Tautomeric Equilibria Studies by Mass Spectrometry

Tautomerism in organic chemistry has been extensively studied in condensed phase by spectrometric methods, mainly by IR and NMR techniques. Mass spectrometry studies start 40 years ago but just recently it has been recognized the importance of the mass spectral data for the study of tautomerism in the gas phase.
Mass spectrometry can provide valuable information in regard to tautomeric equilibria when studying mass spectra among the members of different families of organic compounds.
The relevance of the mass spectral data resides on several facts but there are two that are of key importance:
1-	Mass spectral fragmentation assignments should be tautomer specific since the corresponding abundances ratios are supposed to be correlated to the keto/enol contents.
2-	Ionization in the ion source is supposed to have no effect on the position of the equilibrium so that the results reflect the tautomers content in the gas phase previous to ionization.
Some of the carbonylic compounds do not exhibit noticeable tautomerism so the fragment abundances assigned to the enol form is very low or not measurable. Since enolization is more noticeable in the case of thio-derivatives (which correlates adequately with the oxygenated analogues), the study of their mass spectra is an interesting choice to reach some degree of generalization. 
In addition, experimental findings are supported by semiempirical theoretical calculations, which probed to be adequate not only for supporting tendency correlations among the members of a compound family but also to calculate heats of tautomerization in gas phase.
Reports using mass spectrometry for tautomerism are becoming less common. One of the reasons is that now it would appear that the interpretation of MS results is not as straightforward as it was once believed, even though in a recent review it was written that: “Mass spectrometry is the most informative and practical method for studying and identifying tautomers in the gas phase” [1]. 
In fact, mass spectrometry seems to be very informative for studying and identifying tautomers, because in this case external factors like solvents, intermolecular interactions, etc., can be excluded by transferring the tautomeric system into gas phase, where the process becomes truly unimolecular [1].
This review covers the study of Tautomerism by Mass Spectrometry in the last four decades. 
&#xa

Computational Study of Acid-Catalyzed Reactions in Zeolites

Aldol condensation is a very important reaction in organic synthesis because it leads to the formation of C-C bonds. Because of that, the use of different catalysts and in particular the use of zeolites for the catalysis of this reaction has been previously studied. The first step of aldol condensation is the the acid- catalyzed keto-enol tautomerization of the aldehyde or ketone. In this thesis, we study all the possible locations of BA sites in the vicinity of each of the defined inequivalent T site positions in FER and MOR zeolites and establish the most stable location of proton siting at force field and periodic DFT level. The reactions involving the small carbonyl compounds, acetaldehyde and acetone, are studied at the specific acid site locations in both zeolites in order to discover which are the active sites that can stabilize the reactants and therefore how the existing catalyst can be improved. Besides the H-bonding and other interactions, the confinement effect are of equal importance in the determination of factors that influence the reactivity of these complexes. In order to understand the keto-enol tautomeric mechanism in zeolites and identify the transition states, constrained geometry optimizations were performed of acetaldehyde in FER and MOR using periodic DFT. From this we determined the formation of enol product via and an one and two-step concerted mechanism. The calculations reveal that C-β deprotonation is the kinetic bottleneck for enol formation. The concerted mechanism was performed at each of the inequivalent T position in both zeolites. We found that proton transfer is a consequence of a cooperation between the acid site and its total environment acting on the molecular adsorbate. The adsorption and stability of the intermediates is dependent upon the heterogeneity of acid sites and their local geometry, the pore channels and cavities and interactions such as dispersive and H-bonding that do not reflect, and are often independent of, acid strength. Thirdly, we studied the keto-enol tautomerization of acetaldehyde in FER and MOR in the presence of a single water or methanol molecular and found the activation barriers to reduce further with an increase in stability of the adsorbed enol form with larger reverse barriers in the larger pores of FER. We establish the importance of the specific role of the H-bonding using these solvent molecules. In the smaller pores of MOR, the presence of a solvent supresses the catalytic interconversion due to steric repulsion. Lastly, we explored the location of monovalent alkali ions in FER and found that the most stable location of the cations is in the FER cavity and dependent upon the Al position. We studied the effect of hydration on the mobility of the cesium ion in the cavities of FER using static DFT calculations supplemented with ab initio molecular dynamics. We estabished the cesium ion prefers to coordinate with the framework oxygens of the zeolite rather than oxygen atoms of the water molecules as well as the position of the cesium ion is affected by the Al siting. The coordination number of cesium is ~ 10 with the ion interacting with only 1-3 water molecules. In addition, we identified a self-organization of water molecules across the channels forming a H-bonding network

Tautomerism and Fragmentation of Biologically Active Hetero Atom (O, N)-Containing Acyclic and Cyclic Compounds Under Electron Ionization

In this thesis a total of 86 compounds containing the hetero atoms oxygen and nitrogen were studied under electron ionization mass spectrometry (EIMS). These compounds are biologically active and were synthesized by various research groups. The main attention of this study was paid on the fragmentations related to different tautomeric forms of 2- phenacylpyridines, 2-phenacylquinolines, 8-aryl-3,4-dioxo-2H,8H-6,7-dihydroimidazo- [2,1-c][1,2,4]triazines and aryl- and benzyl-substituted 2,3-dihydroimidazo[1,2-a]pyrimidine-5,7-(1H,6H)-diones. Also regio/stereospecific effects on fragmentations of pyrrolo- and isoindoloquinazolinones and naphthoxazine, naphthpyrrolo-oxazinone and naphthoxazino-benzoxazine derivatives were screened. Results were compared with NMR data, when available. The first part of thesis consists of theory and literature review of different types of tautomerism and fragmentation mechanisms in EIMS. The effects of tautomerism in biological systems are also briefly reviewed. In the second part of the thesis the own results of the author, based on six publications,are discussed. For 2-phenacylpyridines and 2-phenacylquinolines the correlation of different Hammett substituent constants to the relative abundances (RA) or total ion currents (% TIC) of selected ions were investigated. Although it was not possible to assign most of the ions formed unambiguously to the different tautomers, the linear fits of their RAs and % TICs can be related to changing contributions of different tautomeric forms. For dioxoimidazotriazines and imidazopyrimidinediones the effects of substituents were rather weak. The fragmentations were also found useful for obtaining structural information. Some stereoisomeric pairs of pyrrolo- and isoindoloquinazolines and regiomeric pairs of naphtoxazine derivatives showed clear differences in thir mass spectra. Some mechanisms are suggested for their fragmentations.Siirretty Doriast

Quantum Calculations of Aldol Condensation in Acidic Zeolites

We have used Density Functional Theory to model the mixed aldol condensation reaction catalyzed by acidic zeolites. We have studied the convergence of barriers for the keto-enol tautomerization of acetone in cluster models of HZSM-5 and HY ranging in size from 3-37T. A key finding was that activation barriers for keto-enol tautomerization of acetone in both zeolites (~20 kcal/mol) are significantly higher than those for the condensation reaction between the acetone enol and formaldehyde in 11T cluster models of HZSM-5 and HY. Moreover we found that three zeolite clusters of HZSM-5, similarly sized but including different structural features of the zeolite framework, gave very different activation barriers. These results indicated that a more rigorous approach to constructing cluster models of zeolites was needed. We have developed two different approaches to build cluster models of zeolites and used two acid-zeolite-catalyzed processes related to the conversion of biomass as platforms to systematically investigate cluster-size convergence. Our central finding is that clusters generated with multi-centered spherical cutoffs yield converged reaction energies with smaller system sizes than clusters generated by counting framework bonds. The delta approach to constructing finite clusters of zeolite crystals provides a well-defined prescription and employs a single length scale (d = 5 Å) to converge reaction energies to within chemical accuracy (±1 kcal/mol). Although reaction energies were convergent at d = 5 Å, it is not clear that a single length scale is sufficient to converge activation barriers. We used two reaction systems as platforms to establish convergence of activation barriers using delta clusters. We find that a δ ≥ 4 Å cutoff is sufficient to converge activation barriers to within chemical accuracy (±1 kcal/mol). After convergence was established, we studied the acid-zeolite-catalyzed mixed aldol condensation of acetone with more biomass-relevant aldehydes, such as hydroxymethyl furfural and furfural, in δ = 4 Å clusters of HZSM-5. We have found that the mechanism for condensation in HZSM-5 is concerted, unlike that of the homogeneous acid catalyzed mechanism. Ultimately, we conclude that the keto/enol tautomerization of acetone remains rate-determining in the case of condensation with formaldehyde, furfural or hydroxymethyl furfural in HZSM-5

Nightmare from which you will never awake: Electronic to vibrational spectra

This dissertation is comprised of seven chapters: Chapter 1 provides the theoretical background of ab initio methods and density functional theory, which are relevant to the computational methodologies presented in the following chapters. Chapter 2 examines the anharmonicity associated with weakly bound metal cation dihydrogen complexes using the vibrational self-consistent field (VSCF) method and characterizes the interaction between a hydrogen molecule and a metal cation. Chapter 3 illustrates a study of molecular hydrogen clustering around the lithium cation and their accompanied vibrational anharmonicity employing VSCF. Chapter 4 provides a qualitative interpretation of solvent-induced shifts of amides and simulated electronic absorption spectra using the combined time-dependent density functional theory/effective fragment potential method (TDDFT/EFP). Chapter 5 elucidates an excited-state solvent assisted quadruple hydrogen atom transfer reaction of a coumarin derivative using micro solvated quantum mechanical (QM) water and macro solvated EFP water. Chapter 6 presents a dispersion correction to the QM-EFP1 interaction energy. Finally, a general conclusion of this dissertation work and prospective future direction are presented in Chapter 7

Theory of Aqueous Solvation: Uninterrupted, Cyclic Hydrogen-Bonding Essential for Accurate Keto-Enol Energies and Grotthuss Tautomerism of Acetone

Keto-enol tautomerization (KET) is a fundamental process impacting a range of molecular phenomena in organic and biochemistry. However, the accurate computation of solution-phase KET energies remains a challenge, even for prototypical acetone. In Part I, keto-enol tautomers of acetone were incorporated into solvent clusters that interact via uninterrupted, cyclic hydrogen-bonding (UCHB) networks. An empirical model was created to predict accurate KET energies, Etaut, of simple carbonyl compounds. Based on the availability of experimental data and structural simplicity, acetone was selected as a prototype. A discrete-continuum strategy was employed – accounting simultaneously for local noncovalent interactions and bulk-phase effects – wherein acetone, bound to water clusters of size (H2O)n n = 1–4, was paired with implicit solvent, represented by the polarized continuum model (PCM). Geometry optimizations and harmonic vibrational frequency calculations were completed using the B3LYP, ωΒ97Χ-D, and M06-2X hybrid density functionals paired with Dunning’s correlation-consistent basis sets cc-pV[D,T]Z with maug-, jul-, and aug- diffuse functions. Results were compared to second-order Møller–Plesset perturbation theory (MP2) and the experimental value of Etaut = -11.36 ± 0.04 kcal/mol determined by spectrophotometric bromination. In the context of the dissertation, chemical accuracy is defined to be 1.0 kcal/mol. When using the pseudo-aromatic solvent model, MP2 predicted Etaut within chemical accuracy using the maug-cc-PVTZ basis set, and all density functionals with maug-cc-pVTZ achieved errors below 1.50 kcal/mol for Etaut. In Part II, the solvent model of tautomerization was extended to transition structure (TS) complexes of acetone and explicit water. The same density functionals and MP2 with the same basis sets were employed. Utilizing the concept of a Grotthuss mechanism to mediate proton transfer, models with a single Grotthuss chain provided reductions in activation energies from 60 kcal/mol to less than 40 kcal/mol while UCHB solvated models provided further reductions to less than 35 kcal/mol. Both the addition of Grotthuss chains and incorporation into UCHB solvent networks were necessary to achieve stabilization. In efforts to model acid-catalyzed tautomerism, an excess proton was added to the UCHB structures at three separate sites on acetone. Inclusion of acetone into a solvent cluster allowed for delocalization of the proton defect along the UCHB network. At the B3LYP/jul-cc-pVDZ level of theory, an activation energy of 21.8 kcal/mol was predicted, accounting for 92% of the experimental value of 23.6 kcal/mol, reported by Kresge and coworkers. Nonetheless, the influence of a cyclic solvent network was essential in allowing redistribution of the proton defect. Incorporation of the carbonyl group on acetone into a solvent network both stabilized the keto and enol forms to achieve chemical accuracy and stabilized the TS of protonated Grotthuss chains to improve agreement with experimental values. Results indicate the necessity of UCHB networks for calculating KET energies and the emergence of a novel mechanism for acid-catalyzed enolization of ketones, namely Grotthuss tautomerism. My dissertation demonstrates the necessity of extending Pople’s diagram of computational chemistry by adding the physical model as a third dimension. In doing so, the new paradigm for computational chemistry forges agreement between computation and experiment and sets the foundation to expand my work to complex organic functionality and ultimately to a generalized theory of aqueous solvation

Excited state dynamics of bis-dehydroxycurcumin tert-butyl ester, a diketo-shifted derivative of the photosensitizer curcumin

Bis-dehydroxycurcumin tert-butyl ester (K2T23) is a derivative of the natural spice curcumin. Curcumin is widely studied for its multiple therapeutic properties, including photosensitized cytotoxicity. However, the full exploitation of curcumin phototoxic potential is hindered by the extreme instability of its excited state, caused by very efficient non radiative decay by means of transfer of the enolic proton to the nearby keto oxygen. K2T23 is designed to exhibit a tautomeric equilibrium shifted toward the diketo conformers with respect to natural curcumin. This property should endow K2T23 with superior excited-state stability when excited in the UVB band, i.e., in correspondence of the diketo conformers absorption peaks, making this compound an interesting candidate for topical photodynamic therapy of, e.g., skin tumors or oral infections. In this work, the tautomeric equilibrium of K2T23 between the keto-enolic and diketo conformers is assessed in the ground state in several organic solvents by UV-visible absorption and by nuclear magnetic resonance. The same tautomeric equilibrium is also probed in the excited-state in the same environments by means of steady-state fluorescence and time-correlated single-photon counting measurements. These techniques are also exploited to elucidate the excited state dynamics and excited-state deactivation pathways of K2T23, which are compared to those determined for several other curcuminoids characterized in previous works of ours. The ability of K2T23 in photosensitizing the production of singlet oxygen is compared with that of curcumin

Role of tautomerism in RNA biochemistry

Heterocyclic nucleic acid bases and their analogs can adopt multiple tautomeric forms due to the presence of multiple solvent-exchangeable protons. In DNA, spontaneous formation of minor tautomers has been speculated to contribute to mutagenic mispairings during DNA replication, whereas in RNA, minor tautomeric forms have been proposed to enhance the structural and functional diversity of RNA enzymes and aptamers. This review summarizes the role of tautomerism in RNA biochemistry, specifically focusing on the role of tautomerism in catalysis of small self-cleaving ribozymes and recognition of ligand analogs by riboswitches. Considering that the presence of multiple tautomers of nucleic acid bases is a rare occurrence, and that tautomers typically interconvert on a fast time scale, methods for studying rapid tautomerism in the context of nucleic acids under biologically relevant aqueous conditions are also discussed.National Institutes of Health (U.S.) (Grant P01 CA26731)National Institutes of Health (U.S.) (Grant R37 CA080024)National Institutes of Health (U.S.) (Grant P30 ES002109)National Institutes of Health (U.S.) (Training Grant T32 ES007020

Computational Investigations of Catalyzed Organic Reactions: Carbocatalysis, Biocatalysis, Metal and Organo Catalysis

This thesis comprises most of the computational results obtained during the three year Chemistry Ph.D course, during which the research activity mainly focused on investigating catalyzed reaction mechanisms. Catalysis is a vast phenomenon and this dissertation does not presume to cover its extent, nor to be a mere list of computational investigations. The purpose is to stress out that computational organic chemistry is a tool to be exploited to explain how and why some reactions prefer to cover one path rather than another by interpreting computation outcomes. Among the immense world of catalysts, the activity of carbon nanoparticles, enzymes, metal complex and proline in catalyzed organic reactions were investigated. Commercially available software for molecular computations were used to carry out the investigations. The thesis is divided in few parts; the former (Part I) provides some insights into the computational methods used during the PhD activity where Quantum-Mechanics (QM), Molecular-Mechanics (MM) and hybrid QM/MM methods are briefly described. Parts II-V gather the results obtained during the PhD activity. In Part II, two examples of carbo-catalyzed reactions are reported, while Part III and IV collect the computational evidences achieved by analysing the reaction mechanism of enzymatic and metal- (or organo-) catalyzed reactions respectively. The last Part (V) includes two, among the many, side works that were carried out during the PhD course. A résumé of the computational results is reported in Part VI

Ruthenium-thymine acetate binding modes: Experimental and theoretical studies

Ruthenium complexes have proved to exhibit antineoplastic activity, related to the interaction of the metal ion with DNA. In this context, synthetic and theoretical studies on ruthenium binding modes of thymine acetate (THAc) have been focused to shed light on the structure-activity relationship. This report deals with the reaction between dihydride ruthenium mer-[Ru(H)2(CO)(PPh3)3], 1 and the thymine acetic acid (THAcOH) selected as model for nucleobase derivatives. The reaction in refluxing toluene between 1 and THAcOH excess, by H2 release affords the double coordinating species k1-(O)THAc-, k2-(O,O)THAc-[Ru(CO)(PPh3)2], 2. The X-ray crystal structure confirms a simultaneous monohapto, dihapto- THAc coordination in a reciprocal facial disposition. Stepwise additions of THAcOH allowed to intercept the monohapto mer-k1(O)THAc-Ru(CO)H(PPh3)3] 3 and dihapto trans(P,P)-k2(O,O)THAc-[Ru(CO)H(PPh3)2] 4 species. Nuclear magnetic resonance (NMR) studies, associated with DFT (Density Function Theory)-calculations energies and analogous reactions with acetic acid, supported the proposed reaction path. As evidenced by the crystal supramolecular hydrogen-binding packing and 1H NMR spectra, metal coordination seems to play a pivotal role in stabilizing the minor [(N=C(OH)] lactim tautomers, which may promote mismatching to DNA nucleobase pairs as a clue for its anticancer activity