ULTRAVIOLET PHOTOCHEMISTRY OF THYMINE IN AQUEOUS SOLUTION

Abstract— We have investigated the ultraviolet photochemistry of thymine in aqueous solution. Four isomeric dimers are produced, and the yield of each has been measured as a function of thymine concentration, oxygen concentration, and temperature. At low thymine concentration, dimerization proceeds via the triplet state, while at high concentration it arises mainly from aggregates, probably from a singlet precursor. We have determined the ratios of rate constants for the triplet state mechanism and the quantum yield for dimerization from aggregates. The quantum yield for dimerization from the triplet state in thymine is smaller by a factor of about 10 than that in uracil, which in turn is smaller by another factor of 10 than that in orotic acid. It increases with the energy of the exciting radiation in a manner similar to the behaviour of uracil and orotic acid. On the other hand, dimer formation from aggregates is independent of photon energy. Dimerization from aggregates decreases with increasing temperature, while the total production of dimers from the triplet state is independent of temperature.     

Thermodynamic study of the dimerization of 8-anilino-1-naphthalenesulfonic acid by isothermal titration calorimetry

Dimerization of the fluorescence probe, 8-anilino-1-naphthalenesulfonic acid (ANS) in aqueous media have been studied by isothermal titration calorimetry (ITC). ITC experiments carried out at different pHs show that dimerization constants are highly pH dependent, decreasing their values with increasing pH. No dimerization is detected over pH 7. Analyzing the dependence of K_dim on pH, using a model that only considers dimers between zwitterionic molecules of ANS, a value of 5.6 for the pK of anilinium moiety is obtained. It is in agreement with the pK determined spectrophotometrically. The dimerization process is enthalpically disfavored and entropically driven at all pH and temperatures studied, indicating that hydrophobic effect has an important role on the formation of dimers. Although dimerization constants are low, dimerization equilibria must be taken into account when the energetics of the interaction of ANS to a protein is studied at pH below 7.     

Water dimer equilibrium constant of saturated vapor

The value and temperature dependence of the dimerization constant for saturated water vapor are determined. A general expression that links the second virial coefficient and the dimerization constant is obtained. It is shown that the attraction between water monomers and dimers is fundamental, especially at T > 350 K. The range of application for the obtained results is determined.     

The use of similarity profiles in studying cluster formation in molecular beams: Evidence for the role of pre-existing dimers

Studies of the influence of source temperatures and pressures on the distributions of water, ammonia and sulfur dioxide clusters are reported. The experiments reveal that nearly identical cluster distributions occur in cases where the pressure of dimer is maintained constant according to a simple equation involving stagnation temperature and pressure. In similar experiments covering the same range of pressures and temperatures, widely differing cluster distributions are obtained under conditions where the dimer concentration is not fixed. Our results suggest that large clusters proceed largely from pre-existing dimers, and that very few new ones are created early enough in the expansion to effect cluster growth. The gas-phase heat of dimerization of sulfur dioxide is determined to be 4.3 ± 0.3 kcal/mole.     

Elementary peptide motifs in the gas phase: FTIR aggregation study of formamide, acetamide, N-methylformamide, and N-methylacetamide

Cold, isolated peptide model compounds and their aggregates are generated in pulsed supersonic jet expansions and detected by FTIR spectroscopy in the amide-A region, complemented by amide-I spectra. The most stable, symmetric dimer of formamide is unambiguously assigned in the gas phase for the first time, also by comparison to the analogous acetamide dimer. Efficient quenching of a hot-state Fermi resonance by cooling of the dimers is invoked. As the preferred relative orientation of the C=O and N-H groups in N-methylated formamide and acetamide is trans, these compounds show a fundamentally different dimerization pattern. Their most stable dimers, which would be analogous to those of formamide and acetamide, remain undetected as a consequence of kinetic control in the jet. Accurate benchmark quantities for multidimensional vibrational treatments of these peptide models are derived, and the influence of methyl groups on the N-H stretching dynamics is discussed.     

Photophysical studies of the pheophorbide a dimer

This work reports on a monomer-dimer equilibrium state of pheophorbide a in solution. A methodology for controlling the equilibrium constant by use of temperature and solvent variation is described. The absorption spectrum of the dimer is calculated, using different prepared equilibria of monomer and dimer in solution. We propose that these aggregates provide a good model for understanding the dimerization process in tetrapyrroles.     

Thermodynamics of association for benzene-benzyl alcohol,benzene-phenethyl alcohol,and fluorobenzene-benzyl alcohol in dilute aqueous solution

Vapor pressure measurements have been made on dilute aqueous solutions of benzene-benzyl alcohol (BZOH), benzene-phenethyl alcohol (PEOH), and fluorobenzene-BZOH at 15, 25, 35, and 45°C. The benzene results have been interpreted with a mass action model which attributes deviations from ideality to the formation of benzene dimers and heterodimers with BZOH and PEOH. The benzene heterodimers form endothermically at 25°C with large and negative heat capacity changes. The dimerization constant for the benzene-BZOH dimer reaches a maximum of 0.57 M^–1 at about 37°C, while the benzene-PEOH dimer reaches a maximum of 0.60 M^–1 around 30°C. The fluorobenzene results have been interpreted with a mass action model which, in addition to fluorobenzene dimers and heterodimers, includes the formation of a fluorobenzene-BZOH trimer. Thermodynamic properties for these aggregates are reported and compared with results obtained in previous studies.     

Characterization of a novel water-soluble 3,4,9,10-perylenetetracarboxylic diimide in solution and in self-assembled zirconium phosphonate thin films

The properties of N,N'-bis(2-phosphonoethyl)-3,4,9,10-perylenetetracarboxylic diimide (PPDI), a water-soluble perylene dye, have been studied in solution and in thin films. Absorption spectra showed that PPDI exists in the monomeric form in water/ethanol (1:1) and water/dimethyl sulfoxide (DMSO) (3:7) mixtures, but forms dimers in water and higher aggregates in ethanol. The PPDI monomer is highly fluorescent, in contrast to the dimers and aggregates, which are nonfluorescent. The monomer/dimer equilibrium was conveniently followed in a water/ethanol (7:3) mixture by varying the dye concentration. An equilibrium constant of K = 1.25 x 10(5) M(-1) was estimated for the dimerization process in this solvent mixture. The addition of cetyl trimethylammonium bromide (CTAB), a cationic surfactant, to aqueous solutions of PPDI resulted in the dissociation of the dimers, showing that the dye was incorporated into the micellar phase. Self-assembled thin films of PPDI were grown on both silica gel particles and flat surfaces, using zirconium phosphonate chemistry. The growth of multilayered films on flat surfaces was monitored by ellipsometry (silicon substrates) and UV/Vis spectroscopy (quartz slides), and was linear with the number of deposition cycles. No fluorescence was detected from the PPDI films, and the absorption spectra of the films were quite similar to the spectrum of the compound in ethanol, indicating that the dye molecules were stacked in the films. Mixed monolayers containing PPDI and N,N'-bis(2-phosphonoethyl)-1,4,5,8-naphthalenediimide (PNDI) on quartz were also prepared. Monolayers obtained by codeposition from solutions containing both PPDI and PNDI were richer in PPDI, even when the solution contained a large excess of the naphthalene derivative, showing that pi-stacking of PPDI is an important driving force in the formation of the films.     

Synthesis of a New Cationic Pyropheophorbide Derivative and Studies of its Aggregation Process in Aqueous Solution

Abstract— A new water-soluble cationic pyropheophorbide was prepared from pyropheophorbide a by a Curtius rearrangement. The self-aggregation process of this chlorhydrate of aminopyropheophorbide was investigated from the changes observed in its spectroscopic properties when passing from ethanol to aqueous solutions. The formation of aggregates was characterized in the absorption spectrum by a broadening of the Qy band, which is slightly shifted to the red, a significant increase in signals of circular dichroism and a drastic quenching of the fluorescence intensity at 674 nm. Analysis of the nonlinear variation of the fluorescence intensity with the dye concentration in Tris-buffered solutions shows that dimerization is the dominant aggregation process. The dimerization equilibrium constant(at 25_AoC, pH 7.5 in 5 m M Tris buffer, 10 m M NaCl) was determined to be 3.10₆ M _-l. NMR measurements performed in DMSO at various dye concentrations showed that only the chemical shifts of some atoms are affected by these changes, indicating the part of the ring involved in the overlap of the two molecules in the dimer.A molecular modeling study of the packing arrangement of the aminopyropheophorbide molecules in aggregates performed by both semi-empirical quantum chemical PM3 and force field MM2 methods provided a structure consistent with these spectroscopic data.     

Synthesis of new porphyrins with peripheral conjugated chelates and their use for the preparation of porphyrin dimers linked by metal ions

This article describes the preparation of several new porphyrins bearing chelating peripheral groups fully conjugated with the macrocyclic pi-system. Treatment of a 2-nitro-meso-tetraarylporphyrin with phosphite gave a cyclic enamine, whose formylation gave an enaminoaldehyde. The thio analogue was obtained on treatment with Lawesson's reagent. The same reagent was also used to obtain the isomeric thioenaminoketone chelates. A enaminoketone ligand was prepared from a porphyrinic pyrrolone. All these ligands, as internal nickel complexes, could be metalated with palladium to yield porphyrinic dimers. The dimers obtained from enaminoketones and thioketones show a trans geometry, while in the enaminoaldehyde and -thioaldehyde series the cis isomer is thermodynamically favored. The bathochromic shifts of the electronic spectra of the aldehyde-derived dimers illustrate the strong electronic effect of peripheral metalation and dimerization. However, in the case of the pyrrolone-derived ligand, opposite effects were observed, due to partial reconstitution of the porphyrin chromophore on complexation. As with the dimers derived from enaminoketones, the dimers derived from the new ligands show typical splitting (up to 190 mV) of the electrochemical waves confirming large porphyrin-porphyrin interactions.     

Structural aspects of two-stage dimerization in an ionic C60 complex with bis(benzene)chromium: Cr(C6H6)2.C60.C6H4Cl2

Single crystals of the ionic C60 complex with bis(benzene)chromium: {Cr(I)(C6H6)2(.+)}.(C60.-)).C6H4Cl2 (1) were obtained. The crystal structure of 1 shows the presence of monomeric C60.- radical anions at 250 K and the formation of single-bonded (C60-)2 dimers at 90 K. The dimerization is realized in two types of the C60.-) pairs with different interfullerene center-to-center distances of 10.052 and 10.279 A arranged in zigzag chains along the a-direction. As a result, two symmetrically independent (C60-)2 dimers found in 1 at 90 K have different environments, intercage C-C bond lengths and C60- center-to-center distances. Such differences should provide different thermal stability of these dimers and result in the appearance of two stages at the dimerization. Indeed, according to SQUID measurements, the magnetic moment of 1 decreases stepwise at the dimerization in two temperature ranges at 240-200 and 200-160 K.     

Structural evolution of aqueous NaCl solutions dissolved in supercritical carbon dioxide under isobaric heating by mid and near infrared spectroscopy

The local order in aqueous NaCl solutions diluted in supercritical carbon dioxide at constant pressure as a function of NaCl concentration and temperature has been investigated using near and mid infrared absorption spectroscopy. The near IR results have allowed us to estimate the water concentration in CO(2) rich phase, whereas the state of water aggregation in CO(2) phase was investigated using mid IR spectroscopy. The analysis of the band shape variations of the OD stretching mode of HOD led us to conclude that below 100 degrees C, water molecules dissolved in CO(2) exist only under their monomeric form, whatever the salt concentration is, whereas hydrogen-bonded species, namely, dimers start to appear at higher temperatures. Larger aggregates have a negligible concentration in the range of temperature-pressure investigated. Using near and mid infrared data, we have calculated the concentrations of water species in the CO(2) phase. Upon heating, it was found that the concentration of dimers considerably increases at the expense of the monomers and only dimers are detected in carbon dioxide at highest temperatures. Changing the salt concentration affects significantly the concentration of monomers and decreases strongly the dimers population as the solution becomes progressively saturated in salt. In the saturated solution, at 340 degrees C, the dimer concentration is at least two times smaller than in the binary water-CO(2) mixture. These findings are in qualitative agreement with existing thermodynamics data showing that addition of NaCl to the binary H(2)O-CO(2) system shifts the range of partial miscibility of water and CO(2) towards higher pressure and temperature.     

New approach to IR study of monomer-dimer self-association: 2,2-dimethyl-3-ethyl-3-pentanol in tetrachloroethylene as an example

The dimerization of 2,2-dimethyl-3-ethyl-3-pentanol in tetrachloroethylene in the diluted region has been studied at four temperatures by IR spectroscopy. The aforementioned solute compound is chosen because self-association beyond dimerization is hampered by the steric hindrance generated by the bulky sidechains. The integrated absorbances of the monomer bands were treated based on Eq. (9) to obtain its molar absorptivity and dimerization constant. The same dimerization constant as well as the molar absorptivity of dimer band can be obtained based on Eq. (13) from the data treatment of the integrated absorbances of the dimer band. The disparity between two values of dimerization constant determined by two independent sources offers an opportunity to check the consistency of the determination. The standard enthalpy and entropy of dimerization have also been calculated by means of van't Hoff plot, respectively, from the data of temperature-dependent dimerization constants obtained from the monomer bands and dimer bands.     

Thermodynamic properties of the benzene-phenol dimer in dilute aqueous solution

Precise vapor pressure-solubility measurements have been obtained for dilute solutions of benzene and phenol in water at 15, 25, 35 and 45°C. All of the results are consistent with a mass action model that attributes deviations from ideal solution behavior to the formation of benzene dimers and hetero-dimers between benzene and phenol. The benzene-phenol dimer forms endothermically at 25°C, with a very large negative heat capacity, and a formation constant that reaches a maximum value of 0.66 l-mol^?1 at approximately 35°C. Thermodynamic properties of the benzene-phenol dimer are reported and compared with those of other aggregates that are believed to be stabilized primarily by hydrophobic interactions.     

Carboxylated zinc-phthalocyanines--II. Dimerization and singlet molecular oxygen sensitization in hexadecyltrimethylammonium bromide micelles.

The dimerization of the diamide of zinc-tetracarboxyphthalocyanine was studied spectroscopically in hexadecyltrimethylammonium bromide (CTAB) micelles at surfactant concentrations from 0.026 to 0.1 M and dye concentrations between 0.1 and 10 microM. The apparent dimerization constant in CTAB 0.1 M is 8.6 x 10(5) M-1, while the intramicellar dimerization constant is 1.8 x 10(3). The dimer absorption spectrum was also obtained. Singlet molecular oxygen sensitization was studied by steady state photolysis using 1,3-diphenylisobenzofurane as scavenger in 0.1 M CTAB. The usual sensitization mechanism is extended to include dimer reactions. Singlet molecular oxygen sensitization yields for monomer and dimer in the micelles are 0.7 and 0.1, respectively. With the reported values it is possible to calculate the average yield of singlet molecular oxygen production at any surfactant and dye concentrations.     

IR Study of Monomer–Dimer Self-association of 2,2-Dimethyl-3-ethyl-3-pentanol in n-Octane: Determination of the Molar Absorptivities of Monomer and Dimer Bands, and Dimerization Constants Using Novel Equations

The monomer–dimer self-association equilibrium of 2,2-dimethyl-3-ethyl-3-pentanol in n-octane has been studied by IR spectroscopy at four temperatures (288, 298, 308, and 318 K). The solute was chosen to restrict the self-association between solute molecules to dimerization only, owing to steric hindrance of the bulky chains in the vicinity of the OH group. Two linear equations have been derived for the treatment of the experimental data. One of these equations was used to treat the data of the concentration dependent integrated absorbance of the monomer bands for each temperature to obtain the monomer molar absorptivity, ε _m, and dimerization constant, K. The other equation was used to treat the data of concentration-dependent dimer bands to obtain the dimer molar absorptivity, ε _d, and K. Thus, the dimerization constant was determined by two methods. Since the same thermodynamic quantity K is obtained from either the monomer bands or the dimer bands, the difference between them at a given temperature can serve as an assessment of the quality of the experiment. The standard enthalpy and entropy of dimerization were also obtained from a van’t Hoff plot.     

A DFT study on the dimerization of C62, H2-C62, and F2-C62

On the basis of calculations using the density functional theory, we show that C(62), a recently synthesized nonclassical fullerene, will presumably undergo dimerization with various isomers at elevated temperatures. This is shown by calculating the dimerization energy and the activation barrier of the dimerization. Eight possible isomers of the dimer were identified, all of which are more stable than the two isolated monomers. The relative stability of various isomers depends upon the kind of C=C bonds within the four-membered carbon ring involved in the dimerization. In addition, similar calculations were performed for the monomers and dimers of H(2)-C(62) and F(2)-C(62). Six isomers were identified for each of the dimers. Although less pronounced than the case of the C(62) dimer, all isomers of the H(2)-C(62) dimer are appreciably more stable than the individual monomers. Although a large steric repulsion due to F atoms significantly reduces the stability of F(2)-C(62) dimer, its two isomers are still more stable than separate monomers.     

Aggregation of acetic and propionic acid in argon matrices--a matrix isolation and computational study

Monomeric acetic acid MA and propionic acid MP were isolated in argon matrices at 10K by using a pulse deposition technique. The dimerization of the monomers was induced by warming the matrices from 10 to 40 K. Under these conditions the diffusion of small trapped molecules is rapid and the dimerization could be monitored directly by IR spectroscopy. Both carboxylic acids form the symmetrical dimers B with two strong C=O...HO hydrogen bridges as the thermodynamically most stable dimers. With acetic acid a less stable dimer AA could be obtained if high concentrations of acetic acid in argon were used during the deposition of the matrix. On annealing this dimer rearranges to the more stable BA. In contrast, propionic acid does not form a corresponding less stable dimer under any experimental condition. These observations are rationalized on the basis of DFT and ab initio calculations.     

Substituent effects on the assembly of helical cyanine dye aggregates in the minor groove of a DNA template

Double-helical DNA was used as a template for the assembly of helical cyanine dye aggregates. The aggregates consist of cofacial dimers aligned end-to-end in the minor groove of the DNA. The effect of methoxy or fluoro substituents placed on the periphery of the cyanine dye heterocycles on aggregation both in water and on the DNA template was studied by UV-vis and circular dichroism spectroscopy. Methoxy groups were found to be stronger promoters of aggregation than fluoro, and a dimethoxy dye exhibited a higher propensity to aggregate compared with an unsymmetrical methoxy/fluoro dye. Semiempirical calculations supported the experimental observation of methoxy substitution favoring aggregation. These results indicate that dispersion and hydrophobic effects contribute more to dimerization/aggregation than do electron donor-acceptor effects.     

The role of the methylene blue and toluidine blue monomers and dimers in the photoinactivation of bacteria

The interactions between the phenothiazine dyes, methylene blue (MB) and toluidine blue (TB), and bacteria (Staphylococcus aureus, Streptococcus pneumoniae, Enterococcus faecalis, Hemophilus influenzae, Escherichia coli and Pseudomonas aeruginosa) were studied spectrophotometrically. This demonstrated that a metachromatic reaction took place between the dyes and bacteria. Furthermore, bacteria induced additional dimerization of MB and TB. The effective dimerization constants of MB and TB were evaluated in the presence of each bacterial strain at a concentration of 10(8) CFU/ml. The analysis of the effective dimerization constants for MB and TB in the presence of bacteria indicated that the ability to form dimers was greater for TB than for MB. Gram-negative bacteria induced the dye dimerization more intensely than gram-positive bacteria. There was a correlation between the ability of each dye to form dimers in the presence of bacteria and the relative photobactericidal efficacy of each dye against these bacteria. These results provide evidence confirming the essential role of the dye dimers in bacterial photodamage.