'Genome order index' should not be used for defining compositional constraints in nucleotide sequences

A “genome order index,” defined as S = a² + c² + t² + g², where a, c, t, and g are the nucleotide frequencies of A, C, T, and G, respectively, was used to suggest that there exist genome-specific constraints on nucleotide composition. We show that the “evidence” for constraint, S < 1/3, is in fact a mathematical property that is always true regardless of data. Moreover, we show that S is strictly equivalent to and derivable from the Shannon H-function and has no advantage over it.     

Study of the effect of Cal-Red on the secondary structure of human serum albumin by spectroscopic techniques

The effect of Cal-Red on the structure of human serum albumin (HSA) was studied using Resonance light scattering (RLS), Fourier transformed Infrared (FT-IR) and Circular dichroism (CD) spectroscopic methods. The RLS spectroscopic results show that the RLS intensity of HSA was significantly increased in the presence of Cal-Red. The binding parameters of HSA with Cal-Red were studied at different temperatures of 289, 299, 309 and 319 K at pH 4.1. It is indicated by the Scatchard plots that the binding constant K decreased from 4.03 × 10⁸ to 7.59 × 10⁷ l/mol and the maximum binding number N decreased from 215 to 152 with increasing the temperature, respectively. The binding process was exothermic and spontaneous, as indicated by the thermodynamic analyses, and the major part of the binding energy is hydrophobic interaction. The enthalpy change ΔH⁰, the free energy change ΔG⁰ and the entropy change ΔS⁰ of 289 K were calculated to be −42.75 kJ/mol, −47.56 kJ/mol and 16.66 J/mol K, respectively. The alterations of protein secondary structure in the presence of Cal-Red in aqueous solution were quantitatively calculated from FT-IR and CD spectroscopy with reductions of -helices content about 5%, β-turn from 10% to 2% and with increases of β-sheet from 38% to 51%.     

Thermodynamic studies of the solvation of Ph4AsPh4B in mixed solvents (MeOH—DMF)

The thermodynamic data (ΔG⁰, ΔH⁰ and TΔS⁰) of the solvation of tetraphenylarsonium-tetraphenylborate (Ph₄AsPh₄B) and its neutral parts, tetraphenylgermanium (Ph₄Ge) and tetraphenylmethane (Ph₄C) in methanol—N,N-dimethylformamide mixed solvents are discussed.

The values of the free energy of transfer, Δ^s_MG⁰, are calculated from measurements of the solubilities of Ph₄AsPh₄B, Ph₄Ge and Ph₄C in the successive fractions of MeOH in DMF at three different temperatures (15, 25, 35°C). The values of Δ^s_MH⁰ and TΔ^s_MS⁰ for the derivatives are calculated from Δ^s_MG⁰ values.

The values of Δ^s_MG⁰, Δ^s_MH⁰ and TΔ^s_MS⁰ of tetraphenylarsonium and tetraphenylborate ions have also been carefully calculated. The ratios of Δ^s_MG⁰ values (Δ^s_MG⁰ = ΔG⁰(+)/ΔG⁰(−)) were found to be greater than unity. Similarly, the ratios of Δ^s_MH⁰ and TΔ^s_MS⁰ for the positive and negative ions were found to be greater than unity.     

Influence of non-covalent interactions on the thermodynamic stereoselectivity of the protonation of some dipeptides

ΔG⁰, ΔH⁰ and ΔS⁰ protonation values of some pairs of diastereoisomeric dipeptides have been determined by potentiometry and calorimetry in aqueous solution at 25°C and I = 0.1 mol dm⁻³ (KNO₃). On the basis of the results obtained it has been possible to assess the role played by two different non-covalent interactions, namely the electrostatic interaction and the solvophobic interaction, on the thermodynamic stereoselectivity in the proton complex formation, shown by the systems investigated.     

Preparation of novel ion exchange polyurethane foam and its application for separation and determination of palladium in environmental samples

The new strong anion exchanger (PUFIX) from polyurethane foam was prepared by coupling of the primary amine of the foam matrix with ethyl iodide. PUFIX was characterized using different tools (IR spectra, elemental analysis, density and thermal analysis). The sorption properties of the new anion exchanger (PUFIX) and chromatographic behaviour for separation and determination of palladium(II) ions at low concentrations from aqueous iodide or thiocyanate media were investigated by a batch and dynamic processes. The maximum sorption of Pd(II) was in the pH range of 0.3–2. The kinetics of sorption of the Pd(II) by the PUFIX was found to be fast with average values of half-life of sorption (t_1/2) of 3.32 min. The variation of the sorption of Pd(II) with temperature gives average values of ΔH, ΔS, ΔG and ΔE to be −38.3 kJ mol⁻¹, −100.7 J K⁻¹ mol⁻¹, −8.3 and 11.8 kJ mol⁻¹, respectively. The sorption capacity of PUFIX was 1.69 mmol g⁻¹ for Pd(II), preconcentration factors of values ≈250 and the recovery 99–100% were achieved (R.S.D. ≈ 1.24%). The lower detection limit, 1.28 ng mL⁻¹ was evaluated using spectrophotometric method (R.S.D. ≈ 2.46%).     

Fluorometric investigation on the interaction of oleanolic acid with bovine serum albumin

The interactions between oleanolic acid and bovine serum albumin (BSA) have been studied by fluorescence, circular dichroism (CD), UV–vis absorption and Fourier transform infrared spectroscopy (FTIR) under physiological conditions. Spectroscopic analysis of the emission quenching at different temperatures has revealed that the quenching mechanism of bovine serum albumin by oleanolic acid is static quenching mechanism. The binding sites number n and binding constants K are obtained at various temperatures. The distance r between oleanolic acid and the protein is evaluated according to the theory of Forster energy transfer. The results by FTIR, CD and UV–vis absorption spectra experiment indicate that the secondary structures of protein have been perturbed in the presence of oleanolic acid. The thermodynamic parameters ΔH⁰, ΔG⁰, and ΔS⁰ are calculated according to van’t Hoff equation, which indicates that the hydrogen bonds and van der-waals are the intermolecular forces stabilizing the complex. Molecular modeling studies the interaction BSA with oleanolic acid.     

Affinity electrochromatography of acidic drugs using a liposome-modified capillary

Liposomes can be effectively deposited on the inner surface of a capillary wall by flushing the electrophoretic system with a liposome suspension followed by air-drying of the capillary and removal of the excess of loosely bound liposomes by a 0.1 M NaOH wash. It was demonstrated that capillaries prepared in this way could be used for studies of analyte (drug)–liposome binding. The results were expressed as free binding energy changes [Δ(ΔG⁰)] relatively to an arbitrarily selected standard (acetylsalicylic acid). The results were compared to [Δ(ΔG⁰)] changes obtained from binding studies effected by capillary electrophoresis using a stable liposome plug in a capillary with minimized endoosmotic flow. Good agreement of data reported in the literature (without correction for the residual endoosmotic flow), our previous data obtained in a similar way (however, after the correction for the residual endoosmotic flow) and data obtained by the immobilized liposome affinity electrochromatography reported in this communication was achieved.     

On the conformational stability and dimerization of phosphotransferase enzyme I from Escherichia coli

The activity of enzyme I (EI), the first protein in the bacterial PEP:sugar phosphotransferase system, is regulated by a monomer–dimer equilibrium where a Mg²⁺-dependent autophosphorylation by PEP requires the homodimer. Using inactive EI(H189A), in which alanine is substituted for the active-site His189, substrate binding effects can be separated from those of phosphorylation. Whereas 1 mM PEP (with 2 mM Mg²⁺) strongly promotes dimerization of EI(H189A) at pH 7.5 and 20 °C, 5 mM pyruvate (with 2 mM Mg²⁺) has the opposite effect. A correlation between the coupling of N- and C-terminal domain unfolding, measured by differential scanning calorimetry, and the dimerization constant for EI, determined by sedimentation equilibrium, is observed. That is, when the coupling between N- and C-terminal domain unfolding produced by 0.2 or 1.0 mM PEP and 2 mM Mg²⁺ is inhibited by 5 mM pyruvate, the dimerization constant for EI(H189A) decreases from >10⁸ to <5 × 10⁵ or 3 × 10⁷ M⁻¹, respectively. With 2 mM Mg²⁺ at 15–25 °C and pH 7.5, PEP has been found to bind to one site/monomer of EI(H189A) with K_A′10⁶ M⁻¹ (ΔG′=−33.7±0.2 kJ mol⁻¹ and ΔH=+16.3 kJ mol⁻¹ at 20 °C with ΔC_p=−1.4 kJ K⁻¹ mol⁻¹). The binding of PEP to EI(H189A) is synergistic with that of Mg²⁺. Thus, physiological concentrations of PEP and Mg²⁺ increase, whereas pyruvate and Mg²⁺ decrease the amount of dimeric, active, dephospho-enzyme I.     

Thermodynamic properties of solutions of benzoic and citric acids in formamide at different tempertures

The standard thermodynamic quantities, ΔG⁰, ΔH⁰, and ΔS⁰, associated with the ionization process of benzoic acid in formamide have been evaluated. The standard potentials of the Ag(s)/AgCNS(s)/CNS⁻ and the Ag(s)/Ag₃Ci(s)/Ci³⁻ electrode, and the standard thermodynamic quantities for the electrode processes have been calculated in formamide, at different temperatures.     

Solubility and thermodynamic data of manganese hydrogen phosphate in the system MnO---P2O5---H2O at 35, 40, 45 and 50°C

Manganese hydrogen phosphate monohydrate, MnHPO₄·H₂O, a new phase, is synthesized. Its solubility is investigated in the temperature range 35–50°C and pH range 3.4–7.5. K_sp, ΔH⁰, ΔS⁰ and ΔG⁰ for the dissolution are reported. The decrease in solubility with increase in pH is explained as due to a surface coating of insoluble basic phosphate.     

Reactions of oxidizing radicals with 2- and 3-aminopyridines: a pulse radiolysis study

Reactions of OH radicals and some one-electron oxidants with 2-aminopyridine (2-AmPy) and 3-aminopyridine (3-AmPy) were studied in aqueous solutions using pulse radiolysis technique. The OH adduct of 2-AmPy at pH 9 has an absorption maximum at 360 nm along with a weak absorption band in the visible region and was found to be reactive with oxygen. The rate constant for its reaction with O₂ was determined to be 1.0×10⁸ dm³ mol⁻¹ s⁻¹. At pH 4 also, the OH adduct of 2-AmPy has an absorption band at 360 nm. However, there are differences in the absorption at other wavelengths. From the plot of ΔOD vs. pH at 340 nm, the pK_a of the OH adduct was determined to be 6.5. Among the specific oxidants, only SO₄^−√ radicals were able to oxidize 2-AmPy. In the case of 3-aminopyridine (3-AmPy), the transient species formed by OH radical reaction at pH 9 has an absorption maximum at 410 nm with shoulder bands on both the sides. Its absorption spectrum at pH 4 was different indicating the existence of a pK value for the OH adduct. pK_a of 3-AmPy-OH radical adduct species was evaluated to be 5.7. This adduct species was also found to be reactive with oxygen (k=7.6×10⁶ dm³ mol⁻¹ s⁻¹). Specific one-electron oxidants like N₃^√, Br₂^−√ C₂^−√ and SO₄^−√ were able to oxidize 3-AmPy indicating that it is easier to oxidize 3-AmPy as compared to 2-AmPy.     

Vibrational spectra and density functional study of propylgermane

Raman and infrared spectra of propylgermane, CH₃CH₂CH₂GeH₃, and its Ge-deuterated analog, CH₃CH₂CH₂GeD₃, were investigated in their gaseous, liquid and solid states. The normal coordinate treatment was carried out by density functional theory (DFT) calculation, using B3LYP/6-31G^* and 6-311++G^** basis sets, and the corresponding fundamental vibrations were assigned. The trans (T) and gauche (G) forms around the central C–C bond coexisted in the gaseous and liquid states and only the T form existed in the solid state. From the temperature dependent measurements of the Raman spectra in the liquid state, the enthalpy difference was found to be ΔH(T−G)=−0.36±0.02 kcalmol⁻¹ with the T form being more stable. The energy differences between the isomers obtained by DFT calculations were ΔE(T−G)=−0.46 kcalmol⁻¹ and ΔE(T−G)=−0.87 kcalmol⁻¹ by the 6-31G^* basis set and 6-311++G^** basis set, respectively.     

Structure and conformational properties of carbonylbisimidosulfuryl fluoride, O=C(N=S(O)F2)2

The molecular structure and conformational properties of O=C(N=S(O)F₂)₂ (carbonylbisimidosulfuryl fluoride) were determined by gas electron diffraction (GED) and quantumchemical calculations (HF/3-21G* and B3LYP/6-31G*). The analysis of the GED intensities resulted in a mixture of 76(12)% syn–syn and 24(12)% syn–anti conformer (ΔH⁰=H⁰(syn–anti)−H⁰(syn–syn)=1.11(32) kcal mol⁻¹) which is in agreement with the interpretation of the IR spectra (68(5)% syn–syn and 32(5)% syn–anti, ΔH⁰=0.87(11) kcal mol⁻¹). syn and anti describe the orientation of the S=N bonds relative to the C=O bond. In both conformers the S=O bonds of the two N=S(O)F₂ groups are trans to the C–N bonds. According to the theoretical calculations, structures with cis orientation of an S=O bond with respect to a C–N bond do not correspond to minima on the energy hyperface. The HF/3-21G* approximation predicts preference of the syn–anti structure (ΔE=−0.11 kcal mol⁻¹) and the B3LYP/6-31G* method results in an energy difference (ΔE=1.85 kcal mol⁻¹) which is slightly larger than the experimental values. The following geometric parameters for the O=C(N=S)₂ skeleton were derived (r_a values with 3σ uncertainties): C=O 1.193 (9) Å, C–N 1.365 (9) Å, S=N 1.466 (5) Å, O=C–N 125.1 (6)° and C–N=S 125.3 (10)°. The geometric parameters are reproduced satisfactorily by the HF/3-21G* approximation, except for the C–N=S angle which is too large by ca. 6°. The B3LYP method predicts all bonds to be too long by 0.02–0.05 Å and the C–N=S angle to be too small by ca. 4°.     

Theoretical studies and rate constant calculations of the reactions C2F5CHO with OH radicals and Cl atoms

The hydrogen abstraction reactions of C₂F₅CHO with OH radicals and Cl atoms have been investigated theoretically by a dual-level direct dynamics method. In this study, the optimized geometries and frequencies of the stationary points are calculated at the MP2/cc-pVDZ level of theory. The energies of the stationery points and the selected points along the minimum energy paths are further refined at the MC-QCISD level using the MP2 geometries. Complexes with energies less than those of the reactants or products are located at the entrance or the exit channels of the two reactions. This result indicates that both of reactions proceed via indirect reaction mechanisms. The enthalpies of formation for the reactant C₂F₅CHO and the product radical C₂F₅CO are estimated by isodesmic reactions at the MC-QCISD//MP2/cc-pVDZ level. At the same level, the rate constants are calculated by canonical variational transition state theory (CVT) incorporating with the small-curvature tunneling correction (SCT) in the temperature range 200–1000 K. Good agreement between the calculated and experimental rate constants is obtained at the room temperature. Due to the lack of the kinetic data of these reactions, the fitted three-parameter expressions based on the CVT/SCT rate constants within 200–1000 K are k₁ = 1.64 × 10⁻²⁴ T^4.33 exp (−566.1/T) and k₂ = 6.33 × 10⁻¹⁵ T^1.35 exp (550.3/T) cm³ molecule⁻¹ s⁻¹, respectively.     

Heat capacities of NaNO3 and KNO3 from 350 to 800 K

The heat capacities of NaNO₃ and KNO₃ were determined from 350 to 800 K by differential scanning calorimetry. Solid-solid transitions and melting were observed at 550 and 583 K for NaNO₃ and 406 and 612 K for KNO₃, respectively. The entropies associated with the solid-solid transitions were measured to be (8.43± 0.25) J K⁻¹ mole⁻¹ for NaNO₃ and (13.8±0.4) J K⁻¹ mole⁻¹ for KNO₃. At 298.15 K the values of C⁰_P S⁰_P, {H⁰(T)-H⁰(0)}/T and -{G⁰(T)-H⁰(0)}/T, respectively, are 91.94, 116.3, 57.73, and 58.55 J K⁻¹ mole⁻¹ for NaNO₃ and 95.39, 133.0, 62.93, and 70.02 J K⁻¹ mole⁻¹ for KNO₃. Values for S⁰_T, {H⁰(T)-H⁰(0)}/T, and -{G⁰(T)-H⁰(0)}/T were calculated and tabulated from 15 to 800 K for NaNO₃ and KNO₃.     

Model reaction related to cytochrome P-450: effect of substitution on the rate of naphthalene oxidation

A kinetic method for measuring the relative rates of hydroxylation of naphthalene derivatives/cyclohexene has been developed. With this technique a linear relationship between the logarithm of the rates of oxidation products and the oxidation potentials of the naphthalene derivatives has been observed. Plots of σ Hammett and σ⁺ Hammett–Brown with logarithm of relative rates have been linear and shown ρ = −0.98 and ρ⁺ = −0.58, respectively. This contrast aromatic oxidation in protic solvents in which the oxidation products are naphthoquinones and provides further evidence for the intermediacy of carbocation in the hemin catalyzed hydroxylation of aromatic rings.     

A calorimetrical study of the polynuclear Zn(II) and Pb(II) and the polymeric Ni(II) and Cd(II) complexes of 2-mercaptoethanol and 3-mercapto-1,2-propanediol

The ΔG, ΔH and ΔS values for the dissociation of 2-mercaptoethanol (MEL) and 3-mercapto-1,2-propanediol and for the formation of complexes between these ligands and the metal ions Ni²⁺, Zn²⁺, Cd²⁺ and Pb²⁺ have been determined calorimetrically in 0.5 M KNO₃ and at 25°C.     

Thermal stability and related thermodynamic properties of N-ethylthiourea

The enthalpy and entropy of sublimation of N-ethylthiourea were obtained from the temperature dependence of its vapour pressure measured by both the torsion–effusion and the Knudsen effusion method in the temperature range 360–380 K. The compound undergoes no solid-to-solid phase transition or decomposition below 380 K. The pressure against reciprocal temperature resulted in lg(p, kPa) = (13.40 ± 0.27) − (6067 ± 102) /T(K). The molar sublimation enthalpy and entropy at the mid interval temperature were Δ_subH_m(370 K) = (116.1 ± 2.0) kJ mol⁻¹ and Δ_subS_m(370 K) = (218.0 ± 5.2) J mol⁻¹ K⁻¹, respectively. The same quantities derived at 298.15 K were (118.8 ± 2.1) kJ mol⁻¹ and (226.1 ± 5.5) J mol⁻¹ K⁻¹, respectively.     

Heat capacity of copper hydride

The heat capacity of copper hydride has been measured in the temperature range 2–60 and 60–250 K using two adiabatic calorimeters. Special procedure for the purification of CuH has been applied and a careful analysis of sample contamination has been performed. The experimental results have been extrapolated up to 300 K due to instability of the copper hydride at room temperature. From the temperature dependence of heat capacity the values of entropy S°(T), thermal part of enthalpy H°(T)−H°(0) and Gibbs function [−(G°(T)−H°(0))] have been calculated assuming S°(0)=0. The standard absolute entropy, standard entropy of formation from the elements and enthalpy of decomposition of copper hydride from the elements have been calculated and found to be 130.8 J K⁻¹ mol⁻¹ (H₂), −85.1 J K⁻¹ mol⁻¹ (H₂), −55.1 kJ mol⁻¹ (H₂), respectively. These new results gave the possibility of discussion on thermodynamic properties of copper hydride. Debye temperature has been for the first time determined experimentally.     

Adsorption of oligooxypropylenated amines at the aqueous solution—air interface: Homologous series of piperidine and morpholine derivatives

The surface tension isotherms for pure oligooxypropylenated piperidine and morpholine at the aqueous solution—air interface were determined and interpreted. The surface excess concentration, Γ, the surface area per molecule, A, and the standard free energy of adsorption, ΔG°, were calculated according to a new empirical adsorption equation. The standard free energy contribution for the oxypropylene group (PO) in morpholine derivatives,ΔG° (PO) = −3.34 kJ mol⁻¹, is substantially lower than that for the PO group located in the piperidine derivatives, i.e. ΔG° (PO)= −3.12 kJ mol⁻¹.