Excited state proton transfer in guanine in the gas phase and in water solution: a theoretical study

Theoretical investigations were performed to study the phenomena of ground and electronic excited state proton transfer in the isolated and monohydrated forms of guanine. Ground and transition state geometries were optimized at both the B3LYP/6-311++G(d,p) and HF/6-311G(d,p) levels. The geometries of tautomers including those of transition states corresponding to the proton transfer from the keto to the enol form of guanine were also optimized in the lowest singlet pipi* excited state using the configuration interaction singles (CIS) method and the 6-311G(d,p) basis set. The time-dependent density function theory method augmented with the B3LYP functional (TD-B3LYP) and the 6-311++G(d,p) basis set was used to compute vertical transition energies using the B3LYP/6-311++G(d,p) geometries. The TD-B3LYP/6-311++G(d,p) calculations were also performed using the CIS/6-311G(d,p) geometries to predict the adiabatic transition energies of different tautomers and the excited state proton transfer barrier heights of guanine tautomerization. The effect of the bulk aqueous environment was considered using the polarizable continuum model (PCM). The harmonic vibrational frequency calculations were performed to ascertain the nature of potential energy surfaces. The excited state geometries including that of transition states were found to be largely nonplanar. The nonplanar fragment was mostly localized in the six-membered ring. Geometries of the hydrated transition states in the ground and lowest singlet pipi* excited states were found to be zwitterionic in which the water molecule is in the form of hydronium cation (H3O(+)) and guanine is in the anionic form, except for the N9H form in the excited state where water molecule is in the hydroxyl anionic form (OH(-)) and the guanine is in the cationic form. It was found that proton transfer is characterized by a high barrier height both in the gas phase and in the bulk water solution. The explicit inclusion of a water molecule in the proton transfer reaction path reduces the barrier height drastically. The excited state barrier height was generally found to be increased as compared to that in the ground state. On the basis of the current theoretical calculation it appears that the singlet electronic excitation of guanine may not facilitate the excited state proton transfer corresponding to the tautomerization of the keto to the enol form.     

Excited-state proton transfer behavior of 7-hydroxy-4-methylcoumarin in AOT reverse micelles

The excited-state proton transfer and phototautomerization of 7-hydroxy-4-methylcoumarin (7H4MC) dye has been studied in the confined water pools of AOT reverse micelles using steady-state and time-resolved fluorescence measurements. In the "dry" reverse micelles ([water]/[AOT], w(0) = 0), only the neutral form of the dye is present both in the ground and the excited states. At higher w(0) values, three prototropic forms, namely, neutral, anionic, and tautomeric, can be identified in the excited state, although only the neutral form of the dye is present in the ground state. From steady-state fluorescence results and time-resolved area-normalized emission spectra (TRANES), it is indicated that the anionic and tautomeric forms of the dye are the excited-state reaction products and that they arise apparently independently from the excited neutral form of the dye. In bulk water, however, there is no evidence of the tautomeric species and only the anionic form is observed in the excited state. The fluorescence quenching results of the three forms of 7H4MC by the different quenchers, potassium iodide, aniline, and N, N-dimethylaniline, suggest that the distribution of 7H4MC molecules in the reverse micelles is not diverse but that the different prototropic forms arise from the same population of the excited dye in the interfacial region.     

Influence of solvent properties on fluorescence probes. 7-amino- and 7-n-dimethylamino-4-methylcoumarin

The shift of the maximum wavenumber of 7-amino- and 7-N-dimethylamino-4-methylcoumarin as a function of solvent properties is investigated and compared to that of other probes. The observed changes are interpreted on the basis of solvent polarity and, specially, of solvent cohesion, unifying previous interpretations by Kosower and Reeves.     

Excited-state proton transfer in 7-hydroxy-4-methylcoumarin along a hydrogen-bonded water wire

TDDFT, RI-CC2, and CIS calculations have been performed for the nondissociative excited-state proton transfer (ESPT) in the S1 state of 7-hydroxy-4-methylcoumarin (7H4MC) along a H-bonded water wire of three water molecules bridging the proton donor (OH) and the proton acceptor (C[double bond]O) groups (7H4MC.(H2O)3). The observed structural reorganization in the water-wire cluster is interpreted as a proton-transfer (PT) reaction along the H2O solvent wire. The shift of electron density within the organic chromophore 7H4MC due to the optical excitation appears to be the driving force for ESPT. All the methods used show that the reaction path occurs in the 1pipi* state, and no crossing with a Rydberg-type 1pisigma* state is found. TDDFT and RI-CC2 calculations predict an exoergic reaction of the excited-state enol-to-keto transformation. The S1 potential energy curve reveals well-defined Cs minima of enol- and keto-clusters, separated by a single barrier with a height of 17-20 kcal/mol. After surmounting this barrier, spontaneous PT along the water wire is observed, leading without any further barrier to the keto structure. The TDDFT and RI-CC2 methods appear to be reliable approaches to describe the energy surfaces of ESPT. The CIS method predicts an endoergic ESPT reaction and an energy barrier, which is too high.     

Phosphorous disulfide and its ions in the electronic ground state: a gas phase theoretical study

Ab initio molecular orbital theory and density functional theory calculations were performed on the electronic ground states of the open-shell PS₂ molecule and its singly charged ions. A comparison of the optimized molecular structures indicates as the stepwise one-electron reduction of the PS₂⁺ ion, to yield PS₂ and PS₂⁻, provokes a symmetric elongation of both PS bonds along with a bending of its linear equilibrium geometry. The ionization potential (IP), adiabatic electron affinity (EA_ad), and atomization energy (AE) of the open-shell PS₂ molecule were calculated at different levels of theory. The following values were obtained at the more realistic UMP4SDTQ/6-311+G(3df)//UHF/6-311+G(3df) level of theory: IP=8.32 eV, EA_ad=3.03 eV and AE=12.40 eV. At the same level of theory, the calculated vertical detachment energy (VDE) of the PS₂⁻ anion is 3.22 eV. The donor–acceptor complexes formed in the gas-phase upon interaction of either one or two ammonia molecules with PS₂⁺ were also investigated. The calculated gas-phase binding energies indicate that the formation of the bis-adduct is favored over that of the mono-adduct by a binding energy gain of about 20 kcal/mol.     

Structure and isomerization of arenonium ions of dichlorobenzenes in the gas phase. A theoretical study

Ab initio MP2 calculations of all isomeric arenoium ions (AI) ofortho-, meta-, andpara-dichlorobenzenes in the gas phase were carried out with full optimization of geometry with the 6–31 G^* basis set. The calculated proton affinities depend substantially on the position of geminal center in the corresponding dichlorobenzenonium ion and decrease in the series 1,2-dichloro-4H-benzenonium>1,2-dichloro-3H-benzenonium>1,2-dichloro-2H-benzenonium; 1,3-dichloro-4H-benzenonium>1,2-dichloro-3H-benzenonium >1,3-dichloro-5H-benzenonium>1,3-dichloro-3H-benzenonium; 1,4-dichloro-2H-benzenonium >1,4-dichloro-4H-benzenonium. The structures of transition states and activation energies (E _a) of almost all 1,2-shifts of H and Cl atoms in Al were determined. The activation energies of migrations of H atoms are about 6 kcal mol⁻¹ less than those of migrations of Cl atoms in similar structures. The isomerization routes and relations between the rate constants for isomerization of dichlorobenzenes through Al were established. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1726–1731, September, 1998.     

Systematic theoretical investigations on the tautomers of thymine in gas phase and solution

The tautomers of thymine are systematically calculated using various methods. The order of the relative stability, dipole moment as well as solvent effect of the 13 isomers are investigated. The one-step transition process by proton transfer in gas phase and in solution (H₂O or CH₃OH), which acts as both proton donor and acceptor, are exhaustively studied, meanwhile, the internal rotation between two related isomers in the gas phase is also investigated. Furthermore, the energy barrier of each transition is calculated and the results show that both H₂O and CH₃OH could reduce the energy barrier. Comparisons between the activation energies of all the producing processes of each tautomer as well as temperature effect on the producing processes are made. The calculation results also indicated that the diketo is the most stable isomer both in gas phase and in solution, additionally, it is thermodynamically as well as dynamically favored.     

A photoionization study of [C4H7]+ ions in the gas phase

The ionization and [C₄H₇]⁺ appearance energies for a series of C₄H₇CI and C₄H₇Br isomers have been measured by dissociative photoionization mass spectrometry. Cationic heats of formation, based on the stationary electron convention, are derived. No threshold ion is observed with a heat of formation corresponding to the trans-1-methylallyl cation, although there is evidence for formation of the less stable cis isomer. A 298 K heat of formation of 871 kJ mol^?1 is obtained for the cyclopropylcarbinyl cation, with the cyclobutyl cation having a higher value of 886 kJ mol^?1. At the HF/6-31G^** level, ab initio molecular orbital calculations show the 2-butenyl, isobutenyl and homoallyl cations to be stable forms of [C₄H₇]⁺, being less stable than the trans-1-methylallyl cation by 101 kJ mol^?1, 159 kJ mol^?1 and 164 kJ mol^?1, respectively. However, threshold formation is not observed for any of these ions, the fragmentation of appropriate precursor molecules producing [C₄H₇]⁺ ions with lower energy structures.     

Excited state properties and quadratic optical nonlinearities in charged organic chromophores: theoretical analysis

As it has been found experimentally [K. Clays and B. Coe, Chem. Mater. 15, 642 (2003); B. J. Coe et al., 126, 10418 (2004)], elongation of the conjugation path length and N-arylation in stilbazolium chromophores both lead to substantial enhancement of the molecular optical nonlinearities. In the present contribution the authors perform a quantum chemical analysis of the excited state properties and quadratic nonlinear optical responses of a series of this type of dyes. Nonlinear optical responses are estimated by both finite-field and two-state model approaches that demonstrate an excellent qualitative mutual agreement. Time-dependent density functional theory calculations on the isolated cations predict redshift in the energy of the intramolecular charge transfer transition that is overestimated for cations with the longer conjugation path length. At the same time, in comparison with the Stark spectroscopy measurements the differences between the excited and ground state dipole moments are grossly underestimated for all compounds. The inclusion of solvent effect by polarizable continuum model affords a better agreement with experiment for these quantities. The authors' calculations demonstrate the crucial dependence of the electronic excitation properties on the way of the investigated compound geometry optimization. The origin of such dependence is discussed.     

Acetylene cyclotrimerization by early second-row transition metals in the gas phase. A theoretical study

The acetylene cyclotrimerization reaction mediated by the left-hand-side bare transition metal atoms Y, Zr, Nb, and Mo has been studied theoretically, employing DFT in its B3LYP formulation. The complete reaction mechanism has been analyzed, identifying intermediates and transition states. Both the ground spin state and at least one low-lying excited state have been considered to establish whether possible spin crossings between surfaces of different multiplicity can occur. Our results show that the overall reaction is highly favorable from a thermodynamic point of view and ground state transition states lie always below the energy limit represented by ground state reactants. After the activation of two acetylene molecules and formation of a bis-ligated complex, the reaction proceeds to give a metallacycle intermediate, as the alternative formation of a cyclobutadiene complex is energetically disfavored. All the examined reaction paths involve formation of a metallacycloheptatriene intermediate that in turn generates a metal-benzene adduct from which finally benzene is released. Similarities and differences in the behaviors of the considered four metal atoms have been examined.     

A theoretical study on the mechanism and thermodynamics of ozone-water gas phase reaction

Ozone water reaction including a complex was studied at the MP2/6-311++G(d,p) and CCSD/6-311++G(2df,2p)//MP2/6-311++G(d,p) levels of theory. The interaction between water oxygen and central oxygen of ozone produces stable H₂O-O₃ complex with no barrier. With decomposition of this complex through H-abstraction by O₃ and O-abstraction by H₂O, three possible product channels were found. Intrinsic reaction coordinate, topological analyses of atom in molecule, and vibrational frequency calculation have been used to confirm the preferred mechanism. Thermodynamic data at T = 298.15 K and atmospheric pressure have been calculated. The results show that the production of hydrogen peroxide is the main reaction channel with ΔG = ?21.112 kJ mol^-1.     

Ring opening reaction of protonated polyfluorinated benzenes in the gas phase. A theoretical MNDO study

The MNDO calculations of protonated polyfluorobenzenes [Ph-F_n]H⁺ indicate the possibility of a relatively free migration of the hydrogen proton with energy barriers of 125–145 kJ mol^?1. At a higher degree of substitution (n) the protonation of the ipso carbon atom occupied by fluorine becomes energetically feasible, along with analogous migrations of fluorine, which, however, are energetically the most advantageous (ΔE_a ～ 230 kJ mol^?1). In addition to bridged fluoronium ions, relatively stable cyclic intermediates were also found, which make possible a rearrangement to the difluoromethylenecyclopentadienyl cation and thus the elimination of CF₂ observed in collision-induced dissociation mass spectra.     

Multiple fluorescence spectra and stable encapsulation of 7-hydroxy-4-methylcoumarin and rhodamine 6g in silicate glasses by the sol-gel method

7-Hydroxy-4-methylcoumarin(4-methylumbelliferone, HMC) and Rhodamine 6G(R6G) were encapsulated into silicate polymeric glass prepared by the sol-gel method under acidic, basic, and neutral conditions from tetraethyl orthosilicate. The fluorescence spectra of these molecules encapsulated into the xerogel state depend on the used catalysts. Three types of fluorescence emissions having peak wavelengths of ca. 390 nm, 470 nm, and 550 run, respectively, were observed simultaneously in the xerogel state composed of HMC and R6G which were prepared by acid catalysts. The encapsulated HMC remains stable for more than one year in the prepared xerogel. The results open the way to the development of simultaneous three-band laser emissions. The observation of the fluorescence spectrum of HMC is useful for a molecular level photophysical probe elucidating the structural changes oftetraethyl orthosilicate during sol to gel to xerogel transitions.     

Excited singlet state properties of anthracenedione photosensitizers.

The absorption, fluorescence and S1 state kinetics of anthracycline antitumour drugs (e.g. daunomycin, adriamycin) and several imino- and/or amino-substituted derivatives are investigated. The study, which includes all anthracyclines which possess photocytocidal activity, is extended to the disubstituted aminoanthracenedione, mitoxantrone, a red-light-absorbing antitumour drug whose activity, both in vitro and in vivo, is enhanced by photoactivation. The S1 state of the anthracycline imino and amino derivatives, in aqueous buffer at pH 7.4, is characterized by bi-exponential decay kinetics which indicates the presence of two ground state populations differing in the extent of hydrogen bonding. The ammonium group of the sugar moiety of anthracyclines contributes to the quenching of the S1 state population through a prototropic mechanism.     

Theoretical study on the properties of linear and cyclic amides in gas phase and water solution

The structural and energetic properties of a group of selected amides, of well-known importance for the design of efficient clathrate inhibitors, are calculated with Hartree-Fock and density functional theory, B3LYP, theoretical levels, and a 6-311++g** basis set in the gas phase and a water solution. The conformational behavior of the molecules is studied through the scanning of the torsional potential energy surfaces and by the analysis of the differences in the energetic and structural properties between the isomers. The properties of the amides in water solution are determined within a self-consistent reaction field approach with a polarizable continuum model that allows the calculation of the different contributions to the free energy of solvation. The calculated barriers to rotation are in good agreement with the available experimental data and the comparison of the gas and water results shows the strong effect of the solute polarization. The properties of different amide-water complexes are calculated and compared with available experimental information.     

Excited state properties of sizable molecules in solution: from structure to reactivity

We review some recent advances in quantum mechanical methods devised specifically for the study of excited electronic state of large size molecules in solution. The adopted theoretical/computational framework is rooted in the density functional theory (DFT) and its time-dependent extension (TD-DFT) for the characterization of ground and excited states, in the polarizable continuum model (PCM) for the treatment of bulk solvent effects, and in time-dependent quantum mechanical methods for chemical dynamics. Selected applications to the simulation of absorption spectra, to the interpretation of time-resolved experiments, and to the computation of dissociative electron transfer rates are presented and discussed.     

Mass spectrometric and theoretical study of polyiodides: the connection between solid state, solution, and gas phases

Polyiodides have been transferred intact from acetonitrile solution to the gas phase and analyzed by mass spectrometry. A range of ions were observed, including [I(11)](-), [I(13)](-), and [I(15)](-), which have higher iodine/iodide ratios than any previously characterized ions. Theoretical calculations show that branched structures are strongly favored, a result which is in excellent agreement with with gas phase fragmentation studies (MS/MS) and also previous solid state studies. This study demonstrates the utility of mass spectrometry to provide structural information in the absence of other spectroscopic handles.     

Nitrosation of thiols and thioethers in the gas phase: A combined theoretical and experimental study

Recent studies have demonstrated the biological importance of the interaction of nitric oxide with proteins such as cytochrome-c or hemoglobin. In particular, the possibility that the nitrosonium cation, NO(+), could reversibly bind to sulfide atom type was proposed. At pH values of biological relevance, nitrosation was proposed to occur through the action of NO(+) carriers such as nitrosothiols or nitrosamines. In this context, the gas phase chemistry of protonated nitrosothiols is studied in the present work by a combination of mass spectrometry and computational methods.