Teresa Fornaro

Istituto Nazionale di Astrofisica, Osservatorio Astrofisico di Arcetri, Post-Doc

Followers

Following

Co-authors

Public Views

Main scientific activity pertains to Astrobiology, focusing on experimental and theoretical studies for detection of biomarkers on Mars. These studies primarily support the scientific investigations and technology development of Mars Organics Molecule Analyser (MOMA) instrument on board the European Space Agency (ESA) ExoMars 2020 space mission, devoted to detection of a wide range of organic molecules, operating in two modes, i.e. laser desorption ionization- and gas chromatography- mass spectrometry.
Specifically, new protocols are developed in laboratory to adsorb biomarkers onto mineral matrices, in order to study the physico-chemical interactions characterizing such molecule-mineral complexes, and prepare Mars soil analogues for payload tests.
The thermodynamics of the adsorption process is examined both experimentally, determining equilibrium adsorption isotherms, and computationally through quantum mechanical and surface complexation modelling, by using CRYSTAL and GEOSURF software, respectively.
Sample characterization is carried out experimentally by means of several analytical techniques, such as Infrared and Raman vibrational spectroscopies, UV-vis spectrophotometry, High Performance Liquid Chromatography - Mass Spectrometry (HPLC-MS), Ion Chromatography (IC), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), X-Ray Diffraction (XRD).
The experimental measurements are integrated by computational quantum mechanical spectroscopy studies in order to assess the various contributions to the overall spectroscopic signals due to different molecule-mineral interactions and correctly assign the experimental spectroscopic features. This is achieved by using a virtual multi-frequency spectrometer covering rotational, vibrational, electronic, as well as magnetic resonance spectral ranges, implemented in the GAUSSIAN suite of programs.
Moreover, photochemistry of molecules adsorbed on minerals is investigated under Martian-like conditions through UV irradiation processing. The degradation kinetics under Martian-like conditions is inspected taking into account possible catalytic and/or protective effects of minerals.
After preparation, UV processing and characterization of Martian analogues, high-sensitivity tests of MOMA instrument are performed at NASA - Goddard Space Flight Centre (USA), to evaluate the detection limits of MOMA instrument for organic molecules that are considered biomarkers of extant or extinct life, and optimize the instrument parameters in order to improve detection efficiency.
In addition, experience is gained in the development of liquid extraction protocols of biomarkers adsorbed on minerals for in situ biosensor-based life detection technologies, specifically the Life Marker Chip (LMC) instrument on board ExoMars space mission, which is an antibody microarray biosensor instrument with optical readout that uses fluorescently labelled antibodies to detect and quantify the presence of polar and non-polar biomolecules extracted from the Martian soil.
Further activity concerns the study of properties of surface materials of primitive carbon-rich asteroids to support NASA OSIRIS-REX sample return space mission. In particular, criteria and procedures for selection of representative analogue material to be present on primitive carbon-rich asteroids are identified. Characterization of surface properties of primitive carbon-rich asteroids is performed to allow a direct comparison with ground-based observations and laboratory spectroscopic studies. Planetary protection activities are carried out in order to study chemical contamination of samples.
Supervisors: John Robert Brucato

less

Interests

Uploads

Papers by Teresa Fornaro

Toward Feasible and Comprehensive Computational Protocol for Simulation of the Spectroscopic Properties of Large Molecular Systems: The Anharmonic Infrared Spectrum of Uracil in the Solid State by the Reduced Dimensionality/Hybrid VPT2 Approach

by Malgorzata Biczysko, Ivan Carnimeo, and Teresa Fornaro

The journal of physical chemistry. A, Jan 18, 2014

Download

Towards Feasible and Comprehensive Computational Protocol for Simulation of the Spectroscopic Properties of Large Molecular Systems: The Anharmonic Infrared Spectrum of Uracil in the Solid State by Reduced Dimensionality/Hybrid VPT2 Approach

by Malgorzata Biczysko, Ivan Carnimeo, and Teresa Fornaro

Feasible and comprehensive computational protocols for simulating the spectroscopic properties of... more Feasible and comprehensive computational protocols for simulating the spectroscopic properties of large and complex molecular systems are very sought after. Indeed, due to the great variety of intra-and inter-molecular interactions which may take place, the interpretation of experimental data becomes more and more difficult as the system under study increases in size and/or is placed in a complex environment, such as condensed phases. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes, with increasing complexity towards condensed phases and monolayers of biomolecules on solid supports. We have resorted to fully anharmonic quantum mechanical computations within the generalized second order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective B3LYP-D3 method, in conjunction with basis sets of double-ζ plus polarization quality. Such approach has been validated in a previous work (PCCP 2014, 16, 10112-10128) for simulating the IR spectra of the monomers of nucleobases and some of their dimers. In the present contribution we have extended such computational protocol to simulate spectroscopic properties of a molecular solid, namely poly-crystalline uracil. Firstly we have selected a realistic molecular model for representing the spectroscopic properties of uracil in the solid state, the uracil heptamer, and then we have computed the relative anharmonic frequencies combining less demanding approaches such as the hybrid B3LYP-D3/DFTBA one, in which the harmonic frequencies are computed at a higher level of theory (B3LYP-D3/N07D) while the anharmonic shifts are evaluated at a lower level of theory (DFTBA), and the reduced dimensionality VPT2 (RD-VPT2) approach, where only selected vibrational modes are computed anharmonically along with the couplings with other modes.

Download

Extraction Protocols for Life Marker Chip-Style Instruments

ABSTRACT Extraction experiments were performed to evaluate suitable sample-extraction and process... more ABSTRACT Extraction experiments were performed to evaluate suitable sample-extraction and processing protocols that will be used by bioanalytical instruments like Life Marker Chip (LMC), focused on the detection of molecules associated with life that will be extracted from the Martian soil. LMC is an antibody microarray biosensor instrument with optical readout, which uses fluorescent labels, analogous to the expected biomarkers, to detect and quantify the presence of polar and non-polar biomolecules, extracted from the Martian soil. The success of the LMC biomarkers detection experiment is dependent on the sample extraction protocol. The currently recommended extraction procedure, optimized for aliphatic biomarkers, consists in sonicating the samples using as solvent system MeOH:H2O with surfactant, which respects all the tightening requirements associated to LMC biosensor. We have examined this procedure for a particular class of biomarkers, the nucleobases adenine, cytosine, uracil and hypoxanthine adsorbed onto martian analogues minerals.

Computer Simulations of Prebiotic Systems

Download

Biomarkers: how detect life on mineral matrix

Life Marker Chip (LMC) is a bioanalytical instrument on board of the ESA Exomars mission to detec... more Life Marker Chip (LMC) is a bioanalytical instrument on board of the ESA Exomars mission to detect specific organic molecules that may be associated with life on Mars. Observation of possible biomarkers is critical for the understanding of prebiotic evolution and to detect signature of past and/or present life on other extraterrestrial body. Biomarkers usually are associated with mineral matrix, so it is necessary to investigate the nature of the interaction of organic molecules with minerals. Our approach is to combine physical-chemical analisys (adsorption isotherm, adsorption kinetics, surface area measurement, etc.) with FTIR and Raman spectroscopy in order to clarify the kind of interaction at molecular level between biomarkers and minerals. In particular we focus our attention on nucleobases that are the precursor of genetic material (DNA, RNA) with several minerals (MgO, forsterite, TiO2, hydroxylapatite, olivine) that mimic extraterrestrial materials. A second objective was to investigate the desorption processes in order to optimize the experimental procedure for the detection of biomarkers in the contest of LMC. In this study we have evaluated the effect of several parameters such as sonication and temperature on the extraction efficiency. Moreover because the desorption process strongly depends on the chemical nature of organics and minerals and on their own interaction, we have also evaluated the capability of different solvent mixtures (water, methanol, etc.) with different polarity and the use of surfactant (Tween 80) to extract previously adsorbed biomolecules. The results obtained could contribute to improve the biomarker extraction procedure in the LMC experiment.

Download

Reliable Vibrational Wavenumbers for C=O and N-H Stretchings of Isolated and Hydrogen-bonded Nucleic Acid Bases

Phys. Chem. Chem. Phys., 2016

The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bon... more The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C[double bond, length as m-dash]O and N-H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values needs to be compensated by reliable computational data, which require the use of approaches going beyond the standard harmonic oscillator model. Test computations performed for model systems (formamide, acetamide and their cyclic homodimers) in the framework of the second order vibrational perturbation theory (VPT2) confirmed that anharmonic corrections can be safely computed by global hybrid (GHF) or double hybrid (DHF) functionals, whereas the harmonic part is particularly challenging. As a matter of fact, GHFs perform quite poorly and even DHFs, while fully satisfactory for C[double bond, length as m-dash]O stretchings, face unexpected difficulties when dealing with N-H stretchings. On these grounds, a linear regression for N-H stretchings has been obtained and validated for the heterodimers formed by 4-aminopyrimidine with 6-methyl-4-pyrimidinone (4APM-M4PMN) and by uracil with water. In view of the good performance of this computational model, we have built a training set of B2PLYP-D3/maug-cc-pVTZ harmonic wavenumbers (including linear regression scaling for N-H) for six-different uracil dimers and a validation set including 4APM-M4PMN, one of the most stable hydrogen-bonded adenine homodimers, as well as the adenine-uracil, adenine-thymine, guanine-cytosine and adenine-4-thiouracil heterodimers. Because of the unfavourable scaling of DHF harmonic wavenumbers with the dimensions of the investigated systems, we have optimized a linear regression of B3LYP-D3/N07D harmonic wavenumbers for the training set, which has been next checked against the validation set. This relatively cheap model, which shows very good agreement with experimental data (average errors of about 10 cm(-1)), paves the route toward a reliable analysis of spectroscopic signatures for larger polynucleotides.

Hydrogen-Bonding Effects on Infrared Spectra from Anharmonic Computations: the Uracil-Water Complexes and Uracil Dimers

The journal of physical chemistry. A, Jan 13, 2015

Hydrogen-bonding interactions lead to significant changes in the infrared (IR) spectrum, like fre... more Hydrogen-bonding interactions lead to significant changes in the infrared (IR) spectrum, like frequency-shifts of the order of magnitude of hundreds of wavenumbers and increases of IR intensity for bands related to vibrational modes of functional groups directly involved in the hydrogen-bonded bridges. We are actively developing a comprehensive and robust computational protocol aimed at the quantitative reproduction of the spectra of bio-organic and hybrid organic/inorganic molecular systems with a proper account of the variety of intra- and inter-molecular interactions. We have resorted to fully anharmonic quantum mechanical computations within the generalized second order vibrational perturbation theory (GVPT2) approach, combined with B3LYP-D3 method, in conjunction with basis sets of double-zeta plus polarization quality. Such approach has been validated in a previous work (PCCP 2014, 16, 10112-10128) for simulating the IR spectra of the monomers of nucleobases and some of their ...

Download

The journal of physical chemistry. A, Jan 18, 2014

Download

Biomarkers: how detect life on mineral matrix

Download

Extraction Protocols for Life Marker Chip-Style Instruments

Anharmonic Ir Spectra of Biomolecules: Nucleobases and Their Oligomers

Proceedings of the 69th International Symposium on Molecular Spectroscopy, 2014

Computer Simulations of Prebiotic Systems

Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, 2014

Download

Development of extraction protocols for life detection biosensor-based instruments

Planetary and Space Science, 2013

and sharing with colleagues.

Download

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Physical Chemistry Chemical Physics, 2014

Computational spectroscopy techniques have become in the last few years an effective means to ana... more Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work we have chosen two popular and inexpensive approaches to model dispersion interactions, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates. † Electronic supplementary information (ESI) available: (i) Harmonic and anharmonic vibrational frequencies and IR intensities for adenine, cytosine, uracil, hypoxanthine and thymine molecules; (ii) statistical analysis of the vibrational frequency discrepancies for monomers; (iii) binding energies and structural parameters for dimers; and (iv) anharmonic vibrational frequencies of uracil and adenine complexes. See

Download

Adsorption of nucleic acid bases on magnesium oxide (MgO)

International Journal of Astrobiology, 2013

The adsorption of organic molecules on mineral matrices might have played a fundamental role in p... more The adsorption of organic molecules on mineral matrices might have played a fundamental role in processes that led to the emergence of life. We investigated the adsorption properties of the nucleobases adenine, cytosine, uracil and hypoxanthine on magnesium oxide (MgO), determining the single solute batch equilibrium adsorption isotherms. Langmuir-type isotherms were fitted to data, assuming a rapid reversible equilibration of adsorption, demonstrated effectively through desorption experiments. The Langmuir equilibrium adsorption constant K and the amount of the solute per unit of adsorbent mass necessary to complete the monolayer b were calculated. The results indicate that MgO is a good adsorbent for nucleobases (adenine > uracil > hypoxantine > cytosine), suggesting a role of metal oxides in concentrating biomolecules in prebiotic conditions that might have favoured the passage from geochemistry to biochemistry.

Download

Infrared spectral investigations of UV irradiated nucleobases adsorbed on mineral surfaces

Icarus, 2013

The interaction between electromagnetic radiation and bio-molecules in heterogeneous environments... more The interaction between electromagnetic radiation and bio-molecules in heterogeneous environments is a prebiotically relevant process. Minerals may have a pivotal role in the prebiotic evolution of complex chemical systems, mediating the effects of electromagnetic radiation, influencing the photostability of bio-molecules, catalyzing important chemical reactions and/or protecting molecules against degradation. In particular, nucleobases are relevant bio-molecules to investigate both in the prebiotic context, because they are coding components of nucleic acids, and from the standpoint of the survival of biological systems in space conditions. Several studies on the photodynamics of nucleobases suggest that their structure could have been naturally selected for the ability to dissipate electronic energy through ultrafast photophysical decay. Considering the putative involvement of minerals in the prebiotic chemistry, it is necessary to study the photostability of nucleobases under space conditions in the presence of mineral matrices, to investigate both the prebiotic processes that might have had a role in the development of the first living entities on Earth and the physical and chemical processes occurring in extraterrestrial environments. We focused our study on the characterization of the nature of the interaction between nucleobases and the surface of the minerals magnesium oxide and forsterite by infrared vibrational spectroscopy. We observed that most of the characteristic bands of pure nucleobases vanished when adsorbed on magnesium oxide. On the contrary, in the case of adenine and uracil adsorbed on forsterite, very intense nucleobase absorption peaks appeared. This phenomenon pertains to the surface selection rules changes related to molecular orientation. Moreover, based on the vibrational shifts, we deduced the molecular interaction sites with the mineral surfaces. Furthermore, we investigated the photostability of nucleobases adsorbed on such minerals through in situ UV irradiation experiments. Experimental results confirm the high intrinsic photostability of such molecules, because a rather low probability of interaction between UV radiation and nucleobases was estimated, and furthermore indicate that cytosine and hypoxanthine have a greater photostability compared to adenine and uracil, both pure and adsorbed onto magnesium oxide and forsterite.

Download

Teresa Fornaro

Uploads

Papers by Teresa Fornaro

Log In