Spectroscopic studies of zinc(II)tetraphenylporphyrin molecular complex with 1,4-dioxane.

The molecular complex of zinc(II)tetraphenylporphyrin with 1,4-dioxane has been obtained. The IR spectra of the [Zn(TPhP)(1,4-dioxane)2] stabile molecular complex between 4000 and 50cm(-1) have been studied. An interpretation is given on the base the "chair" conformation of 1,4-dioxane molecule.

Water molecules in the crystal structure of tricyclic acyclovir.

The biologically important molecule tricyclic acyclovir, presented here as 3-[(2-hydroxyethoxy)methyl]-6-methyl-3H-imidazolo[1,2-a]purin-9(5H)-one dihydrate, C11H13N5O3*2H2O, shows conformational flexibility, which is observed in the solid state as two symmetrically independent molecules with different side-chain conformations. Additionally, one of these molecules exhibits side-chain disorder, such that there are three different conformations in the crystal. Water molecules found in the crystal form (H2O)8 clusters which are located between molecules of tricyclic acyclovir. The complex hydrogen-bond network formed between water and tricyclic acyclovir in the solid state may be related to the solvation of the molecules in solution.

Mg2+ dependence of the structure and thermodynamics of wheat germ and lupin seeds 5S rRNA.

The formation and stability of structural elements in two 5S rRNA molecules from wheat germ (WG) and lupin seeds (LS) as a function of Mg2+ concentration in solution was determined using the adiabatic differential scanning microcalorimetry (DSC). The experimentally determined thermodynamic parameters are compared with calculations using thermodynamic databases used for prediction of RNA structure. The 5S rRNA molecules which show minor differences in the nucleotide sequence display very different thermal unfolding profiles (DSC profiles). Numerical deconvolution of DSC profiles provided information about structural transformations that take place in both 5S rRNA molecules. A comparative analysis of DSC data and the theoretical thermodynamic models of the structure was used to establish a relationship between the constituting transitions found in the melting profiles and the unfolding of structural domains of the 5S rRNA and stability of its particular helical elements. Increased concentrations of Mg2+ ions induces additional internal interactions stabilising 5S rRNA structures found at low Na+ concentrations. Observed conformational transitions suggest a structural model in which the extension of helical region E dominates over the postulated tertiary interaction between hairpin loops. We propose that helix E is stabilised by a sequence of non-standard pairings extending this helix by the formation of tetra loop e and an almost total reduction of loop d between helices E and D. Two hairpin structures in both 5S rRNA molecules: the extended C-C' and the extended E-E'-E" hairpins appear as the most stable elements of the structure. The cooperativity of the unfolding of helixes in these 5S rRNA molecules changes already at 2 mM Mg2+.

Comparative calorimetric studies on the dynamic conformation of plant 5S rRNA: II. Structural interpretation of the thermal unfolding patterns for lupin seeds and wheat germ.

Thermal unfolding of 5S rRNA from wheat germ (WG) and lupin seeds (LS) was studied in solution. Experimental curves of differential scanning calorimetry (DSC) were resolved into particular components according to the thermodynamic model of two-state transitions. The DSC temperature profiles for WG and LS differ significantly in spite of very high similarities in the sequence of both molecules. Those results are interpreted according to a model of the secondary and tertiary molecular structure of 5S rRNA. A comparison of the 'nearest neighbour' model of interaction with the experimental thermodynamic results enables a complete interpretation of the process of the melting of its structures. In light of our observations, the crucial differences between both DSC melting profiles are mainly an outcome of different thermodynamic properties of the first helical fragment 'A' made up of 9 complementary base pairs. It contains 6 differences in the nucleotide sequence of both types of molecules, which still retain 9-meric double helixes. The temperature stability of his helix in WG is much lower than of the LS one. Moreover, the results supply evidence for a strong specific tertiary interaction between the two hairpin loops 'c' and 'e' in both 5S rRNA molecules, modulated by small differences in the thermodynamic properties of both 5S rRNA.

Comparative calorimetric studies on the dynamic conformation of plant 5S rRNA. I. Thermal unfolding pattern of lupin seeds and wheat germ 5S rRNAs, also in the presence of magnesium and sperminium cations.

An attempt has been made to correlate differential scanning calorimetry melting profiles of 5S rRNAs from lupin seeds (L.s.) and wheat germ (W.g.) with their structure. It is suggested that the observed differences in thermal unfolding are due to differences in RNA nucleotide sequence and as a consequence in higher order structures. Interesting effects induced by magnesium cation, perprotonated and permethylated sperminium tetracations are discussed. It is suggested that the difference in the stabilizing effect of the three cations results from different mode of their interactions with RNA. "Pure" electrostatic interactions expected for permethylated tetracations are rather weak due to the steric hindrance around each positively charged nitrogen atom. Electrostatic interactions of the other two cations are significantly enhanced by coordination bonding for magnesium and by hydrogen bonding for protonated sperminium cation.

Thermochemistry of aqueous solutions of alkylated nucleic acid bases. VI. Enthalpies of hydration of 2-alkyl-9-methyladenines.

Enthalpies of solution in water, delta H0sol, and vant'Hoff enthalpies of sublimation, delta H0subl, were determined experimentally for a number of crystalline 2-alkyl derivatives of 9-methyladenine: m2(2,9)Ade, e2m9Ade, pr2m9Ade and but2m9Ade. Standard enthalpies of hydration, delta H0hydr derived from these data were corrected for the calculated cavity terms, delta H0cav, to yield enthalpies of interaction, delta H0int, of the solutes with their hydration shells. The apparent residual contribution of alkyl groups, R, to the enthalpy of interaction delta delta H0int (R) was found to increase linearly with the number of CH2 groups added upon alkyl substitution, whereas this contribution calculated per unit area of the water-accessible molecular surface, SB, of alkyl residues delta delta H0int (R): delta SB(R) appeared constant over the whole series of the compounds investigated. This indicates that alkyl groups substituted at the C(2) carbon atom of the adenine contribute additively to the van der Waals' part of the enthalpy of interaction and do not affect the electrostatic part of the energy of interaction of the solutes with their hydration shells.

Thermochemistry of aqueous solutions of alkylated nucleic acid bases. IV. Enthalpies of hydration of 5-alkyluracils.

Enthalpies of sublimation, DeltaH degrees (subl) and of solution in water, DeltaH degrees (sol) were determined for a series of crystalline 1,3-dimethyl-uracil derivatives substituted at the C5-ring carbon atom with alkyl groups (-C(n)H(2n+1), n = 2-4) and some of their C(5.6)-cyclooligomethylene analogues (-(CH2)(n)-, n = 3-5). From these data. enthalpies of hydration DeltaH degrees (hydr)= DeltaH degrees (sol) - DeltaH degrees (subl) were calculated and corrected for energies of cavity formation in pure liquid water in order to obtain enthalpies of interaction, DeltaH degrees (int) of the solutes with their hydration shells. The latter are discussed together with the recalculated DeltaH degrees (int) for variously methylated uracils, obtained previously according to a simplified correction procedure, in terms of perturbations in the energy and scheme of hydration of the diketopyrimidine ring brought about by alkyl substitution. It was found that each -CH2-group added with an alkyl substitution contributes favorably about -20 kJ mol(-1) toDeltaH degrees (int). This contribution is partially cancelled by the unfavorable contribution to DeltaH degrees (int) connected with removal of some water molecules bound in the first and subsequent hydration layers by an alkyl substituent. This is particularly evident on substitution at the polar side of the diketopyrimidine ring on which water molecules are expected to be bound specifically.

Thermochemistry of aqueous solutions of alkylated nucleic acid bases. III. Enthalpies of hydration of uracil, thymine and their derivatives.

Enthalpies of sublimation DeltaH(0)(subl) crystalline uracil, thymine and their methylated derivatives as well as of N,N-diethylthymine were determinated by the quartz-resonator method and mass spectrometry. Enthalpies of solution at infinite dilution DeltaH(0)(sol) in water of aBcylated compounds were obtained calorimetrically. Hence the calculated enthalpies of hydration: DeltaH(0)(hydrsubal) = DeltaH(0)(sol) - DeltaH(0)(subl), were corrected for energies of cavity formation in pure liquid water to yield enthalpies of interaction DeltaH(0)(sint) of the solutes with their hydration shells. For uracil DeltaH(0)(int) = -59.8 kJ mole(-1) was obtained in this way. This value decreased linearly on N-methyl substitution with a mean increment of about 6.5 kJ mole CH2(-1). After C(5) or C(6) ring substitution it increased by about 3 kJ. These results are discussed in connection with heat of dilution data and theoretical schemes of hydration.

Thermochemistry of aqueous solutions of alkylated nucleic acid bases. I. Apparent molar heat capacities of uracil, thymine and their derivatives.

Apparent molar heat capacities phiC(p(1,3)) of uracil, thymine and a series of their alkylated derivatives: m(1)Ura,m(1,3)(2) Ura, m(1,3)(2)Thy, mi(1,3,6)(3)Ura, m(1,3)(2),e(5)Ura and e(1,3)(2)Thy in dilute aqueous solutions were measured in the temperature range of 293.15-388.15 K, using a differential adiabatic scanning microcalorimeter. They were found to lie (i) much higher than the estimated heat capacities C(p)(s) of solid compounds, (ii) comparable with the respective partial molar heat capacities at infinite dilution, C(o)(p2), and (iii) linearly related to the number nH of hydrogen atoms covalenuy bound to the solute molecules. The increment thus obtained DeltaC(o)(p2)=42.8 J mole(-1) K(-1)n(-1)(H) per each hydrogen atom at 298.15 K proved (i) to coincide closely with those found previously for homologous series of aliphatic amides and hydrocarbons, and (ii) to decrease with a rise of temperature. These findings imply the involvement of hydrophobic hydration of the solutes.