distinguish because of their inherently low symmetry and non-planar nature. Here, we present a detailed study of diamondoid ethers, structurally rigid and fully saturated molecules, which form uniform 2D monolayers on a highly oriented pyrolytic graphite (HOPG) surface. Using scanning tunneling microscopy, various computational tools, and x-ray structural analysis, we identified the most favorable on-surface orientations of these rigid ethers and accounted for the forces driving the self-organization process. The influence of the oxygen atom and London dispersion interactions were found to be responsible for the formation of the observed highly ordered 2D ether assemblies. Our findings provide insight into the on-surface properties and behavior of non-aromatic organic compounds and broaden our understanding of the phenomena characteristic of monolayers consisting of non-planar molecules.

Isothermal and Isoconversional Modeling of Solid-State Nitroso Polymerization.

The solid-state formation of azodioxide polymers from aromatic dinitroso compounds with different spacer groups was used as a model reaction for a comprehensive analysis that included bulk-based, mechanistic, and isoconversional kinetic methods. Dinitroso species were prepared in situ from azodioxides by UV cleavage under cryogenic conditions, after which their thermally induced conversion to azodioxides was followed by Fourier transform IR spectroscopy. The obtained data were used to calculate activation parameters and determine the influence of the spacer on the kinetics. Isoconversional models suggest a distribution of activation energies, pointing to an important (topochemical) effect of the local environment on the reactivity. In general, bulk-based and isoconversional kinetic models gave poorer fits but produced mutually consistent rate parameters. Similar energies and entropies of activation were obtained with all three approaches, suggesting that they all describe the same underlying physical phenomena; that is, the polymerization by bond-making is the dominant process.

Quantum Chemical Calculations of Monomer-Dimer Equilibria of Aromatic C-Nitroso Compounds.

Monomer-dimer equilibria of nitrosobenzene and 2-nitrosopyridine in gas phase and solution were studied by range of quantum chemical methods in an attempt to find the level of theory suitable for modeling dimerization reactions of aromatic C-nitroso compounds in general. The best agreement with the experimental standard reaction Gibbs energies was obtained with a combination of double-hybrid density functionals B2PLYP-D3, PBE0DH, and DSD-PBEB86, and basis sets of triple-ζ quality. Of all other tested functionals, global hybrid PBE0 behaved equally well, and proved to be more than adequate for at least preliminary work. Other tested methods either produced inferior results (MP2, MP4(SDQ), CCSD, G4(MP2), CBS-QBS, CBS-APNO), or were too demanding for practical use (CCSD(T)). Analysis of computationally obtained thermodynamic data reveal intricate details of these reactions. Both E- and Z-dimers have several different conformers, which all have different solvation energies. While in the gas phase the nitrosobenzene E-dimer is more stable that its Z-form, in chloroform, the Z-form is more stable. Gas-phase dimerization entropies are large and negative, so these reactions are strongly temperature dependent. In some cases, like with 2-nitrosopyridines, entropy and enthalpy terms essentially cancel each other out, allowing structural and media effects to significantly influence dimerization equilibria.

The N Terminus of the Prion Protein Mediates Functional Interactions with the Neuronal Cell Adhesion Molecule (NCAM) Fibronectin Domain.

The cellular form of the prion protein (PrPC) is a highly conserved glycoprotein mostly expressed in the central and peripheral nervous systems by different cell types in mammals. A misfolded, pathogenic isoform, denoted as prion, is related to a class of neurodegenerative diseases known as transmissible spongiform encephalopathy. PrPC function has not been unequivocally clarified, and it is rather defined as a pleiotropic protein likely acting as a dynamic cell surface scaffolding protein for the assembly of different signaling modules. Among the variety of PrPC protein interactors, the neuronal cell adhesion molecule (NCAM) has been studied in vivo, but the structural basis of this functional interaction is still a matter of debate. Here we focused on the structural determinants responsible for human PrPC (HuPrP) and NCAM interaction using stimulated emission depletion (STED) nanoscopy, SPR, and NMR spectroscopy approaches. PrPC co-localizes with NCAM in mouse hippocampal neurons, and this interaction is mainly mediated by the intrinsically disordered PrPC N-terminal tail, which binds with high affinity to the NCAM fibronectin type-3 domain. NMR structural investigations revealed surface-interacting epitopes governing the interaction between HuPrP N terminus and the second module of the NCAM fibronectin type-3 domain. Our data provided molecular details about the interaction between HuPrP and the NCAM fibronectin domain, and revealed a new role of PrPC N terminus as a dynamic and functional element responsible for protein-protein interaction.

Structural basis for the protective effect of the human prion protein carrying the dominant-negative E219K polymorphism.

The most common form of prion disease in humans is sCJD (sporadic Creutzfeldt-Jakob disease). The naturally occurring E219K polymorphism in the HuPrP (human prion protein) is considered to protect against sCJD. To gain insight into the structural basis of its protective influence we have determined the NMR structure of recombinant HuPrP (residues 90-231) carrying the E219K polymorphism. The structure of the HuPrP(E219K) protein consists of a disordered N-terminal tail (residues 90-124) and a well-structured C-terminal segment (residues 125-231) containing three α-helices and two short antiparallel ß-strands. Comparison of NMR structures of the wild-type and HuPrPs with pathological mutations under identical experimental conditions revealed that, although the global architecture of the protein remains intact, replacement of Glu²¹9 with a lysine residue introduces significant local structural changes. The structural findings of the present study suggest that the protective influence of the E219K polymorphism is due to the alteration of surface charge distribution, in addition to subtle structural rearrangements localized within the epitopes critical for prion conversion.

Probing early misfolding events in prion protein mutants by NMR spectroscopy.

The post-translational conversion of the ubiquitously expressed cellular form of the prion protein, PrPC, into its misfolded and pathogenic isoform, known as prion or PrPSc, plays a key role in prion diseases. These maladies are denoted transmissible spongiform encephalopathies (TSEs) and affect both humans and animals. A prerequisite for understanding TSEs is unraveling the molecular mechanism leading to the conversion process whereby most α-helical motifs are replaced by ß-sheet secondary structures. Importantly, most point mutations linked to inherited prion diseases are clustered in the C-terminal domain region of PrPC and cause spontaneous conversion to PrPSc. Structural studies with PrP variants promise new clues regarding the proposed conversion mechanism and may help identify "hot spots" in PrPC involved in the pathogenic conversion. These investigations may also shed light on the early structural rearrangements occurring in some PrPC epitopes thought to be involved in modulating prion susceptibility. Here we present a detailed overview of our solution-state NMR studies on human prion protein carrying different pathological point mutations and the implications that such findings may have for the future of prion research.

Synthesis and Characterization of Benzene- and Triazine-Based Azo-Bridged Porous Organic Polymers.

Porous organic polymers incorporating nitrogen-rich functionalities have recently emerged as promising materials for efficient and highly selective CO2 capture and separation. Herein, we report synthesis and characterization of new two-dimensional (2D) benzene- and triazine-based azo-bridged porous organic polymers. Different synthetic approaches towards the porous azo-bridged polymers were tested, including reductive homocoupling of aromatic nitro monomers, oxidative homocoupling of aromatic amino monomers and heterocoupling of aromatic nitro monomers and a series of aromatic diamines of different lengths and rigidity. IR spectroscopy, 13C CP/MAS NMR spectroscopy, powder X-ray diffraction, elemental analysis, thermogravimetric analysis, nitrogen adsorption-desorption experiments and computational study were used to characterize structures and properties of the resulting polymers. The synthesized azo-bridged polymers are all amorphous solids of good thermal stability, exhibiting various surface areas (up to 351 m2 g-1). The obtained results indicated that the synthetic methods and building units have a pronounced effect on the porosity of the final materials. Reductive and oxidative homocoupling of aromatic nitro and amino building units, respectively, lead to 2D azo-bridged polymers of substantially higher porosity when compared to those produced by heterocoupling reactions. Periodic DFT calculations and Grand-canonical Monte Carlo (GCMC) simulations suggested that, within the used approximations, linear linkers of different lengths do not significantly affect CO2 adsorption properties of model azo-bridged polymers.

Synthesis of aromatic polynitroso compounds: Towards functional azodioxy-linked porous polymers.

The polymerization property of aromatic polynitroso compounds could be used to create azodioxy porous networks with possible application for the adsorption of CO2, the main greenhouse gas. Herein, we report the synthesis and characterization of new aromatic polynitroso compounds, with para-nitroso groups attached to the triphenylbenzene, triphenylpyridine, triphenyltriazine and triphenylamine moiety. The synthesis of the pyridine-based trinitroso compound was performed by reduction of the corresponding trinitro derivative to N-arylhydroxylamine followed by oxidation to the trinitroso product. For the synthesis of the benzene- and triazine-based trinitroso compounds, a novel synthetic strategy was implemented, which included cyclotrimerization of the 4-nitrosoacetophenone and 4-nitrosobenzonitrile, respectively. Reduction of the trinitro compound with triphenylamine unit produced the dinitroso product. In a solid state, all synthesized compounds form E-azodioxy oligomers or polymers. While azodioxy polymer with triphenylbenzene moiety is an amorphous solid, other azodioxy oligomers and polymers displayed sharp diffraction peaks pointing to their crystalline nature. A computational study indicated that eclipsed AA configurations are preferred over staggered AB and inclined AA' configurations. The serrated layers may be the most likely outcome when/if 2D layers form an organized polymer network of azodioxy linked triphenyltriazine-based building blocks.

Structural rearrangements at physiological pH: nuclear magnetic resonance insights from the V210I human prion protein mutant.

A major focus in prion structural biology studies is unraveling the molecular mechanism leading to the structural conversion of PrP(C) to its pathological form, PrP(Sc). In our recent studies, we attempted to understand the early events of the conformational changes leading to PrP(Sc) using as investigative tools point mutations clustered in the open reading frame of the human PrP gene and linked to genetic forms of human prion diseases. In the work presented here, we investigate the effect of pH on the nuclear magnetic resonance (NMR) structure of recombinant human PrP (HuPrP) carrying the pathological V210I mutation responsible for familial Creutzfeldt-Jakob disease. The NMR structure of HuPrP(V210I) determined at pH 7.2 shows the same overall fold as the previously determined structure of HuPrP(V210I) at pH 5.5. It consists of a disordered N-terminal tail (residues 90-124) and a globular C-terminal domain (residues 125-231) comprising three α-helices and a short antiparallel ß-sheet. Detailed comparison of three-dimensional structures of HuPrP(V210I) at pH 7.2 and 5.5 revealed significant local structural differences, with the most prominent pH-related structural variations clustered in the α(2)-α(3) interhelical region, at the interface of the ß(1)-α(1) loop, in helices α(1) and α(3), and in the ß(2)-α(2) loop region. The detailed analysis of interactions among secondary structure elements suggests a higher degree of structural ordering of HuPrP(V210I) under neutral-pH conditions, thus implying that spontaneous misfolding of PrP(C) may occur under acidic-pH conditions in endosomal compartments.

Understanding the Effect of Disease-Related Mutations on Human Prion Protein Structure: Insights From NMR Spectroscopy.

Prion diseases or transmissible spongiform encephalopathies constitute a group of fatal neurodegenerative diseases that can be of sporadic, genetic, or acquired origin. The central molecular event of prion diseases is the conformational conversion of the physiological cellular prion protein, PrPC, into a disease-associated form known as prion or PrPSc. Spontaneous generation of prions in genetic prion diseases is caused by mutations in the human prion protein gene (PRNP). Understanding of the earliest conformational changes during misfolding of PrPC in genetic forms of prion diseases may benefit from detailed structural characterization of various human (Hu) PrP variants. Nuclear magnetic resonance (NMR) spectroscopy offers unique opportunities to obtain detailed atomic-level structure information. In this chapter we present an overview of high-resolution NMR studies on several HuPrPs with disease-associated mutations at mildly acidic and physiological pH conditions that provided valuable insights into possible key structural determinants underlying the formation of prions.

Analysis of Prion Protein Structure Using Nuclear Magnetic Resonance Spectroscopy.

Nuclear magnetic resonance (NMR) spectroscopy is a powerful experimental tool for obtaining information on three-dimensional (3D) structures of proteins at atomic resolution. In inherited forms of prion diseases, misfolding of cellular prion protein, PrPC, into its pathological form, PrPSc, is caused by mutations in the human prion protein gene (PRNP). Understanding of the earliest stages of the conformational changes leading to spontaneous generation of prions in inherited forms of prion diseases may benefit from detailed structural analysis of different human (Hu) PrP variants. Here, we describe the protocol for structure determination of HuPrP variants by NMR spectroscopy in solution that consists of preparation of NMR samples, acquisition of NMR data, NMR resonance assignments, and structure calculation.

NMR structural studies of human cellular prion proteins.

Prion diseases or transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative disorders associated with the conformational conversion of the cellular prion protein, PrP(C), into a pathological form known as prion or PrP(Sc). They can be classified into sporadic, inherited and infectious forms. Spontaneous generation of PrP(Sc) in inherited forms of prion diseases is caused by mutations in the human prion protein gene (PRNP). A major goal in prion biology is unraveling the molecular mechanism by which PrP(C) misfolds and leads to development of diseases. Structural characterization of various human PrP (HuPrP) variants may be helpful for better understanding of the earliest stages of the conformational changes leading to spontaneous generation of prions. Here, we review the results of the recent high-resolution nuclear magnetic resonance (NMR) structural studies on HuPrPs with pathological Q212P and V210I mutations linked with Gerstmann-Sträussler-Scheinker (GSS) syndrome and familial Creutzfeldt-Jakob disease (fCJD), respectively, and HuPrP carrying naturally occurring E219K polymorphism considered to protect against sporadic CJD (sCJD). We describe subtle local differences between the three-dimensional (3D) structures of HuPrP mutants and the wild-type (WT) protein, providing new insights into the possible key structural determinants underlying conversion of PrP(C) into PrP(Sc). Also highlighted are the most recent findings from NMR studies about the effect of pH on the structural features of HuPrP with V210I mutation.

Toward the molecular basis of inherited prion diseases: NMR structure of the human prion protein with V210I mutation.

The development of transmissible spongiform encephalopathies (TSEs) is associated with the conversion of the cellular prion protein (PrP(C)) into a misfolded, pathogenic isoform (PrP(Sc)). Spontaneous generation of PrP(Sc) in inherited forms of disease is caused by mutations in gene coding for PrP (PRNP). In this work, we describe the NMR solution-state structure of the truncated recombinant human PrP (HuPrP) carrying the pathological V210I mutation linked to genetic Creutzfeldt-Jakob disease. The three-dimensional structure of V210I mutant consists of an unstructured N-terminal part (residues 90-124) and a well-defined C-terminal domain (residues 125-228). The C-terminal domain contains three α-helices (residues 144-156, 170-194 and 200-228) and a short antiparallel ß-sheet (residues 129-130 and 162-163). Comparison with the structure of the wild-type HuPrP revealed that although two structures share similar global architecture, mutation introduces some local structural differences. The observed variations are mostly clustered in the α(2)-α(3) inter-helical interface and in the ß(2)-α(2) loop region. Introduction of bulkier Ile at position 210 induces reorientations of several residues that are part of hydrophobic core, thus influencing α(2)-α(3) inter-helical interactions. Another important structural feature involves the alteration of conformation of the ß(2)-α(2) loop region and the subsequent exposure of hydrophobic cluster to solvent, which facilitates intermolecular interactions involved in spontaneous generation of PrP(Sc). The NMR structure of V210I mutant offers new clues about the earliest events of the pathogenic conversion process that could be used for the development of antiprion drugs.