Mechanistic details on Pd(II)/5,10,15,20-tetrakis(1-methyl-4-pyridyl)porphyrin complex formation and reactivity in the presence of DNA

Abstract: Kinetics of coordination of Pd(II) by the macrocyclic porphyrin 5,10,15,20-tetrakis(1-methyl-4-pyridyl)porphyrin (H2P4+) is investigated and confirms quantitative formation of a planar PdP4+complex at room temperature (formation rate 0.19 M-1 s-1 at 25 °C, 0.2 M NaCl, pH 3). Then, the binding ability to DNA of the pre-formed PdP4+complex is analysed. To achieve this aim, spectrophotometry, spectrofluorometry and viscometry are used. Thermodynamic parameters for binding, obtained by the temperature dependence of the equilibrium constants, are deltaH = -71 kJ mol-1 and deltaS = -134 J mol-1 K-1. These values, being both highly negative, agree with full PdP4+intercalation into DNA. Moreover, kinetics of the binding reaction is analysed by the T-jump technique (reaction times in the 1-5 ms range). Experiments on the porphyrin ligand retention on negative SDS and positive DTAC micellar surfaces are also done. Taken altogether, these data provide mechanistic details on complex formation and on DNA binding and relevant energies and driving forces. It is found that interaction between PdP4+and base pairs is very strong (KabsDNA = 8.0E5 M-1 at 25 °C, 1.0 M NaCl), not only owing to the high positive charge borne by the complex, but also to the contribution of high hydrophobicity of the porphyrin ring. In the dye/DNA complex, PdP4+is buried into the helix, as confirmed also by fluorescence quenching tests. Both presence and type of metal ion play a major role, as lower affinity and lower induced helix conformation changes are found in the case of the H2P4+/DNA and CuP4+/DNA systems

Thermodynamic analysis of POPs interaction with biosubstrates

Persistent organic pollutants (POPs) as polycyclic aromatic hydrocarbons (PAH), pesticides and herbicides are nowadays ubiquitous [1]. These species are highly lipophilic and all at least suspected of carcinogenic effects [2,3]. However, information on their toxic activity is often related to in vitro/in vivo studies, whereas a detailed analysis of the mechanistic/chemical aspects of the binding to biosubstrates is sometimes missing. To contribute to this field and in the frame of our participation to PNRA (National Antarctic Research Program) we have done some tests on the binding of model targets (two PAHs, two pesticides and two herbicides, Fig. 1) to biosubstrates (natural DNA and bovine serum albumin - BSA). The interaction with micelles and liposomes was also tested, both as to scale the lipophilicity and to get information on the possible accumulation on membranes. The results collected show that the high hydrophobicity of these species turns into very high affinity for DNA. Absorbance and fluorescence titrations suggest complex binding modes that are discussed in relation with the different pollutant/DNA ratio. BSA binding is also found to occur. Ultrafiltration coupled with absorbance spectroscopy enables the percentage of retention (R%) on the micelle/liposome be measured. R% dependence on the molecule and on the type of system (sodium dodecyl sulphate anionic micelles, TritonX-100 neutral micelles, dodecyl trimethyl ammonium chloride positive micelles and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine liposomes) is discussed. References: [1] A. Lo Giudice, P. Casella, V. Bruni, L. Michaud, Ecotoxicology 2013, 22, 240-250. [2] H. Yu, Journal of Enviromental Science and Health 2002, 20, 149-183. [3] M.C.R. Alavanja, M.R. Bonner, Journal of Toxicology and Environmental Health B 2012, 15, 238-263

Building energy modelling and monitoring by integration of IoT devices and Building Information Models

In recent years, the research about energy waste and CO2 emission reduction has gained a strong momentum, also pushed by European and national funding initiatives. The main purpose of this large effort is to reduce the effects of greenhouse emission, climate change to head for a sustainable society. In this scenario, Information and Communication Technologies (ICT) play a key role. From one side, advances in physical and environmental information sensing, communication and processing, enabled the monitoring of energy behaviour of buildings in real-time. The access to this information has been made easy and ubiquitous thank to Internet-of-Things (IoT) devices and protocols. From the other side, the creation of digital repositories of buildings and districts (i.e. Building Information Models - BIM) enabled the development of complex and rich energy models that can be used for simulation and prediction purposes. As such, an opportunity is emerging of mixing these two information categories to either create better models and to detect unwanted or inefficient energy behaviours. In this paper, we present a software architecture for management and simulation of energy behaviours in buildings that integrates heterogeneous data such as BIM, IoT, GIS (Geographical Information System) and meteorological services. This integration allows: i) (near-) real-time visualisation of energy consumption information in the building context and ii) building performance evaluation through energy modelling and simulation exploiting data from the field and real weather conditions. Finally, we discuss the experimental results obtained in a real-world case-study

Indoor Air-Temperature Forecast for Energy-Efficient Management in Smart Buildings

In the last few years, the reduction of energy consumption and pollution became mandatory. It became also a common goal of many countries. Only in Europe, the building sector is responsible for the total 40% of energy consumption and 36% of CO2 pollution. Therefore, new control policies based on the forecast of buildings energy behaviors can be developed to reduce energy waste (i.e. policies for Demand Response and Demand Side Management). This paper discusses an innovative methodology for smart building indoor air-temperature forecasting. This methodology is based on a Non-linear Autoregressive neural network. This neural network has been trained and validated with a dataset consisting of six years indoor air-temperature values of a building demonstrator. In detail, we have studied three characterizing rooms and the whole building. Experimental results of energy prediction are presented and discussed

A scalable middleware-based infrastructure for energy management and visualization in city districts

Following the Smart City views, citizens, policy makers and energy distribution companies need a reliable and scalable infrastructure to manage and analyse energy consumption data in a city district context. In order to move forward this view, a city district model is needed, which takes into account different data-sources such as Building Information Models, Geographic Information Systems and real-time information coming from heterogeneous devices in the district. The Internet of Things paradigm is creating new business opportunities for low-cost, low-power and high-performance devices. Nevertheless, because of the "smart devices" heterogeneity, in order to provide uniform access to their functionalities, an abstract point of view is needed. Therefore, we propose an distributed software infrastructure, exploiting service-oriented middleware and ontology solutions to cope with the management, simulation and visualization of district energy data

Mechanistic studies on the interaction between small molecules and biosubstrates: a multitechnique approach

One of the main aspect of this thesis is to produce and offer to the scientific community mechanistic details on the interaction between small molecules and biosubstrates for complex selected systems of high biomedical interest. For every system, we highlight and discuss the critical aspects for correctly designing the experiments and treating the data. The binding of small molecules to biosubstrates deserves interest from two apparently opposite point of views. On one side, the development of new efficient anticancer agents. On the other hand, the analysis of the effects of possible tumour-genic species. For the first aspect, although the many studies involved, there are still many unsolved problems mainly related to drug resistance and detrimental effects on the patients. Concerning the second aspect, and in the context of our participation to National Antarctic Research Program (PNRA), our attention has been focused on Persistent Organic Pollutants (POPs), which were demonstrated to enhance tumour morbidity. On the whole, we provided detailed discussions on the binding modes of the selected systems, by employing a combination of experimental and computational techniques

Inquinanti organici: test di interazione con biosubstrati e sistemi micellari di due IPA e due pesticidi modello

Con il termine “inquinanti organici” si intende un gruppo di sostanze organiche tossiche, persistenti, bioaccumulabili e disponibili al trasporto per lunghe distanze dal proprio punto di origine. La contaminazione su scala globale è legata alle proprietà chimico-fisiche di questi composti: molti inquinanti sono resistenti alla degradazione chimica e biologica e persistono nel suolo, nelle acque e persino negli organismi viventi per molto tempo. D’altra parte, considerata l’estrema lipofilicità di queste sostanze, il bioaccumulo risulta senza dubbio favorito. Sebbene i livelli più elevati di inquinamento ambientale siano generalmente riscontrati in prossimità dei punti di rilascio, il problema è diventato ormai ubiquitario.Le regioni polari, a dispetto della lontananza dalle attività antropiche, non sono immuni da questo inquinamento. Al contrario, le basse temperature che caratterizzano tali zone e la conseguente limitata velocità metabolica degli organismi determinano un sostanziale accumulo dei contaminanti organici. Il presente lavoro si inserisce proprio in questo contesto, in quanto frutto di una collaborazione interna al Dipartimento di Chimica e Chimica Industriale con la Prof.ssa S. Giannarelli, che partecipa ad un progetto del PNRA - Programma Nazionale di Ricerche in Antartide. Scopo di questo lavoro di tesi è valutare le interazioni di due idrocarburi policiclici aromatici (IPA) e due pesticidi carbammati con biosubstrati naturali (DNA e siero albumina bovina) e approfondire lo studio della loro tossicità misurandone la tendenza ad essere adsorbiti su sistemi micellari e liposomi di diversa natura, i quali rappresentano un modello semplificato di membrane biologiche

Mechanism of a Pd(II)/porphyrin complex formation and studies on its interaction with polynucleotides

Interactions of synthetic and natural nucleic acids with porphyrins have been intensively investigated since the discovery in 1979 that these compounds are able to intercalate into DNA. The flat aromatic structure of porphyrins, both free and in form of metal complexes, coupled with their high absorptivity, make these substances especially suitable for investigations on the mechanisms of drug binding to nucleic acids; moreover, introduction of a metal ion converts a porphyrin into a metallo-intercalator with additional properties. In recent years the field of porphyrin and metal-porphyrin chemistry has expanded significantly, mainly in connection with the use of these molecules in biology and for light harvesting and energy conversion. DNA/porphyrin systems have been analysed using very different methods but many details of the binding still need to be elucidated. We present here a combined thermodynamic and kinetic analysis of the formation of the Pd(II) complex of 5,10,15,20-tetrakis(1-methyl-4-pyridiyl)-porphyne and of its interaction with DNA. The kinetic analysis of the binding of the Pd(II) to 5,10,15,20-tetrakis(1-methyl-4-confirms 1:1 binding stoichiometry and quantitative reaction. As concerns the binding of the complex to DNA, fluorescence and absorbance titrations under different conditions of temperature and salt content concur in indicating that the binding is strong. Kinetic and equilibrium parameters for the complex interaction with the nucleic acid are obtained and the binding mechanism is discussed. An intercalative binding mode is found to be operative

Investigation on the Alcian Blue-tetrakis(methylpyridinium) chloride reactivity in presence of DNA, RNA, G-quadruplex structures and BSA

Phtalocyanines have the potential to act as anticancer drugs, thanks to their interactions with proteins and polynucleotides [1]. Their strong and specific interaction with G-quadruplex structures may be responsible for inhibiting cancer cells proliferation [2]. Phtalocyanines are excellent macrocyclic ligands for transition metals and metal coordination deeply modulates their chemical and photophysical properties. We focused our attention on Alcian Blue-tetrakis(methylpyridinium) chloride (ABTP), a commercially-available Cu(II)-phtalocyanine complex with promising features. The binding properties in presence of several polynucleotides and a protein were investigated at physiological conditions through spectrophotometric and spectrofluorometric techniques, thermal denaturation tests and calorimetric measurements. The measurements were repeated at different temperatures and ionic strengths in order to obtain information on the binding modes. The thermodynamic parameters were evaluated as well. The UV-vis absorption titrations suggested that an interaction does occur with calf thymus DNA, telomeric DNA G-quadruplex (Tel23), double stranded RNA (polyA·polyU) and triple stranded RNA (polyA·2polyU). The results were confirmed by the appearance of induced signals in the circular dichroism spectra. The isothermal titration calorimetry also corroborated the interactions and provided the thermodynamic parameters for the bindings. On the other hand, ABTP does not seem to interact with bovine serum albumin at all. The Foster Resonance Energy Transfer (FRET) was exploited in Real Time Quantitative PCR measurements in order to evaluate the binding’s effect on double helix DNA and G-quadruplex structures. Although the previous measurements indicate that ABTP has a strong affinity for the biosubstrates, it does not affect the stability of the polynucleotides. The overall results suggest an external binding mode, with partial intercalation of the substituents. This hypothesis does agree with the dimension and geometry of the system. The obtained results are encouraging and further investigations will be performed in order deepen the mechanistic details of the processes. Furthermore, quantum chemistry studies are still in progress and will be refined. References: [1] N. Rasouli, N. Sohrabi, Physical Chemistry Research, 2016, 4 (1), 83-94 [2] H. Yaku, T. Murashima, D. Miyoshi, N. Sugimoto, Molecules, 2012, 17, 10586-1061

Effectiveness of neural networks and transfer learning for indoor air-temperature forecasting

Starting in 2007, EU set energy efficiency improvement targets in sectors with high energy-saving potential such as buildings. ICT allows innovative opportunities for energy consumption forecast to integrate with new control policies such as Demand/Response and Demand Side Management to reduce energy waste. However, such technologies must overcome challenges such as the lack of accurate historic data required for predictions. This article proposes an innovative methodology supporting the energy management of HVAC systems, through Smart Building indoor air-temperature forecast. The applicability of innovative neural networks for time-series predictions is explored. These neural networks are first trained on an artificial but realistic dataset based on BIM simulations with real meteorological data. The inference phase is then carried out on a second dataset collected by IoT devices. Finally, Transfer Learning techniques are exploited to improve the performances predictions. Fanger’s model is applied to validate results, showing consistent levels of accuracy and comfort