Thymine in Water

The general interface between the EOM-CC and EFP methods [56] allows one to exploit the advantages of various EOM techniques, such as spin-flip (SF) [93-94], ionization potential (IP) [95-96], or electron affinity (EA) [97] variants. For example, the vertical ionization energies (VIE) of thymine in an aqueous environment were investigated using the EOM-IP-CCSD/EFP method [58]. The ionization of nucleic acid bases is relevant to radiation and photoinduced damage of DNA. 

It is noteworthy that the convergence of the VIE with the number of hydration shells to the bulk value is slow and nonmonotonic, such that the first solvation shell increases the VIE by 0.1 eV, whereas the overall solvent-induced shift is -0.9 eV (see Fig. 5.8). The unexpected effect of the first hydration shell is due to specific interactions of thymine with individual water molecules. In 

investigation of hydrated thymine provides a direct evidence that explicit polarizable solvation model must be used for describing solvation effects on VI Es in nucleic bases. 

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One obvious reason for the apparent lack of reaction of thymine in water is that the quantum yield for splitting of thymine dimer in solution is 0.5-1.0,28 independent of wavelength, and the probable yield for formation would not be higher, by analogy with other pyrimidines, than... 

An excellent review on organic photochemistry in organized media, including aqueous solvent, has been reported.178 The quantum efficiency for photodimerization of thymine, uracil, and their derivatives increased considerably in water compared with other organic solvents. The increased quantum efficiency is attributed to the preassociation of the reactants at the ground state. 

The high rate of dimer formation in frozen solution reflects the necessity for a preferred orientation of the two thymine molecules concerned, but it is still considered that water plays an important part. Thymine in dried films,32,34 and on filter paper33 can be converted to dimer by ultraviolet light, but the maximum conversions are much lower, 1732-55%34 (depending upon the humidity34). 

Pyrimidine is a weaker base than pyridine because of the presence of the second nitrogen. Its conjugate acid is a much stronger acid (pATa = 1.0). The pA a values of the N-l hydrogen in uracil, thymine and cytosine are 9.5, 9.8 and 12.1, respectively. Pyrimidine is a hygroscopic solid (b.p. 123-124 °C, m.p. 20-22 °C) and soluble in water. 

Di-0-(methanesulfonyl)thymidine (248 g, 0.62 M) was added in portions to a stirred solution of sodium hydroxide (74.7 g, 1.87 M) in water (1.6 L). On addition the reaction mixture became a yellow-orange solution. This stirred solution was then heated to reflux for 2 h. Once the reaction mixture had cooled to room temperature, 6 N hydrochloric acid (100 ml) was added. The reaction mixture was concentrated in vacuo by removing 1.3 L of water. The resulting slurry was cooled in an ice bath for 2 h. The solid was then filtered and washed sparingly with ice water, and then vacuum dried to constant weight (103.7 g, 74%). The l-(3,5-anhydro-2-deoxy-p-D-threo-pentofuranosyl)thymine, melting point 188°-190°C (lit. 190°-193°C) was used without further purification. 

Calculation of As was carried out for hole transfer in finite DNA duplexes in water, in which one strand includes a G3(T) G3 sequence, n = 0-6, where G and T are, respectively, guanine and thymine nucleotide bases (in the complementary strand, of course, G and T are paired respectively, with cytosine and adenine bases) [23], The D and A sites (the solute) were taken as the middle unit of each G3 triad, or as alternative models for the n = 0 case, using one or both of the inner members of the G3 units). These structures lead to D/A sites in contact or separated by intervening bases ranging in number from 1 to 8. Using a base stacking separation of 3.4 A yields rDA = (m+ 1) (3.4 A), m = 0-8 (an estimate closely supported by detailed molecular force field calculations). 

When the derivatives are required to convert to the parent 5-FU in vivo, appropriate substituents were introduced across the carbonyl groups in the chemical modification [20-25]. Though the first synthesis of acryloyl derivatives of 5-FU, which is the simplest polymerizable derivative, was done by Gebelein, the monomer has not been purified and collected [23]. In the present case, as shown in Scheme 2, silylated 5-FU was used instead of just 5-FU so as to give selectivity to the 1 TV-acylation similar to that of the acryloyl derivatives of thymine [9]. For the preparation of acryloyl-5-FU (AFU), methacryloyl-5-FU (MAFU) and / -vinylbenzoyl-5FU (VBFU), trimethylsilylated 5-FU (1) was allowed to react with acryloyl chloride, methacryloyl chloride and vinyl-benzoyl-chloride, respectively. The reaction was carried out in water-free acetonitrile solution after the addition of acid chloride at room temperature the solution was stirred for 30 min. This procedure afforded AFU in 16%, MAFU in 56%, and VBFU in 63% yield. 

Very few reports of the excited-state structural dynamics of the purine nucleobases have appeared in the literature. This lack of research effort is probably due to a number of factors. The primary factor is the lack of photochemistry seen in the purines. Although adenine can form photoadducts with thymine, and this accounts for 0.2% of the photolesions found upon UVC irradiation of DNA [67], the purines appear to be relatively robust to UV irradiation. This lack of photoreactivity is probably due to the aromatic nature of the purine nucleobases. A practical issue with the purine nucleobases is their insolubility in water. While adenine enjoys reasonable solubility, it is almost an order of magnitude lower than that of thymine and uracil, the two most soluble nucleobases [143], Guanine is almost completely insoluble in water at room temperature [143],... 

The relevance of the dark state to a biological system in water can be elucidated from studies of hydrated complexes. Through the sequential addition of water molecules to thymine, we can observe the gradual change in photophysics as we build up the solvent environment. 

Figure 6 illustrates some separations of a 20-mer antisense oligonucleotide with a neutral backbone. With the sample diluted in water, a symmetrical peak is obtained for a small 100-mbs injection (data not shown). The buffer is 100 mM CAPS, pH 11.7, with 6 M urea. The solute is separated as an anion, with thymine and guanine being ionized at the high pH. Figure 6 shows the separations at expanded scale. Some subtle but surprising observations are made. In 1 M salt diluent, two impurity peaks on the tail of the main component show improved resolution, while the impurity peak that elutes just before the main... 

The reaction of polyethylenimine with p-nitrophenyl ester 44 was carried out in DMSO at 25 °C in the presence of imidazole. The obtained polymer, A-PEI (45), was soluble in water below pH 2, acidic solvents and DMSO and insoluble in concentrated hydrochloric add, DMF, or other commonly used organic solvents. The synthetic way to the graft polymer containing thymine (T-PEI) (47) is the same as that used for adenine. The results are compiled in Table 17. 

The fluorescence polarization excitation spectrum has been measured for thymine in aqueous solution. " The depolarization at the red edge is attributed to the hidden n, ir transition. Ionization of the lowest excited singlet and triplet states have been determined by the effect of pH on the absorption, fluorescence, and phosphorescence spectra of purines and pyrimidines. " Spectral, polarization, and quantum yield studies of cytidylyl-(3, 5 )-adenosine have also been published. Intermediates in the room-temperature flash photolysis of adenine and some of its derivatives have been identified hydrated electron, radical cations and anions, and neutral radicals resulting from their reactions have been assigned. Photoionization occurs via the triplet state. FMN encapsulated in surfactant-entrapped water pools interacts with polar head groups, entrapped water molecules, and outer apolar solvent. ... 

The irradiation of thymidine (191) and L-lysine (192) in water at 0°C afforded the ring-opened product (193) in 707o yield. This was rapidly converted in water at 90 °C into the thymine (194). This product had been reported previously. ... 

Modeling of the hydration shell of uracil and thymine in small water clusters... 

The intramolecular interaction of the 9-aminoacridine dye quinacrine with the nucleobases attached via a flexible polymethylene linker has been studied by Constant et al. [100]. The dye and nucleobase form r-stacked intramolecular complexes in water and, to a lesser extent, in organic solvents. Complex formation with adenine or thymine results in an increase in the acridine fluorescence intensity, presumably due to decreased solvation by water. In contrast, complexation with guanine results in quenching of the acridine fluorescence, presumably due to electron transfer. 

Synthetic polymers that incorporate thymine take advantage of this dimerization reaction. Water-soluble polymers can be made that contain th)miine in the chain. When the polymer is irradiated with UV light, it is transformed into a material that resists dissolution in water. In this experiment a water-soluble thymine based photoresist is prepared. The basic procedure is outlined in Figure 8. The water soluble photoresist is coated onto a substrate such as a plastic film. 

Photoreactions of Thymines, etc. - Irradiation at 254 nm of the pyrimidine derivative (153) induces a Norrish Type II hydrogen abstraction from a methyl group of the t-butyl substituent. The resultant 1,4-biradical (153a) undergoes cyclization to afford an unstable cyclobutanol. Elimination of water from this species affords the final product identified as the cyclobutane derivative (154). The structure of this product was verified by X-ray diffraction techniques. The Norrish type II reactivity of the pyrimidine derivative (155) at 254 nm in water follows the analogous path to that observed for (153) and yields the cyclized product (156) in 52 % yield. - °... 

Single crystals of thymine derivatives with long alkyl-chain substituents are photochemically reactive and undergo (2 + 2) photodimerisation to yield solely the trans-anti dimer. In solution, however, the photoreaction affords the usual four cycloadducts. Irradiation of the bis-thymine PNA dimer (142) brings about intramolecular cycloaddition to give the adduct (143) in 50% yield. The reaction is carried out in water using irradiation at 254 nm. The results from a study of the photochemical cycloaddition within the thymidilyl system (144) has been reported. Photoadducts have been obtained from the... 

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