Poor hydration enhances the activation energy of the exchange rate of the base-paired imino protons with water at the core part of the DNA duplex

Here we report the exchange rates (k_{e x}) of imino protons of d[^5′p(T¹G²T³T⁴T⁵G⁶G⁷C⁸)^3′]:d[^{3∼'(A15C14A13A12A11C10C9)p5′}] (duplex I) with water at different pH and temperature to give the life-times (τ_o) of the closed state of the base-pairs. The τ_o of the closed state of the base-pairs is uniform (E_a ≈ 25 ± 5 kcal/mol) in the duplex I, and varies between 0.2 – 4 ms. A plot of the natural log of various exchange rates of the imino protons of the base-pair of the duplex I within the pH range of 6.1 to 8.6 as a function of the inverse of temperature gave the activation energy (E_a) of the exchange process of imino protons with the bound water (hydration). It has been found that although τ_o are in the same range but the E_a of the exchange processes of the open state of imino protons with the bound water are very different, and they are strongly dependent upon the location of the nucleotide residues along the DNA duplex: 22.3±3.3 kcal/mol for the core base-pair T⁴-A¹², 16.2±2.4 kcal/mol for the base-pair T⁵-A¹¹, 10.5±1.6 kcal/mol for the base-pair T³-A¹³. 12.3±1.8 kcal/mol for the base-pair G⁶-C¹⁰ and 2.4±0.4 kcal/mol for the base-pair G²-C¹⁴. The comparison of the activation energies of the exchange process of imino protons and water with that of the water abundance in the first spine of hydration between fully-matched duplex I and the analogous G⁷-A⁹ mismatched duplex II, (d[^5′p(T¹G²T³T⁴T⁵G⁶G⁷C⁸)^3′]: d[^3′(A¹⁵C¹⁴A¹³A¹²A¹¹C¹⁰A⁹)p^5′], determined by a combination of NOESY and ROESY experiments, suggests for the first time that the relative exchange of imino protons of the base-pairs in the DNA duplex is more rapid when there is an abundance of water at the first spine of hydration. This result also showed unambiguously that the core of the DNA is by and large devoid of water and the energy penalty of water entering the core is very high. This is consistent with our earlier work which showed that as the water activity in the minor and major groove of DNA increases, the T_m decreases (ref. 1), suggesting the water poisoning as the principal factor for base-pair mismatch, frame-shift and mutation in our DNA replication machinery.     

Ideal Behavior of Water Solutions of Strong Electrolytes and Non-electrolytes at High Concentrations

Contrary to widely held beliefs, many concentrated aqueous solutions of strong electrolytes and nonelectrolytes are shown to behave ideally by calculating the activity of water (a _w) from vapor pressure data. The mole fraction of water (x _w) is equal to the water activity a _w(Raoult’s Law) when the mole fraction of water is calculated by accounting for water strongly bound to the solute, which is then not available to act as solvent. In this case x _w=(55.51−mH _T)/(55.51−mH _T+im), where m is the molality of the solute particles, i is the stoichiometric number of solute particles produced per mole of dissolved solute, and H _T is the thermodynamic hydration number H _T. Published reservations about previous work of this type are addressed. The values of H _T vary little over wide ranges of concentration and correlate with the Hofmeister series, the B coefficient of the Jones-Dole viscosity equation, and other properties of water. Activity coefficients of the bulk or “free” water remain at unity even at high concentrations.     

FT-IR study of the properties of water in Triton N-42 inverse micelles

The distribution of free (bulk) and bound (hydration) water in Triton N-42 inverse micelles has been studied. The percent of bulk water changes from 12% to 27% when solubilization capacity* (V _s /V _o ) increases from 0.5 vol.% to 3.5 vol.%. Triton N-42 inverse micelles contain hydration water of two types: 1) water bound with hydroxyl groups and secondary-bound with ethoxy groups and 2) water primary-bound with ethoxy groups. The quantity of water of each type is calculated as a function of solubilization capacity. The polar group of the surfactant molecule is hydrated by approximately six H₂O molecules when V _s /V _o = 3.5 vol.%.     

Effect of acetonitrile on the hydration of human serum albumin films: a calorimetric and spectroscopic study

A new experimental approach based on the combination of calorimetric and FTIR spectroscopic measurements was proposed to study simultaneously the sorption of water and organic solvent, and corresponding changes in the structure of protein films in the water activity range from 0 to 1.0. Enthalpy changes (ΔH_tot) on the interaction of water with the dried human serum albumin (HSA) in the presence and absence of acetonitrile (AN) have been measured using a Setaram BT-2.15 calorimeter at 298 K. Spectroscopic data on water and organic solvent vapor sorption by the HSA films and the corresponding changes in the protein secondary structure were determined by means of a Bruker Vector-22 FTIR spectrometer. By using a water activity-based comparison we characterised the effect of acetonitrile on the hydration and structure of the HSA films. Acetonitrile (AN) sorption isotherm resembles a smooth curve. HSA film binds about 250 mol AN/mol protein at the lowest water activities. As the water activity increases from 0 to 0.8, the sorption of AN gradually decreases from 250 to 150 mol AN/mol HSA. At a_w > 0.8, the sorption of AN sharply decreases to zero. Acetonitrile decreases markedly the water content at a given a_w. This behavior suggests that the suppression in the uptake of water is due to a competition for water-binding sites on the HSA films by acetonitrile. Changes in the secondary structure of HSA were determined from infrared spectra by analyzing the structure of amide I band. Acetonitrile increases the intensity of the 1654 cm⁻¹ band that was assigned to the α-helix structure. Changes in the intensity of the 1654 cm⁻¹ band agree well with the decrease in water uptake in the presence of AN. An explanation of the acetonitrile effect on the hydration and structure of the HSA films was provided on the basis of hypothesis on water-assisted disruption of polar contacts in the initially dried protein.     

Cyclam as a Structure-Directing Agent in the Crystallization of Aluminophosphate Open Framework Materials from Fluoride Media

Two aluminofluorophosphates have been synthesized using 1,4,8,11-tetraazacyclotetradecane (cyclam) as a structure-directing agent (SDA). The two materials were synthesized hydrothermally and their structures solved by microcrystal diffraction using synchrotron radiation. In both cases, the SDA has been located crystallographically. The first material, [F, Cyclam]-AlPO-CHA, has the molecular formula Al₆P₆O₂₄F₂.C₁₀N₄H₂₆ and has a framework structure related to the mineral chabazite, with the cyclam molecules occluded within chabazite-like cages (space group P-1, a=9.0993(4) Å, b=9.2232(5) Å, c=9.3929(4) Å, α=77.881(2)^o, β=87.205(1)^o, γ=87.777(1)^o, Z=1, wR(F²)=0.1354, R(F)=0.0487). The second material, [F, Cu-Cyclam]-AlPO-SAS, has the molecular formula Al₈P₈O₃₂F₂.[CuC₁₀N₄H₂₄.2H₂O] and has a framework structure closely related to STA-6 (SAS) zeolite structure type, although the usual tetragonal symmetry has been reduced to monoclinic by the presence of the fluoride ions (space group P2₁/n, a=10.3738(4) Å, b=14.8060(5) Å, c=13.4494(5) Å, β=90.275(1)^o, Z=2, wR(F²)=0.1484, R(F)=0.0524). The cyclam is occluded as a copper complex ordered within the cages of the structure.     

Synthesis,characterization and crystal structure of the anilinium β-octamolybdate dihydrate

The anilinium β-octamolybdate dihydrate has been prepared in acidic aqueous solution. TG, DTG, IR and ¹H NMR techniques have been used to identify the compound. It belongs to a series of molybdates of alkyl-N- and -N,N-substituted anilinium cations. Single crystals have been analyzed by X-ray diffraction. Crystal data are: (C₆H₈N)₄[Mo₈O₂₆] · 2H₂O, space group P$\text{1}$, Z = 1, a = 10.007(1), b = 8.014(2), c = 14.645(8)Å, α = 109.81(3), β = 108.59(2), γ = 85.44(2)°, V = 1052.9(6) ų, D_o = 2.49(1), D_x = 2.52 mg m^?3, R = 0.026 and R_w = 0.031 for 5297 observed reflexions. The crystal structure consists of discrete [β-Mo₈O₂₆]^4? polyanions, two crystallographically independent (C₆H₈N)⁺ cations and one independent water molecule. Polyanions are linked to the cations and to the water molecules by hydrogen bonds of types NH…O and OH…O.     

Cyclometallation reactions in complexes of the type Rh(oq)(CO)(P(o-BrC6F4)Ph2): II. The molecular structure of [Rh(oq)Br(P(o-C6F4)Ph2)(H2O)]2 (oq = 8-oxyquinolinate)

The complex [uRh(oq)Br(P(o-Cu₆F₄)Ph₂)(H₂O)]₂ is obtained by refluxing a solution of Rh(oq)(CO)(P(o-BrC₆F₄)Ph₂) (oq = 8-oxyquinolinate) in toluene. The structure of this compound has been determined by X-ray diffraction and refined to R = 0.061 and R_w = 0.065 factors. The cell has monoclinic symmetry, space group P2₁/n; a 19.513(2), b 17.049(1), c 16.898(1) Å and β 99.69(1)°. The structure consists of two independent Rh(oq)Br(P(o-C₆F₄)Ph₂)H₂O) units linked by hydrogen bonds between the coordinated water molecules and oq ligands to form a distorted boat (six atom ring of junction between the two units). In each unit the metal atom has a distorted octahedral coordination, with a four-atom metallocyclic ring (uRhPCCu) with CRhP and RhPC angles 69.3(2) and 85.3(3)°, respectively, in one unit, and 70.0(2) and 81.1(2)° in the other. The water molecule is readily displaced by a variety of phosphorus donor ligands to form the complexes uRh(oq)Br(P(o-Cu₆F₄)Ph₂)P′, P′ = PPh₃, P(p-CH₃C₆H₄)₃ and P(OCH₃)₃, in which the P atoms are in trans-dispositions.     

(Liquid + liquid) equilibria of ternary and quaternary systems with two hydrocarbons, an alcohol, and water at 303.15 K. Systems containing cyclohexane, benzene, ethanol, and water

Tie-line data for the water, ethanol, and cyclohexane [{w₁H₂O + w₂C₂H₅OH + (1−w₁−w₂)C₆H₁₂}] ternary system, where w is the mass fraction, was investigated at T=303.15 K. A quaternary system containing these three compounds and benzene {w₁C₂H₅OH + w₂C₆H₆ + w₃C₆H₁₂ + (1−w₁−w₂−w₃)H₂O} was also studied at the same temperature, while data on its other two partially miscible ternary systems were taken from the literature [the fourth {w₁C₂H₅OH + w₂C₆H₆ + (1−w₁−w₂)C₆H₁₂} is not partially miscible]. From our experimental results we conclude that this quaternary system presents a very small water tolerance and that phase separation could produce a considerable loss of C₂H₅OH drawn into the aqueous phase. On the other hand, the results also show that the aqueous phase generally contains a higher concentration of C₆H₆ than of C₆H₁₂. A comparison with other similar quaternary systems investigated in our laboratory was also made. The ternary experimental results were correlated with the UNIQUAC equation, and predicted with the UNIFAC group contribution method. As previously, the equilibrium data of the three ternary systems (including those taken from the literature) were used to determine interaction parameters for the UNIQUAC equation. These parameters were then averaged in order to predict equilibrium data of this quaternary system. The UNIFAC method was also used with the same purpose. The UNIQUAC equation appears to be more accurate than the UNIFAC method for this ternary system. However, this last model is slightly better for the quaternary system, as can be seen from the values of both residuals.     

Surface behaviour of some phenol para-derivatives adsorbed at the free surface of water

Comparison is made between two methods for the determination of the average orientation angle of molecules adsorbed at the free surface of water; one based on electric surface potential measurements, the other on second harmonic generation. Assuming that the model of energetics of adsorbed molecules is similar to that of a system of non-interacting permanent dipoles in an external homogeneous field, the parameters of the probability density function in the form exp[ —a cos(0-0_o)], a =w/kT, w, being the absolute orientational energy, have been calculated for phenol, p-methyl-, p-nitro-, and p-bromophenol.     

Hydrophobic Effect: Solubility of Non-polar Substances in Water,Protein Denaturation and Micelle Formation

The 'hydrophobic effect' of the dissolution process of non-polar substances in water has been analysed under the light of a statistical thermodynamic molecular model. The model, based on the distinction between non-reacting and reacting systems explains the changes of the thermodynamic functions with temperature in aqueous systems. In the dissolution of non-polar substances in water, it follows from the model that the enthalpy change can be expressed as a linear function of the temperature (ΔH _app =ΔH ^ø +n _w C _p,w T ). Experimental solubility and calorimetric data of a large number of non-polar substances nicely agree with the expected function. The specific contribution of n _w solvent molecules depends on the size of solute and is related to destructuring (n _w >0) of water molecules around the solute. Then the study of 'hydrophobic effect' has been extended to the protein denaturation and micelle formation. Denaturation enthalpy either obtained by van't Hoff equation or by calorimetric determinations again depends linearly upon denaturation temperature, with denaturation enthalpy, ΔH _den , increasing with T . A portion of reaction enthalpy is absorbed by a number n _w of water molecules (n _w >0) relaxed in space around the denatured moieties. In micellization, an opposite process takes place with negative number of restructured water molecules (n _w <0) because the hydrophobic moieties of the molecules joined by hydrophobic affinity occupy a smaller cavity.     

New pentacyclic ring systems: intramolecular cyclization of o,o′-disubstituted bibenzothiazoles

Efficient methods for the preparation of isomeric o,o′-diaminobibenzothiazoles (8a and 11a) and o,o′-diamino-2,2′-dimethylbibenzothiazoles (8b and 11b), potentially valuable building blocks for construction of hitherto unknown dithiazolo annulated pentacyclic heterocycles, have been developed. The dithiazolo annulated benzo[c]cinnolines 9a, 9b, and 12a were prepared from the corresponding diamines by oxidation with PhI(OAc)₂ in good yield. The dithiazolo annulated carbazoles 13 and 14 were efficiently prepared from the corresponding diamines by thermal cyclization in H₃PO₄. The unusual course of reduction and product formation of o,o′-dinitrosubstituted bibenzothiazoles 6a and 6b with SnCl₂ under acidic conditions was rationalized by DFT quantum-mechanical calculations. It was suggested that cyclic products are formed from dinitroso derivatives and open-shell species immediately following on a reduction path.     

Standard pH values for potassium hydrogenphthalate reference buffer solutions in 10, 30 and 50% (w/w) 1,4-dioxane/water mixed solvents at temperatures from 288.15 to 318.15 K

Standard pH(S) values for 0.05 mol kg^?1 potassium hydrogenphthalate (KHpH) reference buffer solutions in 10, 30 and 50% (w/w) 1,4-dioxane/water solvent mixtures within the temperature range 288.15–318.15 K are determined from e.m.f. measurements of the cell without transference Pt|H₂|KHPh + KCl|AgCl|Ag|Pt. The consistency of the results is analysed by a recently described method of multilinear regression of the quantity p(a_Hγ_Cl) as a function of both solution composition and temperature. The standard pH(S) determined can be reproduced to within ±0.01 by the equation pH(S) - 4.004 + 3.309w + 0.408z + 1.037w³ - 14.95zw² + 27.1zw³, where w is the weight fraction of dioxane in the solvent mixture,z = (T –θ)/θ, and θ - 298.15 K. Values of the first ionization constant of phthalic acid (H₂Ph; benzene-1,2-dicarboxylic acid) in the above solvent mixtures are also determined from e.m.f. measurements of the cell without transference Pt|H₂|H₂Ph + KHPh + KCl|AgCl|Ag|Pt.     

Bulk properties and hydration numbers of ammonium nitrate and ammonium chloride in solution: A structural and thermodynamic analysis

The apparent volumes of the salts in the systems H₂O-NH₄Cl (298 K) and H₂O-NH₄NO₃ (273 K, 298 K, and 323 K) are reproduced with an accuracy of 0.03–0.01 cm³/mol by the equation ? = ?⁰ + Aw ₂ ^0.5 + Bw ₂, where w ₂ is the salt content (mass fractions). The study shows that there is a correspondence between the critical (for determining the hydration number) structural parameters-the intrinsic volume of the electrolyte and the volume of water in ion hydration shells-and the limiting (at w ₂ = 1) partial molar volumes of the components. The hydration numbers at infinite dilution are 6.9 for NH₄Cl at 298 K and 9.1, 6.7, and 6.4 for NH₄NO₃ at 273 K, 298 K, and 323 K. The water volume in ion hydration shells decreases in the sequence: No ₃ ^? , Cl^?, and NH ₄ ⁺ . The hydration numbers decrease with increasing salt concentration. The study shows that within a simpler model ? = ?⁰ + aw ₂ ^0.5 , the hydration numbers are temperature independent.     

Full CI calibration of model hamiltonian,large basis set studies of the H2-H2 van der Waals interaction.

The non-variational CEPA2 PNO ansatz, recently employed in detailed studies of the H₂-H₂ van der Waals interaction by Burton and Senff and the full CI extrapolation studies on the same system by Burton are discussed in relation to the explicit full CI study of Harrison and Handy for the planar T configuration of H₂-H₂ (R = 6.5 a_o) in a basis of 80 functions.     

Atomistic modelling of the hydration of CaSO4

Atomistic modelling techniques, using empirical potentials, have been used to simulate a range of structures formed by the hydration of γ-CaSO₄ and described as CaSO₄·nH₂O (0<n<1). The hemihydrate phase (n=0.5) is of commercial importance and has been subjected to much experimental study. These simulation studies demonstrate significant water-matrix interactions that influence the crystallography of the hydrated phase. The existence of two types of hydration site has been predicted, including one within the Ca²⁺coordination sphere. Close correlation between water molecule bonding energy, Ca²⁺-O_w bond length and unit-cell volume have been established. This shows that as the number of water molecules within the unit cell increases, the bonding energy increases and the unit cell contracts. However around n=0.5, this process reaches a turning point with the incorporation of further waters resulting in reduced binding energy and an expanding unit cell.     

Standard enthalpies of dissolution of L-alanine in the water solutions of glycerol, ethylene glycol, and 1,2-propylene glycol at 298.15 K

The integral enthalpies of dissolution Δ_sol H ^m of L-alanine in mixtures of water with glycerol, ethylene glycol, and 1,2-propylene glycol under the concentration of organic solvents up to 0.32 mole fraction were measured by means of calorimetry. The standard values of the dissolution enthalpies (Δ_sol H ^o) and transfer enthalpies (Δ_tr H ^o) of amino acids from water to the mixed solvent were calculated. It was shown that the calculated enthalpic coefficients of pair interactions of L-alanine with cosolvent molecules have positive values. The data obtained are interpreted from the viewpoint of prevalence of different types of interactions in the solutions and influence of the cosolvents nature on the thermo-chemical characteristics of amino acid dissolution.     

Acid-base chemistry of omeprazole in aqueous solutions

Omeprazole is a potent anti-acid drug. Its absorption and mode of action are closely related to its prototropic behavior. In the present study, omeprazole samples from different sources and in different forms were studied spectrophotometrically to obtain pK_a values. In the neutral to alkaline pH region, two consistent pK_a values of 7.1 and 14.7 were obtained from various samples. The assignment of these pK_a values was realized by comparison with the prototropic properties of N(1)-methylated omeprazole substituted on the nitrogen at the 1-position of the benzimidazole ring, which was found to have a pK_a of 7.5. The omeprazole pK_a of 14.7 is assigned to the dissociation of the hydrogen from the 1-position of the benzimidazole ring and the pK_a of 7.1 is assigned to the dissociation from the protonated pyridine nitrogen of omeprazole. The results presented are at variance with those of earlier work.     

Methyl-oxygen bond cleavage in hemilabile phosphine-ether ligand of ruthenium(II) complexes

The preparation and characterization are described for four ruthenium(II) complexes containing hemilabile phosphine-ether ligand o-(diphenylphosphino)anisole (Ph₂PC₆H₄OMe-o) and/or bidentate ligand diphenylphosphino-phenolate ([Ph₂PC₆H₄O-o]⁻) Ru(RCN)₂(κ²-Ph₂PC₆H₄O-o)₂ (1a: R = Me; 1b: R = Et) and [Ru(RCN)₂(κ²-Ph₂PC₆H₄O-o)(κ²-Ph₂PC₆H₄OMe-o)](PF₆) (2a: R = Me; 2b: R = Et). The ruthenium(II) phosphine-ether complexes undergo mild methyl-oxygen bond cleavage. Two different kinds reaction mechanism are proposed to describe the methyl-oxygen bond cleavage, one involving attack of anionic nucleophiles and another involving the phosphine. The new reactions define novel routes to phosphine-phenolate complexes. The structures of complexes 1a, 1b and 2a were confirmed by X-ray crystallography.     

Analysis of kinetic models for the tunnel electron transfer reactions. Reaction kinetics for various radial and angular dependences of the tunneling probability

A new version of the “stepwise” approximation used in kinetic models for the long range electron transfer reactions is suggested. Using this approach the effects on the kinetics of these reactions of such factors are examined as a more complicated dependence (compared to the commonly used exponential one) of the tunneling probability, w, on the distance between the reagents as well as the angular dependence of w. For many practically important situations taking account of the above factors is shown to have no significant effect on the form of the reaction kinetics for both the pairwise and random spatial distributions of the reagents. However, the relations between the parameters a_ef and ν_cf in the expression for the tunneling distance R* = ₂¹a_ef In ν_cft, which can be determined from the experimental kinetics, and similar theoretical parameters ν_o and a that are involved in the expressions for w are found to be different for various types of the radial and the angular dependences of w. It is shown that when the orbitals between which the electron transfer takes place are located at sites removed from the geometric centers of the reactants the values of ν_ef can exceed by many orders of magnitude the characteristic frequency of the electron movement in molecules ν_e ≈ 10¹³ s^?1.     

(Liquid + liquid) equilibria of ternary and quaternary systems containing n-hexane,toluene, m-xylene,propanol, sulfolane,and water at T = 303.15 K

(Liquid + liquid) equilibrium data for ternary and quaternary systems containing n-hexane (C₆H₁₄), toluene (C₇H₈), m-xylene (C₈H₁₀), propanol (C₃H₈O), sulfolane (C₄H₈SO₂), and water (H₂O) were measured at T = 303.15 K. Phase diagrams of {w₁C₄H₈SO₂ + w₂C₇H₈ + (1 − w₁ − w₂)C₆H₁₄}, {w₁C₄H₈SO₂ + w₂C₈H₁₀ + (1 − w₁ − w₂)C₆H₁₄}, {w₁C₄H₈SO₂ + w₂C₃H₈O + w₃C₇H₈ + (1 − w₁ − w₂ − w₃)C₆H₁₄} and also systems containing water: {w₁C₄H₈SO₂ + w₂H₂O + w₃C₇H₈ + (1 − w₁ − w₂ − w₃)C₆H₁₄} and {w₁C₄H₈SO₂ + w₂H₂O + w₃C₈H₁₀ + (1 − w₁ − w₂ − w₃)C₆H₁₄} (w = mass fraction) were obtained at T = 303.15 K. The (liquid + liquid) equilibrium data of the systems were used to obtain interaction parameters in non-random two-liquid (NRTL) and universal quasi-chemical theory (UNIQUAC) activity coefficient models. These parameters can be used to predict equilibrium data of ternary and quaternary systems. The root mean square deviations (RMSDs) using these models were calculated and reported. The partition coefficients and the selectivity factors of solvents for extraction of toluene or m-xylene from n-hexane at T = 303.15 K are calculated and presented. The experimental selectivity factors of sulfolane for the system {w₁C₄H₈SO₂ + w₂C₇H₈ + (1 − w₁ − w₂)C₆H₁₄} at T = 298.15 K and T = 323.15 K were taken from the literature and the influence of temperature on the extraction of toluene was also investigated. The phase diagrams for the ternary and quaternary systems including both the experimental and correlated tie lines are presented. The tie-line data of the studied systems were also correlated using the Hand equation and the correlation parameters are calculated and reported.