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.

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.

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-ß-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 ß-diketonato ligands.

PAHs, PCBs, PBDEs, and OCPs trapped and remobilized in the Lake of Cavazzo (NE Italy) sediments: Temporal trends, quality, and sources in an area prone to anthropogenic and natural stressors.

Under the present climatic emergency, the environmental quality of freshwater reservoirs is an increasingly urgent topic as its deterioration threatens humans and ecosystems. It is evident that pollution by natural and anthropogenic contaminants must be avoided or reduced. The Lake of Cavazzo (NE Italy) is a natural perialpine basin which, from the mid-20th century, has sustained several anthropogenic impacts that added to the effects of the intense regional seismicity. Starting from 2015, in response to concerns raised by local authorities, a multidisciplinary investigation of the lake floor and sub-floor was conducted, including a geophysical survey and the collection of sediment cores. Two of them were studied to detect contamination by Polycyclic Aromatic Hydrocarbons (PAHs) and specific Persistent Organic Pollutants (POPs; i.e. PolyChlorinated Biphenyls - PCBs, PolyBrominated Diphenyl Ethers - PBDEs, and OrganoChlorine Pesticides - OCPs), and to verify the link with known anthropogenic stressors. Results were interpreted in light of previous studies suggesting modified conditions after the '50s, and recognized the effects of the 1976-1977 MW 6.5 seismic sequence in resuspending sediments within the basin. Analyzed pollutants defined a potential critical situation only for few OCPs, above all 2,4'- and 4,4'-DDT isomers. In addition, PBDEs were found at concentrations exceeding those of other heavily polluted alpine lakes. Mass movements (either seismic or human induced) have likely resuspended and transferred pollutants from shallower locations to the lake depocenter, showing the potential of re-exposing contaminated layers to biomagnification processes along the lacustrine food chain. Local inputs of pollutants prevail over distributed sources, suggesting a link with local agricultural or industrial activities. Indeed, works connected to the construction of the hydroelectric power plant in the '50s might have reworked local sediments perturbing their natural accretion. Results of this work might inspire similar studies in other problematic lacustrine areas that sustain both natural and anthropogenic stressors.

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.

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.

Screening environmental risk evaluation of As and trace metals in soils and sediments from a developing area (Bac Giang Province, Northern Vietnam).

Despite the key role that areas close to the rivers Cau and Ngu Huyen Khê (Bac Giang Province, Northern Vietnam) play in the socio-economic development of Vietnam, poor information is available on the level of contaminants and their natural backgrounds in local soils and sediments. To partially fill this gap and to take into account for pressures and impacts on different zones and environment types (river sediments, crop fields, family wells, industrial and urban soils), the samples were collected and analyzed for fifteen trace elements at thirty sites distributed over the province. To overcome the lack of information on natural background and to identify the extent of the deviation from natural conditions, we coupled statistical analysis to contamination indices. The multivariate analysis was used to relate sediment chemical composition with a possible alteration from secondary inputs and to highlight those samples that most deviate from the distribution by category and are potentially more problematic. Geoaccumulation indexes and enrichment factors were calculated to discriminate between natural backgrounds and anthropic sources, SQGs were used for a screening evaluation of environmental risk in the study area. Results showed relatively high concentrations, sometimes exceeding international and national guidelines, and local sources could prevail over geogenic origins. Despite its significant natural contribution all over the study area, As evidenced some cases of anthropogenic contamination, similarly to that observed for Cd, Hg, and Zn. Their high concentrations may be a problem for public health, especially when found in family wells.

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.

Composition-Thermometric Properties Correlations in Homodinuclear Eu3+ Luminescent Complexes.

A family of homodinuclear Ln3+ (Ln3+ = Gd3+, Eu3+) luminescent complexes with the general formula [Ln2(ß-diketonato)6(N-oxide)y] has been developed to study the effect of the ß-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 ß-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 Sr (% 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.

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.

Contribution of the residue at position 4 within classical nuclear localization signals to modulating interaction with importins and nuclear targeting.

Nuclear import involves the recognition by importin (IMP) superfamily members of nuclear localization signals (NLSs) within protein cargoes destined for the nucleus, the best understood being recognition of classical NLSs (cNLSs) by the IMPα/ß1 heterodimer. Although the cNLS consensus [K-(K/R)-X-(K/R) for positions P2-P5] is generally accepted, recent studies indicated that the contribution made by different residues at the P4 position can vary. Here, we apply a combination of microscopy, molecular dynamics, crystallography, in vitro binding, and bioinformatics approaches to show that the nature of residues at P4 indeed modulates cNLS function in the context of a prototypical Simian Virus 40 large tumor antigen-derived cNLS (KKRK, P2-5). Indeed, all hydrophobic substitutions in place of R impaired binding to IMPα and nuclear targeting, with the largest effect exerted by a G residue at P4. Substitution of R with neutral hydrophobic residues caused the loss of electrostatic and van der Waals interactions between the P4 residue side chains and IMPα. Detailed bioinformatics analysis confirmed the importance of the P4 residue for cNLS function across the human proteome, with specific residues such as G being associated with low activity. Furthermore, we validate our findings for two additional cNLSs from human cytomegalovirus (HCMV) DNA polymerase catalytic subunit UL54 and processivity factor UL44, where a G residue at P4 results in a 2-3-fold decrease in NLS activity. Our results thus showed that the P4 residue makes a hitherto poorly appreciated contribution to nuclear import efficiency, which is essential to determining the precise nuclear levels of cargoes.

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.

Circularly Polarized Luminescence of Silica-Grafted Europium Chiral Derivatives Prepared through a Sequential Functionalization.

We describe a new organic/inorganic material emitting circularly polarized luminescence (CPL). The hybrid system was obtained by the following steps: (i) preliminary grafting of the europium N,N-dibutylcarbamate [Eu(O2CNBu2)3] complex onto silica, (ii) substitution of the residual carbamato groups with anionic 1,3-diphenyl-1,3-propanedionato ligands (dbm), and (iii) subsequent introduction of the neutral tridentate chiral ligand 2,6-bis(isopropyl-2-oxazolin-2-yl)pyridine (iPr-PyBox) in the metal coordination sphere. The solid material is stable to air and does not leach either the metal or the ligand. Samples of both enantiomers have been studied, showing mirror-image CPL spectra. The molecular compounds [Eu(dbm)3-(S)-(iPr-PyBox)] and [Eu(dbm)3-(R)-(iPr-PyBox)] were prepared for comparison purposes and their molecular structures studied by single-crystal X-ray diffraction, showing mononuclear derivatives with a coordination number of 9 for europium. Powder X-ray diffraction showed a single crystalline phase. Photoluminescence and CPL evidenced the presence of a single emitting species.

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 ß-diketone dibenzoylmethane (Hdbm), in view of the antenna effect of the ß-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.

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.

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.

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.

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.

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.