Quantum sensing of microRNAs with nitrogen-vacancy centers in diamond

Label-free detection of nucleic acids such as microRNAs holds great potential for early diagnostics of various types of cancers. Measuring intrinsic biomolecular charge using methods based on field effect has been a promising way to accomplish label-free detection. However, the charges of biomolecules are screened by counter ions in solutions over a short distance (Debye length), thereby limiting the sensitivity of these methods. Here, we measure the intrinsic magnetic noise of paramagnetic counter ions, such as Mn2+, interacting with microRNAs using nitrogen-vacancy (NV) centers in diamond. All-atom molecular dynamics simulations show that microRNA interacts with the diamond surface resulting in excess accumulation of Mn ions and stronger magnetic noise. We confirm this prediction by observing an increase in spin relaxation contrast of the NV centers, indicating higher Mn2+ local concentration. This opens new possibilities for next-generation quantum sensing of charged biomolecules, overcoming limitations due to the Debye screening.

Pure and Sc-doped diopside (CaMgSi2O6) vibrational spectra: modelling and experiments

We investigated the structure of pure and Sc-doped synthetic diopside (a monoclinic single-chain silicate nominally CaMgSi2O6); in Sc-doped diopside, Sc3+ substitutes Mg2+ in the structure and, to achieve charge balance, vacancies form at the expense of Ca2+. We compared the structure obtained from ab initio modelling techniques at the density functional theory (DFT) level with the structure solved by employing single crystal X-ray diffraction. Furthermore, we compared IR and Raman spectroscopy experiments with vibrational density of states (VDOS) calculated from the Fourier transform of the velocity autocorrelation function obtained using ab initio (DFT) molecular dynamics simulations. In this framework, we developed a computational tool to assign the vibrational mode associated with a specific frequency. This method consists of projecting velocities along a specific set of internal coordinates such as stretching or bending, in cases involving defects or vacancies, to calculate a partial VDOS (pVDOS) that takes into account only the vibrations associated with selected internal modes, aiding the interpretation of the total VDOS and the experimental spectra in a relevant way. The computed data were validated with the experiments and we observed that doping the diopside structure with Sc produces peak broadening and the occurrence of new peaks in the Raman spectra and that site vacancies are associated with the nearby Sc site. The present work constitutes an interesting starting point to exploit the calculated VDOS/pVDOS to characterize experimental vibrational spectra of complex systems containing local vacancies, substitutions or defects as the Sc-doped diopside.

Aluminium 8-Hydroxyquinolinate N-Oxide as a Precursor to Heterometallic Aluminium-Lanthanide Complexes

A reaction in anhydrous toluene between the formally unsaturated fragment [Ln(hfac)3] (Ln3+ = Eu3+, Gd3+ and Er3+; Hhfac = hexafluoroacetylacetone) and [Al(qNO)3] (HqNO = 8-hydroxyquinoline N-oxide), here prepared for the first time from [Al(OtBu)3] and HqNO, affords the dinuclear heterometallic compounds [Ln(hfac)3Al(qNO)3] (Ln3+ = Eu3+, Gd3+ and Er3+) in high yields. The molecular structures of these new compounds revealed a dinuclear species with three phenolic oxygen atoms bridging the two metal atoms. While the europium and gadolinium complexes show the coordination number (CN) 9 for the lanthanide centre, in the complex featuring the smaller erbium ion, only two oxygens bridge the two metal atoms for a resulting CN of 8. The reaction of [Eu(hfac)3] with [Alq3] (Hq = 8-hydroxyquinoline) in the same conditions yields a heterometallic product of composition [Eu(hfac)3Alq3]. A recrystallization attempt from hot heptane in air produced single crystals of two different morphologies and compositions: [Eu2(hfac)6Al2q4(OH)2] and [Eu2(hfac)6(µ-Hq)2]. The latter compound can be directly prepared from [Eu(hfac)3] and Hq at room temperature. Quantum mechanical calculations confirm (i) the higher stability of [Eu(hfac)3Al(qNO)3] vs. the corresponding [Eu(hfac)3Alq3] and (ii) the preference of the Er complexes for the CN 8, justifying the different behaviour in terms of the Lewis acidity of the metal centre.

Aptamer-based gold nanoparticle aggregates for ultrasensitive amplification-free detection of PSMA

Early diagnosis is one of the most important factors in determining the prognosis in cancer. Sensitive detection and quantification of tumour-specific biomarkers have the potential to improve significantly our diagnostic capability. Here, we introduce a triggerable aptamer-based nanostructure based on an oligonucleotide/gold nanoparticle architecture that selectively disassembles in the presence of the biomarker of interest; its optimization is based also on in-silico determination of the aptamer nucleotides interactions with the protein of interest. We demonstrate this scheme for the case of Prostate Specific Membrane Antigen (PSMA) and PSMA derived from PSMA-positive exosomes. We tested the disassembly of the system by diameter and count rate measurements in dynamic light scattering, and by inspection of its plasmon resonance shift, upon addition of PSMA, finding appreciable differences down to the sub-picomolar range; this points towards the possibility that this approach may lead to sensors competitive with diagnostic biochemical assays that require enzymatic amplification. More generally, this scheme has the potential to be applied to a broad range of pathologies with specific identified biomarkers.

Competing excitation paths in luminescent heterobimetallic Ln-Al complexes: Unraveling interactions via experimental and theoretical investigations

The interest for heterometallic lanthanide-d or-p metal (Ln-M) complexes is growing because of a potential cooperative or synergistic effect related to the proximity of two different metals in the same molecular architecture affording special tunable physical properties. To exploit the potentiality of Ln-M complexes, suitable synthetic approaches, and the in-depth understanding of the effect of each building block on their properties are mandatory. Here, we report the study on a family of heterometallic luminescent complexes [Ln(hfac)₃Al(L)₃], Ln= Eu³⁺ and Tb³⁺. Using different L ligands, we investigated the effect of the steric and electronic properties of the Al(L)₃ fragment, highlighting the general validity of the employed synthetic route. A marked difference in the light emission of [Eu(hfac)₃Al(L)₃] and [Tb(hfac)₃Al(L)₃] complexes has been observed. Thanks to photoluminescence experiments and Density Functional Theory calculations, Ln³⁺ emissions are explained with a model involving two non-interacting excitation paths through hfac or Al(L)₃ ligands.

Heat-Driven Iontronic Nanotransistors

Thermoelectric polyelectrolytes are emerging as ideal material platform for self-powered bio-compatible electronic devices and sensors. However, despite the nanoscale nature of the ionic thermodiffusion processes underlying thermoelectric efficiency boost in polyelectrolytes, to date no evidence for direct probing of ionic diffusion on its relevant length and time scale has been reported. This gap is bridged by developing heat-driven hybrid nanotransistors based on InAs nanowires embedded in thermally biased Na⁺ -functionalized (poly)ethyleneoxide, where the semiconducting nanostructure acts as a nanoscale probe sensitive to the local arrangement of the ionic species. The impact of ionic thermoelectric gating on the nanodevice electrical response is addressed, investigating the effect of device architecture, bias configuration and frequency of the heat stimulus, and inferring optimal conditions for the heat-driven nanotransistor operation. Microscopic quantities of the polyelectrolyte such as the ionic diffusion coefficient are extracted from the analysis of hysteretic behaviors rising in the nanodevices. The reported experimental platform enables simultaneously the ionic thermodiffusion and nanoscale resolution, providing a framework for direct estimation of polyelectrolytes microscopic parameters. This may open new routes for heat-driven nanoelectronic applications and boost the rational design of next-generation polymer-based thermoelectric materials.

Size Selectivity in Heterolanthanide Molecular Complexes with a Ditopic Ligand

The similar reactivity of lanthanides generally leads to statistically populated polynuclear complexes, making the rational design of ordered hetero-lanthanide compounds extremely challenging. Here we report on the site selectivity in hetero-lanthanide tetranuclear complexes afforded by the relatively simple ditopic pyterpyNO ligand (4'-(4-pyridil)-2,2':6',2"-terpyridine N-oxide). The sequential room temperature reaction of RE₂ (tta)₆ (pyterpyNO)₂ (where RE=Y, (1); Eu, (2), Dy, (3) Htta=2-thenoyltrifluoroacetone) with La(tta)₃ dme (dme=dimethoxyethane) yielded Y₂ La₂ (tta)₁₂ (pyterpyNO)₂ (4), Dy₂ La₂ (tta)₁₂ (pyterpyNO)₂ (5) and Eu₂ La₂ (tta)₁₂ (pyterpyNO)₂ (6). Single crystals X-ray diffraction studies showed that 4, 5 and 6 are isostructural, featuring a tetranuclear structure with two different metal coordination sites with coordination numbers 8 (CN8) and 9 (CN9). The two smaller cations are mainly bridged by the O-donor atoms of the NO groups of two pyterpyNO ligands (CN8), while the larger lanthanum centres are bound by a terpyridine unit (CN9). Size selectivity has been studied with structural and magnetic studies in the solid state and through ¹⁹ F NMR and photoluminescence studies in solution, showing a direct dependence on the difference of ionic radii of the ions and yielding a 91 % selectivity for 4. Furthermore, ¹⁹ F NMR, X-ray and PL studies pointed out that the nature of the product is independent from the synthetic route for compound Eu₂ Y₂ (tta)₁₂ (pyterpyNO)₂ (7), keeping the ion selectivity also for a self-assembly reaction. Unexpectedly, these studies have evidenced that selectivity is not exclusively governed by electrostatic interactions related to size dimensions.

Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study

A rationally designed gold-functionalized surface capable of capturing a target protein is presented using the biotin–streptavidin pair as a proof-of-concept. We carried out multiscale simulations to shed light on the binding mechanism of streptavidin on four differently biotinylated surfaces. Brownian Dynamics simulations were used to reveal the preferred initial orientation of streptavidin over the surfaces, whereas classical molecular dynamics was used to refine the binding poses and to investigate the fundamental forces involved in binding, and the binding kinetics. We assessed the binding events and the stability of the streptavidin attachment through a quartz crystal microbalance with dissipation monitoring (QCM-D). The sensing element comprises of biotinylated polyethylene glycol chains grafted on the sensor’s gold surface via thiol-Au chemistry. Finally, we compared the results from experiments and simulations. We found that the confined biotin moieties can specifically capture streptavidin from the liquid phase and provide guidelines on how to exploit the microscopic parameters obtained from simulations to guide the design of further biosensors with enhanced sensitivity.

Acidic pH Promotes Refolding and Macroscopic Assembly of Amyloid β (16-22) Peptides at the Air-Water Interface

Assembly by amyloid-beta (Aβ) peptides is vital for various neurodegenerative diseases. The process can be accelerated by hydrophobic interfaces such as the cell membrane interface and the air-water interface. Elucidating the assembly mechanism for Aβ peptides at hydrophobic interface requires knowledge of the microscopic structure of interfacial peptides. Here we combine scanning force microscopy, sum-frequency generation spectroscopy, and metadynamics simulations to probe the structure of the central fragment of Aβ peptides at the air-water interface. We find that the structure of interfacial peptides depends on pH: at neutral pH, the peptides adopt a less folded, bending motif by forming intra-hydrogen bonds; at acidic pH, the peptides refold into extended β-strand fibril conformation, which further promotes their macroscopic assembly. The conformational transition of interfacial peptides is driven by the reduced hydrogen bonds, both with water and within peptides, resulting from the protonation of acidic glutamic acid side chains.

Stoichiometrically Controlled Assembly of Lanthanide Molecular Complexes of the Heteroditopic Divergent Ligand 4'-(4-Pyridyl)-2,2':6',2″-terpyridine N-Oxide in Hypodentate or Bridging Coordination Modes. Structural, Magnetic, and Photoluminescence Studies

Mononuclear rare-earth tris-β-diketonato complexes RE(tta)₃dme [RE = Y (1), La (2), Dy (3), or Eu (4); Htta = 2-thenoylacetone; dme = 1,2-dimethoxyethane] react cleanly at room temperature in a 1:1 molar ratio with the heteroditopic divergent ligand 4'-(4-pyridyl)-2,2':6',2″-terpyridine N-oxide (pyterpyNO) to yield RE₂(tta)₆(pyterpyNO)_n, where n = 2 for RE = Y (5), Dy (6), or Eu (7) and n = 3 for RE = La (8). The crystal structure of 5 revealed a dinuclear compound with two pyterpyNO's bridging through the oxygen atom in a hypodentate mode leaving the terpyridine moieties uncoordinated. Using a metal:pyterpyNO molar ratio of 2 for RE = Y (9), Dy (10), or Eu (11), it was possible to isolate the molecular complexes RE₄(tta)₁₂(pyterpyNO)₂, while using a 5:3 molar ratio, the product La₅(tta)₁₂(pyterpyNO)₃ (12) can be obtained. ⁸⁹Y nuclear magnetic resonance spectroscopy revealed two different yttrium centers at room temperature for 9. An X-ray diffraction study of 10 showed a symmetrical tetranuclear structure resulting from the coordination of two Dy(tta)₃ fragments to the two hypodentate terpyridines of the dinuclear unit and presenting two different coordination sites for metals with coordination numbers of 8 and 9. Magnetic studies of 6 and 10 revealed the presence of an antiferromagnetic interaction between the two Dy(III) atoms bound by the NO bridges. These compounds displayed a slow relaxing magnetization through Orbach (6) and Raman (10) processes in the absence of an applied magnetic field; the rate increased upon application of a 1 kOe field. 7 and 11 showed a bright red emission typical of Eu³⁺. The two complexes have similar emission properties mainly determined by the employed β-diketonato ligands.

1D-Zigzag Eu3+/Tb3+ Coordination Chains as Luminescent Ratiometric Thermometers Endowed with Multicolor Emission

Two homometallic Coordination Polymers (CPs) with composition [Ln(hfac)₃bipy]_n (Ln³⁺ = Eu³⁺, 1, and Tb³⁺, 2; hfac = hexafluoroacetylacetonato, bipy = 4,4′-bipyridine) were used to develop a family of ratiometric luminescent thermometers containing Eu³⁺ and Tb³⁺ as red and green emitters, respectively. The thermometric properties of pure CPs and of their mixtures having an Eu³⁺/Tb³⁺ molar ratio of 1:1, 1:3, 1:5, and 1:10 (samples: Eu1Tb1, Eu1Tb3, Eu1Tb5, and Eu1Tb10) were studied in the 83–383 K temperature range. Irrespective of the chemical composition, we observed similar thermometric responses characterized by broad applicative temperature ranges (from 100 to 165 K wide), and high relative thermal sensitivity values (S_r), up to 2.40% K⁻¹, in the physiological temperature range (298–318 K). All samples showed emissions endowed with peculiar and continuous color variation from green (83 K) to red (383 K) that can be exploited to develop a colorimetric temperature indicator. At fixed temperature, the color of the emitted light can be tuned by varying composition and excitation wavelength.

Correction: Covalent organic functionalization of graphene nanosheets and reduced graphene oxide via 1,3-dipolar cycloaddition of azomethine ylide

[This corrects the article DOI: 10.1039/D1NA00335F.].

Covalent organic functionalization of graphene nanosheets and reduced graphene oxide via 1,3-dipolar cycloaddition of azomethine ylide

Organic functionalization of graphene is successfully performed via 1,3-dipolar cycloaddition of azomethine ylide in the liquid phase. The comparison between 1-methyl-2-pyrrolidinone and N,N-dimethylformamide as dispersant solvents, and between sonication and homogenization as dispersion techniques, proves N,N-dimethylformamide and homogenization as the most effective choice. The functionalization of graphene nanosheets and reduced graphene oxide is confirmed using different techniques. Among them, energy-dispersive X-ray spectroscopy allows to map the pyrrolidine ring of the azomethine ylide on the surface of functionalized graphene, while micro-Raman spectroscopy detects new features arising from the functionalization, which are described in agreement with the power spectrum obtained from ab initio molecular dynamics simulation. Moreover, X-ray photoemission spectroscopy of functionalized graphene allows the quantitative elemental analysis and the estimation of the surface coverage, showing a higher degree of functionalization for reduced graphene oxide. This more reactive behavior originates from the localization of partial charges on its surface due to the presence of oxygen defects, as shown by the simulation of the electrostatic features. Functionalization of graphene using 1,3-dipolar cycloaddition is shown to be a significant step towards the controlled synthesis of graphene-based complex structures and devices at the nanoscale.

Deterministic synthesis of Cu9S5 flakes assisted by single-layer graphene arrays

The employment of two-dimensional materials, as growth substrates or buffer layers, enables the epitaxial growth of layered materials with different crystalline symmetries with a preferential crystalline orientation and the synthesis of heterostructures with a large lattice constant mismatch. In this work, we employ single crystalline graphene to modify the sulfurization dynamics of copper foil for the deterministic synthesis of large-area Cu₉S₅ crystals. Molecular dynamics simulations using the Reax force-field are used to mimic the sulfurization process of a series of different atomistic systems specifically built to understand the role of graphene during the sulphur atom attack over the Cu(111) surface. Cu₉S₅ flakes show a flat morphology with an average lateral size of hundreds of micrometers. Cu₉S₅ presents a direct band-gap of 2.5 eV evaluated with light absorption and light emission spectroscopies. Electrical characterization shows that the Cu₉S₅ crystals present high p-type doping with a hole mobility of 2 cm² V^-1 s^-1.

Atomistic simulations of gold surface functionalization for nanoscale biosensors applications

A wide class of biosensors can be built via functionalization of gold surface with proper bio conjugation element capable of interacting with the analyte in solution, and the detection can be performed either optically, mechanically or electrically. Any change in physico-chemical environment or any slight variation in mass localization near the surface of the sensor can cause differences in nature of the transduction mechanism. The optimization of such sensors may require multiple experiments to determine suitable experimental conditions for the immobilization and detection of the analyte. Here, we employ molecular modeling techniques to assist the optimization of a gold-surface biosensor. The gold surface of a quartz-crystal-microbalance sensor is functionalized using polymeric chains of poly(ethylene glycol) (PEG) of 2 KDa molecular weight, which is an inert long chain amphiphilic molecule, supporting biotin molecules (bPEG) as the ligand molecules for streptavidin analyte. The PEG linkers are immobilized onto the gold surface through sulphur chemistry. Four gold surfaces with different PEG linker density and different biotinylation ratio between bPEG and PEG, are investigated by means of state-of-the art atomistic simulations and compared with available experimental data. Results suggest that the amount of biotin molecules accessible for the binding with the protein increases upon increasing the linkers density. At the high density a 1:1 ratio of bPEG/PEG can further improve the accessibility of the biotin ligand due to a strong repulsion between linker chains and different degree of hydrophobicity between bPEG and PEG linkers. The study provides a computaional protocol to model sensors at the level of single molecular interactions, and for optimizing the physical properties of surface conjugated ligand which is crucial to enhance output of the sensor.

In silico design, building and gas adsorption of nano-porous graphene scaffolds

Graphene-based nano-porous materials (GNM) are potentially useful for all those applications needing a large specific surface area (SSA), typical of the bidimensional graphene, yet realized in the bulk dimensionality. Such applications include for instance gas storage and sorting, catalysis and electrochemical energy storage. While a reasonable control of the structure is achieved in micro-porous materials by using nano-micro particles as templates, the controlled production or even characterization of GNMs with porosity strictly at the nano-scale still raises issues. These are usually produced using dispersion of nano-flakes as precursors resulting in little control on the final structure, which in turn reflects in problems in the structural model building for computer simulations. In this work, we describe a strategy to build models for these materials with predetermined structural properties (SSA, density, porosity), which exploits molecular dynamics simulations, Monte Carlo methods and machine learning algorithms. Our strategy is inspired by the real synthesis process: starting from randomly distributed flakes, we include defects, perforation, structure deformation and edge saturation on the fly, and, after structural refinement, we obtain realistic models, with given structural features. We find relationships between the structural characteristics and size distributions of the starting flake suspension and the final structure, which can give indications for more efficient synthesis routes. We subsequently give a full characterization of the models versus H₂ adsorption, from which we extract quantitative relationship between the structural parameters and the gravimetric density. Our results quantitatively clarify the role of surfaces and edges relative amount in determining the H₂ adsorption, and suggest strategies to overcome the inherent physical limitations of these materials as adsorbers. We implemented the model building and analysis procedures in software tools, freely available upon request.

Composition-Thermometric Properties Correlations in Homodinuclear Eu3+ Luminescent Complexes

A family of homodinuclear Ln³⁺ (Ln³⁺ = Gd³⁺, Eu³⁺) luminescent complexes with the general formula [Ln₂(β-diketonato)₆(N-oxide)_y] has been developed to study the effect of the β-diketonato and N-oxide ligands on their thermometric properties. The investigated complexes are [Ln₂(tta)₆(pyrzMO)₂] (Ln = Eu (1·C₇H₈), Gd (5)), [Ln₂(dbm)₆(pyrzMO)₂] (Ln = Eu (2), Gd (6)), [Ln₂(bta)₆(pyrzMO)₂] (Ln = Eu (3), Gd (7)), [Ln₂(hfac)₆(pyrzMO)₃] (Ln = Eu (4), Gd (8)) (pyrzMO = pyrazine N-oxide, Htta = thenoyltrifluoroacetone, Hdbm = dibenzoylmethane, Hbta = benzoyltrifluoroacetone, Hhfac = hexafluoroacetylacetone, C₇H₈ = toluene), and their 4,4′-bipyridine N-oxide (bipyMO) analogues. Europium complexes emit a bright red light under UV radiation at room temperature, whose intensity displays a strong temperature (T) dependence between 223 and 373 K. This remarkable variation is exploited to develop a series of luminescent thermometers by using the integrated intensity of the ⁵D₀ → ⁷F₂ europium transition as the thermometric parameter (Δ). The effect of different β-diketonato and N-oxide ligands is investigated with particular regard to the shape of thermometer calibration (Δ vs T) and relative thermal sensitivity curves: i.e.. the change in Δ per degree of temperature variation usually indicated as S_r (% K^–1). The thermometric properties are determined by the presence of two nonradiative deactivation channels, back energy transfer (BEnT) from Eu³⁺ to the ligand triplet levels and ligand to metal charge transfer (LMCT). In the complexes bearing tta and dbm ligands, whose triplet energy is ca. 20000 cm^–1, both deactivation channels are active in the same temperature range, and both contribute to determine the thermometric properties. Conversely, with bta and hfac ligands the response of the europium luminescence to temperature variation is ruled by LMCT channels since the high triplet energy (>21400 cm^–1) makes BEnT ineffective in the investigated temperature range.

A family of homodinuclear Eu³⁺ luminescent complexes with the general formula [Ln₂(β-diketonato)₆(N-oxide)_y] (y = 2, 3) was developed to study the effect of the β-diketonato and N-oxide ligands on the thermometric properties of the complexes. In this way, an effective tuning of the system’s thermometric properties can be achieved.

Effects of Ligand Binding on the Energy Landscape of Acyl-CoA-Binding Protein

Binding of ligands is often crucial for function yet the effects of ligand binding on the mechanical stability and energy landscape of proteins are incompletely understood. Here, we use a combination of single-molecule optical tweezers and MD simulations to investigate the effect of ligand binding on the energy landscape of acyl-coenzyme A (CoA)-binding protein (ACBP). ACBP is a topologically simple and highly conserved four-α-helix bundle protein that acts as an intracellular transporter and buffer for fatty-acyl-CoA and is active in membrane assembly. We have previously described the behavior of ACBP under tension, revealing a highly extended transition state (TS) located almost halfway between the unfolded and native states. Here, we performed force-ramp and force-jump experiments, in combination with advanced statistical analysis, to show that octanoyl-CoA binding increases the activation free energy for the unfolding reaction of ACBP without affecting the position of the transition state along the reaction coordinate. It follows that ligand binding enhances the mechanical resistance and thermodynamic stability of the protein, without changing its mechanical compliance. Steered molecular dynamics simulations allowed us to rationalize the results in terms of key interactions that octanoyl-CoA establishes with the four α-helices of ACBP and showed that the unfolding pathway is marginally affected by the ligand. The results show that ligand-induced mechanical stabilization effects can be complex and may prove useful for the rational design of stabilizing ligands.

Dynamics and structural communication in the ternary complex of fully phosphorylated V2 vasopressin receptor, vasopressin, and β-arrestin 1

G protein-coupled receptors (GPCRs) are critically regulated by arrestins, which not only desensitize G-protein signaling but also initiate a G protein-independent wave of signaling. The information from structure determination was herein exploited to build a structural model of the ternary complex, comprising fully phosphorylated V2 vasopressin receptor (V2R), the agonist arginine vasopressin (AVP), and β-arrestin 1 (β-arr1). Molecular simulations served to explore dynamics and structural communication in the ternary complex. Flexibility and mechanical profiles reflect fold of V2R and β-arr1. Highly conserved amino acids tend to behave as hubs in the structure network and contribute the most to the mechanical rigidity of V2R seven-helix bundle and of β-arr1. Two structurally and dynamically distinct receptor-arrestin interfaces assist the twist of the N- and C-terminal domains (ND and CD, respectively) of β-arr1 with respect to each other, which is linked to arrestin activation. While motion of the ND is essentially assisted by the fully phosphorylated C-tail of V2R (V2RCt), that of CD is assisted by the second and third intracellular loops and the cytosolic extensions of helices 5 and 6. In the presence of the receptor, the β-arr1 inter-domain twist angle correlates with the modes describing the essential subspace of the ternary complex. β-arr1 motions are also influenced by the anchoring to the membrane of the C-edge-loops in the β-arr1-CD. Overall fluctuations reveal a coupling between motions of the agonist binding site and of β-arr1-ND, which are in allosteric communication between each other. Mechanical rigidity points, often acting as hubs in the structure network and distributed along the main axis of the receptor helix bundle, contribute to establish a preferential communication pathway between agonist ligand and the ND of arrestin. Such communication, mediated by highly conserved amino acids, involves also the first amino acid in the arrestin C-tail, which is highly dynamic and is involved in clathrin-mediated GPCR internalization.

Engineering 3D Graphene-Based Materials: State of the Art and Perspectives

Graphene is the prototype of two-dimensional (2D) materials, whose main feature is the extremely large surface-to-mass ratio. This property is interesting for a series of applications that involve interactions between particles and surfaces, such as, for instance, gas, fluid or charge storage, catalysis, and filtering. However, for most of these, a volumetric extension is needed, while preserving the large exposed surface. This proved to be rather a hard task, especially when specific structural features are also required (e.g., porosity or density given). Here we review the recent experimental realizations and theoretical/simulation studies of 3D materials based on graphene. Two main synthesis routes area available, both of which currently use (reduced) graphene oxide flakes as precursors. The first involves mixing and interlacing the flakes through various treatments (suspension, dehydration, reduction, activation, and others), leading to disordered nanoporous materials whose structure can be characterized a posteriori, but is difficult to control. With the aim of achieving a better control, a second path involves the functionalization of the flakes with pillars molecules, bringing a new class of materials with structure partially controlled by the size, shape, and chemical-physical properties of the pillars. We finally outline the first steps on a possible third road, which involves the construction of pillared multi-layers using epitaxial regularly nano-patterned graphene as precursor. While presenting a number of further difficulties, in principle this strategy would allow a complete control on the structural characteristics of the final 3D architecture.

Single-crystal-to-single-crystal post-synthetic modifications of three-dimensional LOFs (Ln = Gd, Eu): a way to modulate their luminescence and thermometric properties

Single-crystal-to-single-crystal post-synthetic modifications of {[Ln₂(H₂L)₃(DMF)₄]·2DMF}_n LOFs (Ln = Gd, Eu) to modulate their luminescence and thermometric properties.

Interconnecting Flexibility, Structural Communication, and Function in RhoGEF Oncoproteins

Dbl family Rho guanine nucleotide exchange factors (RhoGEFs) play a central role in cell biology by catalyzing the exchange of guanosine 5'-triphosphate for guanosine 5'-diphosphate (GDP) on RhoA. Insights into the oncogenic constitutive activity of the Lbc RhoGEF were gained by analyzing the structure and dynamics of the protein in different functional states and in comparison with a close homologue, leukemia-associated RhoGEF. Higher intrinsic flexibility, less dense and extended structure network, and less stable allosteric communication pathways in Lbc, compared to the nonconstitutively active homologue, emerged as major determinants of the constitutive activity. Independent of the state, the essential dynamics of the two RhoGEFs is contributed by the last 10 amino acids of Dbl homology (DH) and the whole pleckstrin homology (PH) domains and tends to be equalized by the presence of RhoA. The catalytic activity of the RhoGEF relies on the scaffolding action of the DH domain that primarily turns the switch I (SWI) of RhoA on itself through highly conserved amino acids participating in the stability core and essential for function. Changes in the conformation of SWI and disorganization of the RhoA regions deputed to nucleotide binding are among the major RhoGEF effects leading to GDP release. Binding of RhoA reorganizes the allosteric communication on RhoGEF, strengthening the communication among the canonical RhoA binding site on DH, a secondary RhoA binding site on PH, and the binding site for heterotrimeric G proteins, suggesting dual roles for RhoA as a catalysis substrate and as a regulatory protein. The structure network-based analysis tool employed in this study proved to be useful for predicting potentially druggable regulatory sites in protein structures.

Activation of PKA via asymmetric allosteric coupling of structurally conserved cyclic nucleotide binding domains

Cyclic nucleotide-binding (CNB) domains allosterically regulate the activity of proteins with diverse functions, but the mechanisms that enable the cyclic nucleotide-binding signal to regulate distant domains are not well understood. Here we use optical tweezers and molecular dynamics to dissect changes in folding energy landscape associated with cAMP-binding signals transduced between the two CNB domains of protein kinase A (PKA). We find that the response of the energy landscape upon cAMP binding is domain specific, resulting in unique but mutually coordinated tasks: one CNB domain initiates cAMP binding and cooperativity, whereas the other triggers inter-domain interactions that promote the active conformation. Inter-domain interactions occur in a stepwise manner, beginning in intermediate-liganded states between apo and cAMP-bound domains. Moreover, we identify a cAMP-responsive switch, the N3A motif, whose conformation and stability depend on cAMP occupancy. This switch serves as a signaling hub, amplifying cAMP-binding signals during PKA activation.

1D hetero-bimetallic regularly alternated 4f-3d coordination polymers based on N-oxide-4,4'-bipyridine (bipyMO) as a linker: photoluminescence and magnetic properties

Heterotopic divergent ligand N-oxide-4,4'-bipyridine (bipyMO) has been herein exploited for the preparation of hetero-bimetallic coordination polymers where Ln(hfac)3 and M(hfac)2 nodes regularly alternate (Hhfac = 1,1,1,5,5,5-hexafluoro-2,4-pentanedione), bipyMO being able to selectively use its two potential coordination sites to discriminate the metal ions. The synthesis of three coordination polymers, [Ln(hfac)3M(hfac)2(bipyMO)2]n (Ln = Eu, M = Zn, 1; Ln = Eu, M = Cu, 2, Ln = Dy, M = Co, 3), was carried out by reacting the appropriate [M(hfac)2(bipyMO)]n and [Ln(hfac)3] precursors in toluene in the presence of a given stoichiometric amount of bipyMO. The products were characterized by elemental analysis, X-ray powder diffraction, and FTIR spectroscopy. Single crystal X-ray diffraction studies carried out on 2 showed that it was formed by chains containing the hexa-coordinated 3d metal (Cu(hfac)2[N]2) and the octa-coordinated lanthanide (Eu(hfac)3[O]2) nodes, where [N] and [O] stand for the donor atom of the bridging divergent ligand. The X-ray powder diffraction patterns of the three compounds and the comparison of their cell constant values allowed establishing that the derivatives were isotypic. Photoluminescence (PL) studies on microcrystalline sample powders evidenced a bright red emission for 1 with an absolute PL quantum yield of 0.24. The sensitized emission of Eu3+ can be excited in a wide wavelength range, from UV to visible, up to ≈450 nm. Conversely, europium emissions are not detectable in 2 due to the presence of Cu(hfac)2(bipyMO) moieties whose strong absorption overlaps Eu3+ transitions. Magnetic measurements conducted on 3 revealed the presence of a weak ferromagnetic interaction below 2.1 K. An ac susceptibility study highlighted a slow relaxation of the magnetization of 3 with an applied static magnetic field of 0.1 T, which could be equally fitted with a Orbach-direct or a Raman-direct mechanism. No relaxation dynamics was detected without the application of a static magnetic field.

Gating of TonB-dependent transporters by substrate-specific forced remodelling

Membrane proteins play vital roles in inside-out and outside-in signal transduction by responding to inputs that include mechanical stimuli. Mechanical gating may be mediated by the membrane or by protein(s) but evidence for the latter is scarce. Here we use force spectroscopy, protein engineering and bacterial growth assays to investigate the effects of force on complexes formed between TonB and TonB-dependent transporters (TBDT) from Gram-negative bacteria. We confirm the feasibility of protein-only mediated mechanical gating by demonstrating that the interaction between TonB and BtuB (a TBDT) is sufficiently strong under force to create a channel through the TBDT. In addition, by comparing the dimensions of the force-induced channel in BtuB and a second TBDT (FhuA), we show that the mechanical properties of the interaction are perfectly tuned to their function by inducing formation of a channel whose dimensions are tailored to the ligand.

Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface

Proteins in the proximity of inorganic surfaces and nanoparticles may undergo profound adjustments that trigger biomedically relevant processes, such as protein fibrillation. The mechanisms that govern protein-surface interactions at the molecular level are still poorly understood. In this work, we investigate the adsorption onto a gold surface, in water, of an amyloid-β (Aβ) peptide, which is the amyloidogenic peptide involved in Alzheimer's disease. The entire adsorption process, from the peptide in bulk water to its conformational relaxation on the surface, is explored by large-scale atomistic molecular dynamics (MD) simulations. We start by providing a description of the conformational ensemble of Aβ in solution by a 22 μs temperature replica exchange MD simulation, which is consistent with previous results. Then, we obtain a statistical description of how the peptide approaches the gold surface by multiple MD simulations, identifying the preferential gold-binding sites and giving a kinetic picture of the association process. Finally, relaxation of the Aβ conformations at the gold/water interface is performed by a 19 μs Hamiltonian-temperature replica exchange MD simulation. We find that the conformational ensemble of Aβ is strongly perturbed by the presence of the surface. In particular, at the gold/water interface the population of the conformers akin to amyloid fibrils is significantly enriched, suggesting that this extended contact geometry may promote fibrillation.

Structural Determinants of Constitutive Activation of Gα Proteins: Transducin as a Paradigm

Heterotrimeric guanine nucleotide-binding proteins (Gα proteins) are intracellular nanomachines deputed to signal transduction. The switch-on process requires the release of bound GDP from a site at the interface between GTPase and helical domains. Nucleotide release is catalyzed by G protein Coupled Receptors (GPCRs). Here we investigate the functional dynamics of wild type (WT) and six constitutively active mutants (CAMs) of the Gα protein transducin (Gt) by combining atomistic molecular dynamics (MD) simulations with Maxwell-Demod discrete MD (MDdMD) simulations of the receptor-catalyzed transition between GDP-bound and nucleotide-free states. Compared to the WT, Gt CAMs increase the overall fluctuations of nucleotide and its binding site. This is accompanied by weakening of native links involving GDP, α1, the G boxes, β1-β3, and α5. Collectively, constitutive activation by the considered mutants seems to associate with weakening of the interfaces between α5 and the surrounding portions and the interface between GTPase (G) and helical (H) domains. These mutational effects associate with increases in the overall fluctuations of the G and H domains, which reflect on the collective motions of the protein. Gt CAMs, with prominence to G56P, T325A, and F332A, prioritize collective motions of the H domain overlapping with the collective motions associated with receptor-catalyzed nucleotide release. In spite of different local perturbations, the mechanisms of nucleotide exchange catalyzed by activating mutations and by receptor are expected to employ similar molecular switches in the nucleotide binding site and to share the detachment of the H domain from the G domain.

Small-Molecule Protein-Protein Interaction Inhibitor of Oncogenic Rho Signaling

Uncontrolled activation of Rho signaling by RhoGEFs, in particular AKAP13 (Lbc) and its close homologs, is implicated in a number of human tumors with poor prognosis and resistance to therapy. Structure predictions and alanine scanning mutagenesis of Lbc identified a circumscribed hot region for RhoA recognition and activation. Virtual screening targeting that region led to the discovery of an inhibitor of Lbc-RhoA interaction inside cells. By interacting with the DH domain, the compound inhibits the catalytic activity of Lbc, halts cellular responses to activation of oncogenic Lbc pathways, and reverses a number of prostate cancer cell phenotypes such as proliferation, migration, and invasiveness. This study provides insights into the structural determinants of Lbc-RhoA recognition. This is a successful example of structure-based discovery of a small protein-protein interaction inhibitor able to halt oncogenic Rho signaling in cancer cells with therapeutic implications.

The interaction with gold suppresses fiber-like conformations of the amyloid β (16-22) peptide

Inorganic surfaces and nanoparticles can accelerate or inhibit the fibrillation process of proteins and peptides, including the biomedically relevant amyloid β peptide. However, the microscopic mechanisms that determine such an effect are still poorly understood. By means of large-scale, state-of-the-art enhanced sampling molecular dynamics simulations, here we identify an interaction mechanism between the segments 16-22 of the amyloid β peptide, known to be fibrillogenic by itself, and the Au(111) surface in water that leads to the suppression of fiber-like conformations from the peptide conformational ensemble. Moreover, thanks to advanced simulation analysis techniques, we characterize the conformational selection vs. induced fit nature of the gold effect. Our results disclose an inhibition mechanism that is rooted in the details of the microscopic peptide-surface interaction rather than in general phenomena such as peptide sequestration from the solution.

Smart Grafting of Lanthanides onto Silica via N,N-Dialkylcarbamato Complexes

The grafting and the postgrafting functionalization of lanthanide ions on commercial amorphous silica have been herein carried out by using as a precursor the terbium N,N-dibutylcarbamato derivative [Tb(O2CNBu2)3]. The reaction of the complex with the surface silanols involved only a fraction of the carbamato ligands. The following protolytic substitution of the residual carbamato ligands was carried out by exploiting the Brønsted's acidity of the β-diketone dibenzoylmethane (Hdbm), in view of the antenna effect of the β-diketonato groups, which are commonly used in lanthanide photoluminescence studies. The reaction proceeded at room temperature in a clean and easy way affording the introduction of the chosen functionality in the lanthanide coordination sphere. The same procedure has been followed by using as a precursor the X-ray characterized heterometallic N,N-dibutylcarbamato complex [NH2Bu2]2[Ln4(CO3)(O2CNBu2)12] (Ln = Eu, Tb, Tm). In both cases, X-ray photoelectron spectroscopy evidenced the chemical implantation of the lanthanide ions on the silica surface, and photoluminescence studies pointed out the potentiality of the proposed synthetic approach in the preparation of highly luminescent materials.

Unconventional plasticity of HIV-1 reverse transcriptase: how inhibitors could open a connection "gate" between allosteric and catalytic sites

Targeted molecular dynamics (TMD) simulations allowed for identifying the chemical/structural features of the nucleotide-competitive HIV-1 inhibitor DAVP-1, which is responsible for the disruption of the T-shape motif between Try183 and Trp229 of the reverse transcriptase (RT). DAVP-1 promoted the opening of a connection "gate" between allosteric and catalytic sites of HIV-1 RT, thus explaining its peculiar mechanism of action and providing useful insights to develop novel nucleotide-competitive RT inhibitors.

The structure of neuronal calcium sensor-1 in solution revealed by molecular dynamics simulations

Neuronal calcium sensor-1 (NCS-1) is a protein able to trigger signal transduction processes by binding a large number of substrates and re-shaping its structure depending on the environmental conditions. The X-ray crystal structure of the unmyristoilated NCS-1 shows a large solvent-exposed hydrophobic crevice (HC); this HC is partially occupied by the C-terminal tail and thus elusive to the surrounding solvent. We studied the native state of NCS-1 by performing room temperature molecular dynamics (MD) simulations starting from the crystal and the solution structures. We observe relaxation to a state independent of the initial structure, in which the C-terminal tail occupies the HC. We suggest that the C-terminal tail shields the HC binding pocket and modulates the affinity of NCS-1 for its natural targets. By analyzing the topology and nature of the inter-residue potential energy, we provide a compelling description of the interaction network that determines the three-dimensional organization of NCS-1.

TIP48/Reptin and H2A.Z requirement for initiating chromatin remodeling in estrogen-activated transcription

Histone variants, including histone H2A.Z, are incorporated into specific genomic sites and participate in transcription regulation. The role of H2A.Z at these sites remains poorly characterized. Our study investigates changes in the chromatin environment at the Cyclin D1 gene (CCND1) during transcriptional initiation in response to estradiol in estrogen receptor positive mammary tumour cells. We show that H2A.Z is present at the transcription start-site and downstream enhancer sequences of CCND1 when the gene is poorly transcribed. Stimulation of CCND1 expression required release of H2A.Z concomitantly from both these DNA elements. The AAA+ family members TIP48/reptin and the histone variant H2A.Z are required to remodel the chromatin environment at CCND1 as a prerequisite for binding of the estrogen receptor (ERα) in the presence of hormone. TIP48 promotes acetylation and exchange of H2A.Z, which triggers a dissociation of the CCND1 3′ enhancer from the promoter, thereby releasing a repressive intragenic loop. This release then enables the estrogen receptor to bind to the CCND1 promoter. Our findings provide new insight into the priming of chromatin required for transcription factor access to their target sequence. Dynamic release of gene loops could be a rapid means to remodel chromatin and to stimulate transcription in response to hormones.

Our study investigates changes in the chromatin environment at the Cyclin D1 gene that are a prerequisite for transcriptional initiation in response to estradiol. Gene expression is under control of chromatin structure. Histone variants, including histone H2A.Z, are incorporated into specific genomic sites and participate in transcription regulation. We show that H2A.Z is present at the transcription start-site and downstream enhancer sequences of CCND1 when the gene is poorly transcribed. Stimulation of CCND1 expression required release of H2A.Z concomitantly from both these DNA elements. The TIP48/reptin protein, which is part of several chromatin remodeling complexes, also associated with the CCND1 regulatory elements. Here, TIP48 promotes exchange of H2A.Z, which triggers a dissociation of the CCND1 enhancer from the promoter, thereby releasing a repressive intragenic loop. This release then enables estrogen receptor binding to the CCND1 promoter. Acetylation of H2A.Z is required for these processes. Our findings provide new insight into the priming of chromatin required for transcription factor access to their target sequence. Hence, we propose a new model for early events in transcription activation that were not shown before. Specifically, release of looping could be a rapid means to activate transcription efficiently in response to stimuli, in particular estrogen.

Stereoretentive chlorination of cyclic alcohols catalyzed by titanium(IV) tetrachloride: evidence for a front side attack mechanism

A mild chlorination reaction of alcohols was developed using the classical thionyl chloride reagent but with added catalytic titanium(IV) chloride. These reactions proceeded rapidly to afford chlorination products in excellent yields and with preference for retention of configuration. Stereoselectivities were high for a variety of chiral cyclic secondary substrates including sterically hindered systems. Chlorosulfites were first generated in situ and converted to alkyl chlorides by the action of titanium tetrachloride which is thought to chelate the chlorosulfite leaving group and deliver the halogen nucleophile from the front face. To better understand this novel reaction pathway, an ab initio study was undertaken at the DFT level of theory using two different computational approaches. This computational evidence suggests that while the reaction proceeds through a carbocation intermediate, this charged species likely retains pyramidal geometry existing as a conformational isomer stabilized through hyperconjugation (hyperconjomers). These carbocations are then essentially "frozen" in their original configurations at the time of nucleophilic capture.

Activation of p21 by HDAC inhibitors requires acetylation of H2A.Z

Differential positioning of the histone variant H2A.Z in a p53 dependent manner was shown to regulate p21 transcription. Whether H2A.Z is involved in p21 activity in the absence of p53 is not known. The p21 gene is repressed in estrogen receptor (ER) negative cell lines that are p53−/− and hormone independent for their growth. Here we demonstrate that class I and II pan Histone deacetylase inhibitors (HDACi) induce p21 transcription and reduce cell proliferation of MDA-MB231, an ERα-negative mammary tumor cell line, in a H2A.Z dependent manner. H2A.Z is associated with the transcription start site (TSS) of the repressed p21 gene. Depleting H2A.Z did not lead to transcription of p21 but annihilated the stimulating effect of HDACi on this gene. Acetylation of H2A.Z but not of H3K9 at the p21 promoter correlated with p21 activation. We further show that HDACi treatment reduced the presence of the p400 chromatin remodeler at the p21 TSS. We propose a model in which association of p400 negatively affects p21 transcription by interfering with acetylation of H2A.Z.

H2A.Z-dependent crosstalk between enhancer and promoter regulates cyclin D1 expression

H2A.Z association with specific genomic loci is thought to contribute to a chromatin structure that promotes transcription activation. Acetylation of H2A.Z at promoters of oncogenes has been linked to tumorigenesis. The mechanism is unknown. Here, we show that in triple negative breast cancer cells, H2A.Z bound to the promoter of the constitutively, weakly expressed cyclin D1 oncogene (CCND1), a key regulator of cellular proliferation. Depleting the pool of H2A.Z stimulated transcription of CCND1 in the absence of its cognate transcription factor, the estrogen receptor (ER). During activation of CCND1, H2A.Z was released from the transcription start site (TSS) and downstream enhancer (enh2) sequences. Concurrently, acetylation of H2A.Z, H3 and H4 at the TSS was increased but only H2A.Z was acetylated at enh2. Acetylation of H2A.Z required the Tip60 acetyltransferase to be associated with the activated CCND1 on both TSS and enh2 sites. Depletion of Tip60 prevented CCND1 activation. Chromosome conformation capture experiments (3C) revealed specific contacts between the TSS and enh2 chromatin regions. These results suggest that release of a histone H2A.Z-mediated repression loop activates CCND1 for transcription. Our findings open new avenues for controlling and understanding aberrant gene expression associated with tumorigenesis.

Investigations on the 4-quinolone-3-carboxylic acid motif part 5: modulation of the physicochemical profile of a set of potent and selective cannabinoid-2 receptor ligands through a bioisosteric approach

Three heterocyclic systems were selected as potential bioisosteres of the amide linker for a series of 1,6-disubstituted-4-quinolone-3-carboxamides, which are potent and selective CB2 ligands that exhibit poor water solubility, with the aim of improving their physicochemical profile and also of clarifying properties of importance for amide bond mimicry. Among the newly synthesized compounds, a 1,2,3-triazole derivative (1-(adamantan-1-yl)-4-[6-(furan-2-yl)-1,4-dihydro-4-oxo-1-pentylquinolin-3-yl]-1H-1,2,3-triazole) emerged as the most promising in terms of both physicochemical and pharmacodynamic properties. When assayed in vitro, this derivative exhibited inverse agonist activity, whereas, in the formalin test in mice, it produced analgesic effects antagonized by a well-established inverse agonist. Metabolic studies allowed the identification of a side chain hydroxylated derivative as its only metabolite, which, in its racemic form, still showed appreciable CB2 selectivity, but was 150-fold less potent than the parent compound.

A Direct and Stereoretentive Synthesis of Amides from Cyclic Alcohols

Chlorosulfites prepared in situ using thionyl chloride react with nitrile complexes of titanium (IV) fluoride to give a one-pot conversion of alcohols into amides. For the first time, amides are obtained from cyclic alcohols with stereoretention. Critical to the design of these new Ti(IV) reactions has been the use of little explored Ti(IV) nitrile complexes which are thought to chelate chlorosulfites in the transition state to create a carbocation that is rapidly captured by the nitrile nucleophile via a front-side attack mechanism.

A regulatory mechanism involving TBP-1/Tat-Binding Protein 1 and Akt/PKB in the control of cell proliferation

TBP-1 /Tat-Binding Protein 1 (also named Rpt-5, S6a or PSMC3) is a multifunctional protein, originally identified as a regulator of HIV-1-Tat mediated transcription. It is an AAA-ATPase component of the 19S regulative subunit of the proteasome and, as other members of this protein family, fulfils different cellular functions including proteolysis and transcriptional regulation. We and others reported that over expression of TBP-1 diminishes cell proliferation in different cellular contexts with mechanisms yet to be defined. Accordingly, we demonstrated that TBP-1 binds to and stabilizes the p14ARF oncosuppressor increasing its anti-oncogenic functions. However, TBP-1 restrains cell proliferation also in the absence of ARF, raising the question of what are the molecular pathways involved. Herein we demonstrate that stable knock-down of TBP-1 in human immortalized fibroblasts increases cell proliferation, migration and resistance to apoptosis induced by serum deprivation. We observe that TBP-1 silencing causes activation of the Akt/PKB kinase and that in turn TBP-1, itself, is a downstream target of Akt/PKB. Moreover, MDM2, a known Akt target, plays a major role in this regulation. Altogether, our data suggest the existence of a negative feedback loop involving Akt/PKB that might act as a sensor to modulate TBP-1 levels in proliferating cells.

Examination of the uncertainty in contaminant fate and transport modeling: a case study in the Venice Lagoon

A Monte Carlo analysis is used to quantify environmental parametric uncertainty in a multi-segment, multi-chemical model of the Venice Lagoon. Scientific knowledge, expert judgment and observational data are used to formulate prior probability distributions that characterize the uncertainty pertaining to 43 environmental system parameters. The propagation of this uncertainty through the model is then assessed by a comparative analysis of the moments (central tendency, dispersion) of the model output distributions. We also apply principal component analysis in combination with correlation analysis to identify the most influential parameters, thereby gaining mechanistic insights into the ecosystem functioning. We found that modeled concentrations of Cu, Pb, OCDD/F and PCB-180 varied by up to an order of magnitude, exhibiting both contaminant- and site-specific variability. These distributions generally overlapped with the measured concentration ranges. We also found that the uncertainty of the contaminant concentrations in the Venice Lagoon was characterized by two modes of spatial variability, mainly driven by the local hydrodynamic regime, which separate the northern and central parts of the lagoon and the more isolated southern basin. While spatial contaminant gradients in the lagoon were primarily shaped by hydrology, our analysis also shows that the interplay amongst the in-place historical pollution in the central lagoon, the local suspended sediment concentrations and the sediment burial rates exerts significant control on the variability of the contaminant concentrations. We conclude that the probabilistic analysis presented herein is valuable for quantifying uncertainty and probing its cause in over-parameterized models, while some of our results can be used to dictate where additional data collection efforts should focus on and the directions that future model refinement should follow.