Detailed electron paramagnetic resonance and electron nuclear double resonance experiments on the co-crystalline complex of 1-methylthymine:9-methyladenine (MTMA) have revealed that the major radiation induced products at low temperatures (10 K) are MTMA1, a radical formed by net hydrogen abstraction from the C5 methyl group on thymine, and MTMA2, a radical formed by net hydrogen abstraction of the N1 methyl group on thymine. The following four minor products were also observed: MTMA3, the C4-OH protonated anion of thymine, MTMA4, the C6 H-addition product of thymine, and MTMA5 and MTMA6, radicals formed by net H-addition to C2 and C8 of the adenine base. The geometries, energetics and hyperfine properties of all possible radicals of MT and MA, the primary anions and cations, as well as radicals formed via net hydrogen atom abstraction (deprotonated cations) or addition (protonated anions) were investigated theoretically. All systems were optimized using the hybrid Hartree-Fock density functional theory functional B3LYP, in conjunction with the 6-31G(d,p) basis set of Pople and co-workers. Calculations of the anisotropic hyperfine couplings for all the radicals observed in MTMA are presented, and are shown to compare favorably with the experimentally measured hyperfine couplings. The calculated ionizations potentials indicate that MA would be the preferred oxidation site. However, in MTMA neither the adenine cation nor its N4-deprotonated derivative were observed. The adenine cation in MTMA is not stabilized by deprotonation, and is thus likely subject to recombination. The calculated electron affinities indicate that MT would be the preferred reduction site. Reduction of MT is believed to result in protonation of the anion at C4=O. The calculated hyperfine couplings for the MT anion are very similar to those of the C4-OH protonated anion, and therefore, the theoretical calculations are not useful in deciding the actual protonation state of this reduction product.

This thesis discusses two ensembles, the study of which was dependent upon the controllable production of cold gas-phase samples using supersonic beams. The experiments on DNA bases and base clusters were carried out in Germany at the Max Born Institute. The experiments anticipating the construction of a molecular beam slower were carried out in the United States at the University of Texas at Austin. Femtosecond pump-probe techniques were employed to study the dynamics and electronic character of DNA bases, pairs and clusters in the gas phase. Experiments on DNA base monomers confirmed the dominance of a particular relaxation pathway, the nπ* state. Competition between this state and another proposed relaxation pathway was demonstrated through observations of the DNA base pairs and base-water clusters, settling a recent controversy. Further, it was determined that the excited state dynamics in base pairs is due to intramolecular processes rather than intermolecular processes. Finally, results from base-water clusters confirm that microsolvation permits comparison with biologically relevant liquid phase experiments and with ab initio calculations, bridging a long-standing gap. A purely mechanical technique that does not rely upon quantum or electronic properties to produce very cold, very slow atoms and molecules would be more generally applicable than current approaches. The approach described here uses supersonic beam methods to produce a very cold beam of particles and a rotating paddle-wheel, or rotor, to slow the cold beam. Initial experiments testing the possibility of elastic scattering from a single crystal surface were conducted and the implications of these experiments are discussed. / text

Η φασματοσκοπία Raman θεωρείται αξιόπιστη μέθοδος χαρακτηρισμού της μοριακής δομής της ύλης. Τελευταία δε καταβάλλεται μεγάλη προσπάθεια να αναδειχθεί και ως μη επεμβατική τεχνική ανίχνευσης ουσιών φαρμακευτικού και βιολογικού ενδιαφέροντος. Επειδή όμως το φαινόμενο Raman είναι ασθενές και τα όρια ανίχνευσης των ουσιών αυτών ιδιαίτερα χαμηλά, η συμβατική φασματοσκοπία Raman ανταποκρίνεται με μεγάλη δυσκολία στις απαιτήσεις μιας μη επεμβατικής τεχνικής. Τα τελευταία χρόνια με την ανακάλυψη της επιφανειακής ενίσχυσης της σκέδασης Raman (Surface Enhanced Raman Scattering) και την ανάπτυξη της ομώνυμης τεχνικής SERS αυξήθηκε η πιθανότητα του φαινομένου κατά τάξεις μεγέθους. Στο πλαίσιο αυτό, έχουν αναφερθεί και μελέτες SERS με ανίχνευση σκέδασης Raman ακόμη και από ένα μόνο μόριο (single molecule detection). Προϋπόθεση όμως ανάπτυξης φαινομένου SERS είναι η γειτνίαση της εξεταζόμενης ουσίας με νανοσωματίδια αργύρου (Ag) ή χρυσού (Au). Τα νανοσωματίδια αυτά χρησιμοποιούνται κυρίως είτε υπό μορφή κολλοειδών διαλυμάτων είτε υπό την μορφή νανοδομημένων επιφανειών. Μια επιπλέον παράμετρος που πρέπει να συνυπολογισθεί ώστε η μέθοδος αυτή να χαρακτηριστεί αναλυτική είναι η δυνατότητα πραγματοποίησης με SERS ποσοτικών μετρήσεων. Στην παρούσα εργασία ως “υπόστρωμα” εμφάνισης του φαινομένου SERS χρησιμοποιήθηκαν κολλοειδή διαλύματα Au και Ag (~2 mL), στα οποία προστίθεντο 25-100 μL διαλύματος της προς ανίχνευσης ουσίας. Η χρησιμοποίηση της γεωμετρίας σκέδασης 90ο, της πλέον ενδεδειγμένης για λήψη φασμάτων Raman από υγρά και κολλοειδή διαλύματα νανομετρικής κλίμακας (10-100 nm), έδωσε τη δυνατότητα ανίχνευσης συγκεντρώσεων ουσιών-στόχων ακόμη και της τάξης των fg/mL. Επιπλέον, η χρησιμοποίηση μιας κυψελίδας με συνεχή ταλάντωση σε κάθετη ως προς το επίπεδο σκέδασης διεύθυνση (oscillating or shaking cell), επέτρεψε την πραγματοποίηση ποσοτικών μετρήσεων SERS σε συγκεντρώσεις της τάξης των (sub)-ng & (sub)-pg/mL. Η διάταξη αυτή φωταψίας δείγματος και συλλογής σκεδαζόμενης ακτινοβολίας εφαρμόστηκε σε αντικαρκινικά φάρμακα (Novantrone® & Doxorubicin), αντιβιοτικό (Ciproxin®) και βάσεις του DNA. Στην περίπτωση του αντιβιοτικού με ενεργή ουσία το Ciprofloxacin ελήφθησαν ποσοτικά αποτελέσματα σε διαλύματα τεχνητών δακρύων της τάξης των ng/mL, κάτω από την συνολική κλίμακα της μέσης ανασταλτικής πυκνότητας (minimum inhibitory concentration range) του φαρμάκου. Στόχος και φιλοδοξία είναι η τεχνική αυτή να αναδειχθεί ως μια ταχεία μη επεμβατική αναλυτική μέθοδος μέτρησης φαρμακευτικών ή/και βιολογικών ουσιών σε σωματικά υγρά (π.χ. σίελος, δάκρυα, …), για την μελέτη της φαρμακοκινητικής, την έγκαιρη διάγνωση ασθενειών καθώς και τη μελέτη ελεγχόμενης αποδέσμευσης ενεργών ουσιών από πολυμερικές μήτρες σε πολύ μικρές συγκεντρώσεις. Επιπλέον, έγινε προσπάθεια μελέτης/ανίχνευσης μορίων Ε18 primary rat cortical cells με την χρήση του SERS σε συνθήκες προσομοίωσης ηλεκτροχημικού εμφυτεύματος. Για τον λόγο αυτό σχεδιάστηκε και αναπτύχθηκε ένας μικρο-επωαστής (micro-incubator) που επιτρέπει αφ’ ενός μεν τη συντήρηση των κυττάρων σε περιβάλλον κατάλληλο για τη μελέτη τους (layer of Neurobasal-culture medium with a 95% air & 5% CO2 gas flow at 37oC), αφ’ ετέρου δε την προσαρμογή του σε χώρο υποδοχής δείγματος ενός φασματοφωτόμετρου μικρο-Raman για τη λήψη φασματοηλεκτροχημικών μετρήσεων Raman/SERS. Το κύριο σημείο ενδιαφέροντος στο οποίο εστιάσαμε στην παρούσα εργασία αναφέρεται στην διερεύνηση ανίχνευσης βασικών/θεμελιωδών μορίων των κυττάρων στo θρεπτικό υγρό του πειράματος για την ταχεία εκτίμηση ενδεχόμενης αποδέσμευσης DNA που θα αντικατόπτριζε την κατάσταση των κυττάρων. / Laser Raman spectroscopy plays an increasing important role in polymer science, biophysics/biochemistry and life science. Based on vibrational transitions, it has long been regarded as a valuable non destructive tool for the identification of chemical and biological samples as well as the elucidation of molecular structure, surface processes and interface reactions. Spontaneous Raman scattering is however an inherently weak process characterized by extremely small cross sections. Even so, the Raman signal can be highly enhanced when the analyte is placed on or near either to nano-rough noble-metal substrates or to nano-structured colloidal clusters of noble metals. This nano-enhanced scattering process is known as Surface Enhanced Raman Scattering, SERS. With SERS, extremely small amounts of substances can be detected; even single molecule detection has been reported. This constitutes a challenge of applying SERS to extremely low concentration measurements. Nevertheless, the quantitative evaluation by means of SERS was proved difficult, due largely to lack of nano-sized noble metal structures with analytically suitable stability and reproducibility. The commonly used SERS substrates are nanostructured colloids or roughened surfaces of mainly silver and gold undergoing visible or NIR excitation. A note is made of the fact that the Raman scattering geometry that is actually largely used is the backscattering geometry. For solids this is better achieved via a microscope objective, while for liquids via a macro lens. However, the best scattering geometry for Raman light collection from liquids and nanostructured colloids is the right angle scattering; that is, the scattered light is collected at 90o from the excitation light. Having all above in mind, in order to perform quantitative SERS measurements we have designed and developed an oscillating cell making use of the right angle Raman scattering geometry. Originally, the development of the oscillating or “shaking” cell allows large sample sectional surface monitoring, better mixing and homogeneity giving rise to SERS signal reproducibility. In addition, the application of the advantageous for nanocolloidal solutions right angle Raman scattering collection geometry enables SERS measurements at extremely low concentrations. We demonstrated the use this new surface enhanced Raman scattering excitation/collection configuration to monitor the level of the antitumor drugs mitoxantrone and doxorubicin as well as the antibiotic ciprofloxacin at very low concentrations performing fast SERS & SERRS measurements. We have also quantified the concentration of the active agents in aqueous solutions as well as in artificial tears by a partial least-squares (PLS) chemo metric regression algorithm. All above reveal the potential of this technique in the monitoring of the controlled release of active agents from polymeric matrices as well as in the quantitative analysis of drugs in corporal fluids. The only need is to add in a test tube containing 0.5 mL of a nanocolloidal noble metal solution3 about 25-100 μL of a sampling fluid. Finally, in an attempt to detect “living” cells by SERS, to identify DNA components released in a cell culture medium as a “touch mark” of cell death and to perform even single molecule detection, a home-made micro-incubator was designed to allow Raman measurements of neuron cells under the microscope. Commercial micro incubators feature higher optical path between coverslips than the required (<1-1,5 cm) for typical micro-Raman systems even bearing long working distance objectives. It was at that sense a prerequisite to design, construct and optimize a micro-incubator to fit a conventional micro-Raman configuration. The designed micro-incubator meets well-defined stable conditions (temperature, culture solution and atmosphere).