Easy to Use DFT Approach for Computational pKa Determination of Carboxylic Acids.

In pKa computational determination, the challenge in exploring and fostering new methodologies and approaches goes in parallel with the amelioration of computational performances. In this paper a "ready to use methodology" has been compared to other strategies, such as the re-shaping in solvation cavity (Bondi radius re-shaping), wanting to assess its reliability in predicting the pKa of a broad list of carboxylic acids. Thus, the functionals B3LYP and CAM-B3LYP have been selected, using SMD as continuum solvation model. Exploiting our previous results, two water molecules were made explicit on the reaction centre. Data show that our model (CAM-B3LYP/2H2 O) is capable to accurately predict pKa, leading to mean absolute error (MAE) values lower than 0.5. Noteworthy, good results were achieved in computing the pKa of substituents bearing nitro and cyano groups. Focusing on B3LYP, eventually remarkable outputs were obtained only when Bondi correction was applied to the complex with two water molecules. Hence, massive outcomes were obtained in foreseeing the trichloro and trifluoro acetic acid pKa. These findings demonstrated that no complex level of theory nor external factor is required to accurately predict carboxylic acids pKa, with MAE well below 0.5 units.

New Insights in the Computational pKb Determination of Primary Amines and Anilines.

Extensive research has already provided reliable methods for the in silico prediction of pKa, while a trustworthy strategy for pKb determination is still being sought. Indeed, the approaches previously exploited for computing pKa have shown their weakness in predicting pKb. In the light of the exceptional reliability demonstrated in the pKa calculation of a wide panel of organic acids, in this work, we exploited our "easy to use methodology", based on the direct approach, to predict the pKb of primary amines. Herein, CAM-B3LYP was compared to WB97XD and B3PW91, exploring the solvation model based on density (SMD) and the polarizable continuum model (PCM), in the presence of two explicit water molecules. Noteworthy, CAM-B3LYP and WB97XD returned completely different solvent accessible surfaces (SAS) and electron potential maps (EPM) for the bases and the conjugated acids, independently from the nature of the substituents. Once again, CAM-B3LYP/SMD/2H2O method confirmed its remarkable reliability, leading to a minimum average error (MAE) lower than 0.3. This outstanding result strengthens the trustworthiness of our method, already successfully applied to predict the pKa of different substituted phenols and carboxylic acids. Thus, our "easy-to-use" process can predict also the pKb of primary ammines and anilines, always ensuring consistent outputs.

Towards the "Eldorado" of pKa Determination: A Reliable and Rapid DFT Model.

The selection of a "perfect tool" for the theoretical determination of acid-base dissociation constants (Ka) is still puzzling. Recently, we developed a user-friendly model exploiting CAM-B3LYP for determining pKa with impressive reliability. Herein, a new challenge is faced, examining a panel of functionals belonging to different rungs of the "Jacob's ladder" organization, which classifies functionals according to their level of theory. Specifically, meta-generalized gradient approximations (GGAs), hybrid-GGAs, and the more complex range-separated hybrid (RSH)-GGAs were investigated in predicting the pKa of differently substituted carboxylic acids. Therefore, CAM-B3LYP, WB97XD, B3PW91, PBE1PBE, PBEPBE and TPSSTPSS were used, with 6-311G+(d,p) as the basis set and the solvation model based on density (SMD). CAM-B3LYP showed the lowest mean absolute error value (MAE = 0.23) with relatively high processing time. PBE1PBE and B3PW91 provided satisfactory predictions (MAE = 0.34 and 0.38, respectively) with moderate computational time cost, while PBEPBE, TPSSTPSS and WB97XD led to unreliable results (MAE > 1). These findings validate the reliability of our model in predicting carboxylic acids pKa, with MAE well below 0.5 units, using a simplistic theoretical level and a low-cost computational approach.

Track Structure of Light Ions: The Link to Radiobiology.

It is generally recognized that the biological response to irradiation by light ions is initiated by complex damages at the DNA level. In turn, the occurrence of complex DNA damages is related to spatial and temporal distribution of ionization and excitation events, i.e., the particle track structure. It is the aim of the present study to investigate the correlation between the distribution of ionizations at the nanometric scale and the probability to induce biological damage. By means of Monte Carlo track structure simulations, the mean ionization yield M1 and the cumulative probabilities F1, F2, and F3 of at least one, two and three ionizations, respectively, were calculated in spherical volumes of water-equivalent diameters equal to 1, 2, 5 and 10 nm. When plotted as a function of M1, the quantities F1, F2 and F3 are distributed along almost unique curves, largely independent of particle type and velocity. However, the shape of the curves depends on the size of the sensitive volume. When the site size is 1 nm, biological cross sections are strongly correlated to combined probabilities of F2 and F3 calculated in the spherical volume, and the proportionality factor is the saturation value of biological cross sections.

KuQuinone as a Highly Stable and Reusable Organic Photocatalyst in Selective Oxidation of Thioethers to Sulfoxides.

A chemoselective photocatalytic system to perform thioether oxidation to sulfoxide is presented. The light-induced oxidation process is here promoted by a metal-free quinoid catalyst, namely 1-hexylKuQuinone (KuQ). Reactions performed in a fluorinated solvent (i.e., HFIP), using O2 as the oxidant, at room temperature, lead to complete thioanisole conversion to methyl phenyl sulfoxide in 60 min. Remarkably, the system can be recharged and recycled without a loss of activity and selectivity, reaching turnover numbers (TONs) higher than 4000. Excellent catalytic performances and full selectivity have also been obtained for the photocatalytic oxidation of substituted thioanisole derivatives, aliphatic, cyclic, and diaryl thioethers. Likewise, the oxidation of heteroaromatic organosulfur compounds can be accomplished, with longer reaction times.

A matter of space: how the spatial heterogeneity in energy deposition determines the biological outcome of radiation exposure.

The outcome of the exposure of living organisms to ionizing radiation is determined by the distribution of the associated energy deposition at different spatial scales. Radiation proceeds through ionizations and excitations of hit molecules with an ~ nm spacing. Approaches such as nanodosimetry/microdosimetry and Monte Carlo track-structure simulations have been successfully adopted to investigate radiation quality effects: they allow to explore correlations between the spatial clustering of such energy depositions at the scales of DNA or chromosome domains and their biological consequences at the cellular level. Physical features alone, however, are not enough to assess the entity and complexity of radiation-induced DNA damage: this latter is the result of an interplay between radiation track structure and the spatial architecture of chromatin, and further depends on the chromatin dynamic response, affecting the activation and efficiency of the repair machinery. The heterogeneity of radiation energy depositions at the single-cell level affects the trade-off between cell inactivation and induction of viable mutations and hence influences radiation-induced carcinogenesis. In radiation therapy, where the goal is cancer cell inactivation, the delivery of a homogenous dose to the tumour has been the traditional approach in clinical practice. However, evidence is accumulating that introducing heterogeneity with spatially fractionated beams (mini- and microbeam therapy) can lead to significant advantages, particularly in sparing normal tissues. Such findings cannot be explained in merely physical terms, and their interpretation requires considering the scales at play in the underlying biological mechanisms, suggesting a systemic response to radiation.

An Accurate Approach for Computational pKa Determination of Phenolic Compounds.

Computational chemistry is a valuable tool, as it allows for in silico prediction of key parameters of novel compounds, such as pKa. In the framework of computational pKa determination, the literature offers several approaches based on different level of theories, functionals and continuum solvation models. However, correction factors are often used to provide reliable models that adequately predict pKa. In this work, an accurate protocol based on a direct approach is proposed for computing phenols pKa. Importantly, this methodology does not require the use of correction factors or mathematical fitting, making it highly practical, easy to use and fast. Above all, DFT calculations performed in the presence two explicit water molecules using CAM-B3LYP functional with 6-311G+dp basis set and a solvation model based on density (SMD) led to accurate pKa values. In particular, calculations performed on a series of 13 differently substituted phenols provided reliable results, with a mean absolute error of 0.3. Furthermore, the model achieves accurate results with -CN and -NO2 substituents, which are usually excluded from computational pKa studies, enabling easy and reliable pKa determination in a wide range of phenols.

Unveiling KuQuinone Redox Species: An Electrochemical and Computational Cross Study.

The study of the electrochemical properties of variegated quinones is a fascinating topic in chemistry. In fact, redox reactions occurring with quinoid scaffolds are essential for most of their applications in biological systems, in photoelectrochemical devices, and in many other fields. In this paper, a detailed investigation of KuQuinones' redox behavior is presented. The distinctiveness of such molecules is the presence in the structure of two condensed naphthoquinone units, which implies the possibility to undergo multiple one-electron reduction processes. Solvent, supporting electrolyte, and hydrogen bond donor species effects have been elucidated. Changing the experimental parameters provoked significant shift of the redox potential for each reduction process. In particular, additions of 2,2,2-trifluoroethanol as a hydrogen bond donor in solution as well as Lewis acid coordination were crucial to obtain important shifts of the redox potentials toward more favorable values. UV-vis-NIR spectroelectrochemical experiments and DFT calculations are also presented to clarify the nature of the reduced species in solution.

Similar, Yet Different: Long-Range Metal-Metal Coupling and Electron-Transfer Processes in Metal-Free 5,10,15,20-Tetra(ruthenocenyl)porphyrin.

The electronic structure, redox properties, and long-range metal-metal coupling in metal-free 5,10,15,20-tetra(ruthenocenyl)porphyrin (H2TRcP) were probed by spectroscopic (NMR, UV-vis, magnetic circular dichroism (MCD), and atmospheric pressure chemical ionization (APCI)), electrochemical (cyclic voltammetry, CV, and differential pulse voltammetry, DPV), spectroelectrochemical, and chemical oxidation methods, as well as theoretical (density functional theory, DFT, and time-dependent DFT, TDDFT) approaches. It was demonstrated that the spectroscopic properties of H2TRcP are significantly different from those in H2TFcP (metal-free 5,10,15,20-tetra(ferrocenyl)porphyrin). Ruthenocenyl fragments in H2TRcP have higher oxidation potentials than the ferrocene groups in the H2TFcP complex. Similar to H2TFcP, we were able to access and spectroscopically characterize the one- and two-electron oxidized mixed-valence states in the H2TRcP system. DFT predicts that the porphyrin π-system stabilizes the [H2TRcP]+ mixed-valence cation and prevents its dimerization, which is characteristic for ruthenocenyl systems. However, formation of the mixed-valence [H2TRcP]2+ is significantly less reproducible than the formation of [H2TRcP]+. DFT and TDDFT calculations suggest the ruthenocenyl fragment dominance in the highest occupied molecular orbital (HOMO) energy region and the presence of the low-energy MLCT (Rc → porphyrin (π*)) transitions in the visible region with energies higher than the predominantly porphyrin-centered Q-bands.

Lignosulfonate Microcapsules for Delivery and Controlled Release of Thymol and Derivatives.

Thymol and the corresponding brominated derivatives constitute important biological active molecules as antibacterial, antioxidant, antifungal, and antiparasitic agents. However, their application is often limited, because their pronounced fragrance, their poor solubility in water, and their high volatility. The encapsulation of different thymol derivatives into biocompatible lignin-microcapsules is presented as a synergy-delivering remedy. The adoption of lignosulfonate as an encapsulating material possessing relevant antioxidant activity, as well as general biocompatibility allows for the development of new materials that are suitable for the application in various fields, especially cosmesis. To this purpose, lignin microcapsules containing thymol, 4-bromothymol, 2,4-dibromothymol, and the corresponding O-methylated derivatives have been efficiently prepared through a sustainable ultrasonication procedure. Actives could be efficiently encapsulated with efficiencies of up to 50%. To evaluate the applicability of such systems for topical purposes, controlled release experiments have been performed in acetate buffer at pH 5.4, to simulate skin pH: all of the capsules show a slow release of actives, which is strongly determined by their inherent lipophilicity.

Amphiphilic Porphyrin Aggregates: A DFT Investigation.

Owing to the attractive potential applications of porphyrin assemblies in photocatalysis, sensors, and material science, studies presently concerning porphyrin aggregation are widely diffused. π-π stacking, H-bonding, metal coordination, hydrophobic effect, and electrostatic forces usually drive porphyrin interaction in solution. However, theoretical studies of such phenomena are still limited. Therefore, a computational examination of the different porphyrin aggregation approaches is proposed here, taking into account amphiphilic [5-{4-(3-trimethylammonium)propyloxyphenyl}-10,15,20-triphenylporphyrin] chloride, whose aggregation behavior has been previously experimentally investigated. Different functionals have been adopted to investigate the porphyrin dimeric species, considering long-range interactions. Geometry optimization has been performed, showing that for the compound under analysis, H-type and cation-π dimers are the most favored structures that likely co-exist in aqueous solution. Of note, frontier orbital delocalization showed an interesting interaction between the porphyrin units in the dimer at the supramolecular level.

Risk of post-operative venous thromboembolism in patients with meningioma.

The surgical resection of meningiomas can be complicated by venous thromboembolism (VTE) in the post-operative period, but the exact incidence of this event is not known. Aim of this study was to assess the occurrence of VTE in patients operated for meningioma who underwent a post-operative clinical and objective screening for VTE. Patients undergoing meningioma resection between 2000 and 2010 who accepted to be investigated for VTE in the post-operative period were included in the study. The screening included daily clinical assessment, pulmonary perfusion scintigraphy (Q-SCAN) on day 2 and venous compression ultrasonography (CUS) of the lower limbs within day 7. The univariate and multivariate statistical analysis of risk factors for VTE included sex, age, presence of comorbidities, pre- and post-operative Karnofsky Performance scale (KPS), post-operative neurological worsening and post-operative walking ability. Two-hundred and seventy-five patients were included in the study. VTE was diagnosed in 82 patients (29.8%). Univariate analysis revealed that age ≥ 65 years, cardiovascular comorbidities, pre- and post-operative KPS < 80/100, post-operative neurological worsening and impaired post-operative walking ability were significantly associated with VTE. Multivariate analysis confirmed only age ≥ 65 years (p = 0.011) and post-operative KPS < 80/100 (p = 0.002) as independent risk factors for VTE. Patients operated for meningioma have a 30% risk of VTE. Age ≥ 65 years and post-operative KPS < 80 were independent risk factors for VTE.

KuQuinones Equilibria Assessment for Biomedical Applications.

A small library of pentacyclic quinoid compounds, called KuQuinones (KuQs), has been prepared through a one-pot reaction. KuQuinones complex structure is made up by two naphthoquinone units connected by a five-membered ring. Due to KuQs structural features, keto-enol tautomerization in solution likely occurs, leading to the generation of four different species, i.e., the enol, the enolate, the external enol and the diquinoid species. The interchange among KuQ tautomers leads to substantial spectral variations of the dye depending on the experimental conditions used. The comprehension of tautomeric equilibria of this new class of quinoid compounds is strongly required in order to explain their behavior in solution and in biological environment. UV-vis, 1H NMR spectroscopies, and DFT calculations resulted appropriate tools to understand the nature of the prevalent KuQuinone species in solution. Moreover, due to the structural similarity of KuQuinones with camptothecin (CPT), a largely used anticancer agent, KuQs have been tested against Cisplatin-resistant SKOV3 and SW480 cancer cell lines. Results highlighted that KuQs are highly active toward the analyzed cell lines and almost nontoxic for healthy cell, indicating a high specific activity.

Experimental subarachnoid haemorrhage results in multifocal axonal injury.

The great majority of acute brain injury results from trauma or from disorders of the cerebrovasculature, i.e. ischaemic stroke or haemorrhage. These injuries are characterized by an initial insult that triggers a cascade of injurious cellular processes. The nature of these processes in spontaneous intracranial haemorrhage is poorly understood. Subarachnoid haemorrhage, a particularly deadly form of intracranial haemorrhage, shares key pathophysiological features with traumatic brain injury including exposure to a sudden pressure pulse. Here we provide evidence that axonal injury, a signature characteristic of traumatic brain injury, is also a prominent feature of experimental subarachnoid haemorrhage. Using histological markers of membrane disruption and cytoskeletal injury validated in analyses of traumatic brain injury, we show that axonal injury also occurs following subarachnoid haemorrhage in an animal model. Consistent with the higher prevalence of global as opposed to focal deficits after subarachnoid haemorrhage and traumatic brain injury in humans, axonal injury in this model is observed in a multifocal pattern not limited to the immediate vicinity of the ruptured artery. Ultrastructural analysis further reveals characteristic axonal membrane and cytoskeletal changes similar to those associated with traumatic axonal injury. Diffusion tensor imaging, a translational imaging technique previously validated in traumatic axonal injury, from these same specimens demonstrates decrements in anisotropy that correlate with histological axonal injury and functional outcomes. These radiological indicators identify a fibre orientation-dependent gradient of axonal injury consistent with a barotraumatic mechanism. Although traumatic and haemorrhagic acute brain injury are generally considered separately, these data suggest that a signature pathology of traumatic brain injury-axonal injury-is also a functionally significant feature of subarachnoid haemorrhage, raising the prospect of common diagnostic, prognostic, and therapeutic approaches to these conditions.

Quantitative assessments of traumatic axonal injury in human brain: concordance of microdialysis and advanced MRI.

Axonal injury is a major contributor to adverse outcomes following brain trauma. However, the extent of axonal injury cannot currently be assessed reliably in living humans. Here, we used two experimental methods with distinct noise sources and limitations in the same cohort of 15 patients with severe traumatic brain injury to assess axonal injury. One hundred kilodalton cut-off microdialysis catheters were implanted at a median time of 17 h (13-29 h) after injury in normal appearing (on computed tomography scan) frontal white matter in all patients, and samples were collected for at least 72 h. Multiple analytes, such as the metabolic markers glucose, lactate, pyruvate, glutamate and tau and amyloid-ß proteins, were measured every 1-2 h in the microdialysis samples. Diffusion tensor magnetic resonance imaging scans at 3 T were performed 2-9 weeks after injury in 11 patients. Stability of diffusion tensor imaging findings was verified by repeat scans 1-3 years later in seven patients. An additional four patients were scanned only at 1-3 years after injury. Imaging abnormalities were assessed based on comparisons with five healthy control subjects for each patient, matched by age and sex (32 controls in total). No safety concerns arose during either microdialysis or scanning. We found that acute microdialysis measurements of the axonal cytoskeletal protein tau in the brain extracellular space correlated well with diffusion tensor magnetic resonance imaging-based measurements of reduced brain white matter integrity in the 1-cm radius white matter-masked region near the microdialysis catheter insertion sites. Specifically, we found a significant inverse correlation between microdialysis measured levels of tau 13-36 h after injury and anisotropy reductions in comparison with healthy controls (Spearman's r = -0.64, P = 0.006). Anisotropy reductions near microdialysis catheter insertion sites were highly correlated with reductions in multiple additional white matter regions. We interpret this result to mean that both microdialysis and diffusion tensor magnetic resonance imaging accurately reflect the same pathophysiological process: traumatic axonal injury. This cross-validation increases confidence in both methods for the clinical assessment of axonal injury. However, neither microdialysis nor diffusion tensor magnetic resonance imaging have been validated versus post-mortem histology in humans. Furthermore, future work will be required to determine the prognostic significance of these assessments of traumatic axonal injury when combined with other clinical and radiological measures.

Electronic properties of mono-substituted tetraferrocenyl porphyrins in solution and on a gold surface: assessment of the influencing factors for photoelectrochemical applications.

Two unsymmetric meso-tetraferrocenyl-containing porphyrins of general formula Fc3 (FcCOR)Por (Fc=ferrocenyl, R=CH3 or (CH2)5 Br, Por=porphyrin) were prepared and characterized by a variety of spectroscopic methods, whereas their redox properties were investigated using cyclic voltammetry (CV) and differential pulse voltammetry (DPV) approaches. The mixed-valence [Fc3 (FcCOR)Por](n+) (n=1,3) were investigated using spectroelectrochemical as well as chemical oxidation methods and corroborated with density functional theory (DFT) calculations. Inter-valence charge-transfer (IVCT) transitions in [Fc3 (FcCOR)Por](+) were analyzed, and the resulting data matched closely previously reported complexes and were assigned as Robin-Day class II mixed-valence compounds. Self-assembled monolayers (SAMs) of a thioacetyl derivative (Fc3 (FcCO(CH2)5 SCOCH3 )Por) were also prepared and characterized. Photoelectrochemical properties of SAMs in different electrolyte systems were investigated by electrochemical techniques and photocurrent generation experiments, showing that the choice of electrolyte is critical for efficiency of redox-active SAMs.

Tau elevations in the brain extracellular space correlate with reduced amyloid-ß levels and predict adverse clinical outcomes after severe traumatic brain injury.

Axonal injury is believed to be a major determinant of adverse outcomes following traumatic brain injury. However, it has been difficult to assess acutely the severity of axonal injury in human traumatic brain injury patients. We hypothesized that microdialysis-based measurements of the brain extracellular fluid levels of tau and neurofilament light chain, two low molecular weight axonal proteins, could be helpful in this regard. To test this hypothesis, 100 kDa cut-off microdialysis catheters were placed in 16 patients with severe traumatic brain injury at two neurological/neurosurgical intensive care units. Tau levels in the microdialysis samples were highest early and fell over time in all patients. Initial tau levels were >3-fold higher in patients with microdialysis catheters placed in pericontusional regions than in patients in whom catheters were placed in normal-appearing right frontal lobe tissue (P = 0.005). Tau levels and neurofilament light-chain levels were positively correlated (r = 0.6, P = 0.013). Neurofilament light-chain levels were also higher in patients with pericontusional catheters (P = 0.04). Interestingly, initial tau levels were inversely correlated with initial amyloid-ß levels measured in the same samples (r = -0.87, P = 0.000023). This could be due to reduced synaptic activity in areas with substantial axonal injury, as amyloid-ß release is closely coupled with synaptic activity. Importantly, high initial tau levels correlated with worse clinical outcomes, as assessed using the Glasgow Outcome Scale 6 months after injury (r = -0.6, P = 0.018). Taken together, our data add support for the hypothesis that axonal injury may be related to long-term impairments following traumatic brain injury. Microdialysis-based measurement of tau levels in the brain extracellular space may be a useful way to assess the severity of axonal injury acutely in the intensive care unit. Further studies with larger numbers of patients will be required to assess the reproducibility of these findings and to determine whether this approach provides added value when combined with clinical and radiological information.

TOPAS simulations of the response of a mini-TEPC: benchmark with experimental data.

Objective. Microdosimetry offers a fast tool for radiation quality (RQ) verification to be implemented in treatment planning systems in proton therapy based on variable LET or RBE to move forward from the use of a fixed RBE of 1.1. It is known that the RBE of protons can increase up to 50% higher than that value in the last few millimetres of their range. Microdosimetry can be performed both experimentally and by means of Monte Carlo (MC) simulations. This paper has the aim of comparing the two approaches.Approach. Experimental measurements have been performed using a miniaturized Tissue equivalent proportional counter developed at the Legnaro National Laboratories of the Italian National Institute for Nuclear Physics with the aim of being used as RQ monitors for high intensity beams. MC simulations have been performed using the microdosimetric extension of TOPAS which provides optimized parameters and scorers for this application.Main results. Simulations were compared with experimental microdosimetric spectra in terms of shape of the spectra and their average values. Moreover, the latter have been investigated as possible estimators of LET obtained with the same MC code. The shape of the spectra is in general consistent with the experimental distributions and the average values of the distributions in both cases can predict the RQ increase with depth.Significance. This study aims at the comparison of microdosimetric spectra obtained from both experimental measurements and the microdosimetric extension of TOPAS in the same radiation field.

KuQuinones: a ten years tale of the new pentacyclic quinoid compound.

Quinones are widespread in nature, as they participate, mainly as redox mediators, in several biochemical processes. Up to now, various synthetic quinones have been recommended in the literature as leading molecules in energy, biomedical and catalytic fields. In this brief review, we retraced our research activity in the last ten years, mainly dedicated to the study of a new class of peculiar pentacyclic conjugated quinoid compounds, synthesized in our group. In particular, their application as sensitive materials in photoelectrochemical devices and in biosensors, as photocatalysts in selective oxidation reactions, and their anticancer activity is here reviewed.

Energy imparted and ionisation yield at the nanometre scale: results for extended beams.

The metrological problem of interpreting ionisation-based micro- and nanodosimetric measurements in terms of quantities proportional to energy imparted becomes particularly relevant when the sensitive volume (SV) size is in the nanometre range. At these scales, a constant W-value cannot be assumed, and the stochastics of the energy transfer per single collision could play a more important role. This problem was recently analysed by our group by means of track-structure Monte Carlo simulations with the Geant4-DNA code, finding a strong correlation between the energy imparted and ionisation yield also for SV diameters of 1 nm. As the previous study was limited to primary beams of radius zero crossing the sensitive sphere along its diameter, it is the aim of the present work to extend the analysis to beams with a radius larger than the dimensions of the SV, to better assess the role played by secondary electrons.