Effects of Pressure and pH on the Physical Stability of an I-Motif DNA Structure

The thermodynamic stability of a cytosine(C)-rich i-motif tract of DNA, which features pH-sensitive [C..H..C]⁺ moieties, has been studied as function of both pressure (0.1–200 MPa) and pH (3.7–6.2). Careful attention was paid to correcting citrate buffer pH for known variations that stem from changes in pressure. Once pH-corrected, (i) at pH >4.6 the i-motif becomes less stable as pressure is increased (K_D decreases), giving a small negative volume change for dissociation (Δ_DV°) of the i-motif – a conclusion opposite to that which would be drawn if the buffer pH was not corrected for the effects of pressure; (ii) the i-motif's melting temperature increases by more than 30 K between pH 6.5 and 4.5, the consequence of an enthalpy for dissociation (Δ_DH°) of 77(3) and 90(3) kJ (mol H⁺)⁻¹ at 0.1 and 200 MPa, respectively; (iii) below pH 4.6 at 0.1 MPa (pH 4.3 at 200 MPa) the melting temperature decreases as a result of double protonation of cytosine pairs, and Δ_DH° and Δ_DV° change signs; and (iv) the combination of Δ_DH° and Δ_DV° lead to the melting temperature at pH 4.3 being 3 K higher at 200 MPa than at 0.1 MPa.     

Theoretical studies of intramolecular electron transfer reactions: Distance and free energy dependences

Electron tunneling through a square potential energy barrier is used to calculate the distance-dependent factors of electron transfer (ET) processes in metal-monolayer-metal junctions, donors and acceptors dispersed in rigid organic glasses, intramolecular ET in rigid donorbridge—acceptor species in solution and redox centers attached to electrodes through adsorbed monolayers. This tunneling model of distancedependent non-adiabatic factors is incorporated in the intersecting state model (ISM). The result is a simple semiclassical theory which is used to calculate the rates of non-adiabatic ET reactions. When the electron is originally located in a π* molecular orbital of the donor and the reaction free energy is no lower than approximately −50 kJ mol⁻¹, no adjustable parameters are necessary to calculate the intramolecular ET rates from a donor, through a rigid bridge, to an acceptor. Such calculated rates are within an order of magnitude of the experimental values. The model can also account for the ET rates of more exothermic reactions provided that the value of an empirical parameter, which is constant for structurally related reactants and solvents of similar polarity, is estimated. The physical meaning of this parameter is related to the dynamics of the reactions. The profiles of the distance and free energy dependences of photoinduced ET rates are closely reproduced. The occurrence of distance-dependent non-adiabatic factors in intermolecular σ*-d ETs is rationalized.     

Electrostatic model for protein adsorption in ion-exchange chromatography and application to monoclonal antibodies,lysozyme and chymotrypsinogen A

A model for the adsorption equilibrium of proteins in ion-exchange chromatography explicitly accounting for the effect of pH and salt concentration in the limit of highly diluted systems was developed. It is based on the use of DLVO theory to estimate the electrostatic interactions between the charged surface of the ion-exchanger and the proteins. The corresponding charge distributions were evaluated as a function of pH and salt concentration using a molecular approach. The model was verified for the adsorption equilibrium of lysozyme, chymotrypsinogen A and four industrial monoclonal antibodies on two strong cation-exchangers. The adsorption equilibrium constants of these proteins were determined experimentally at various pH values and salt concentrations and the model was fitted with a good agreement using three adjustable parameters for each protein in the whole range of experimental conditions. Despite the simplifications of the model regarding the geometry of the protein–ion-exchanger system, the physical meaning of the parameters was retained.     

Temperature and frequency dependencies of the complex dielectric constant of poly(ethylene oxide) under hydrostatic pressure

Electrical impedance measurements have been made in the frequency range 5 Hz to 10 MHz in pure poly(ethylene oxide) having a molecular weight of 600,000 from 12 K nearly up to the melting point of the crystalline phase (about 330 K). A pronounced relaxation peak in the dielectric loss and a corresponding step in the dielectric constant have been observed at about 240 K, which can be readily related to the glass-rubber transition in the amorphous region of the polymer. As the temperature approaches the melting point there are large increases in the real ϵ′ and imaginary e′ parts of the dielectric constant. The frequency dependence of ϵ′ is characterized by a primary relaxation process, whose frequency increases with increasing temperature as a consequence of decrease of the average structural relaxation time. There is strong evidence that this low-frequency dispersion arises mainly from the diffusive transport of ionic charge carriers rather than a purely orientation relaxation process. In addition, the effects of hydrostatic pressures (0–0.25 GPa) on the frequency dependencies of the real ϵ′ and imaginary ϵ′ parts of the dielectric constant have been measured in the temperature range from 254 to 329 K. An advantage of applying pressure is that it shifts the α_𝒶 relaxation peak into an experimentally accessible frequency window of the equipment; the lowering of frequency results from a decrease in the relaxation volume and a consequent reduction in the mobility of the molecular units. Results are discussed in terms of theoretical models of the effect of pressure on the glass transition, providing information on the cooperative dynamics. © 1996 John Wiley & Sons, Inc.     

Isocratic networks in supercritical fluid chromatography II: Selectivities and effective plate numbers

The dependence of the selectivity α and the effective plate number, N, on temperature and pressure is shown in three-dimensional diagrams. The specific system studied was pentane as the mobile phase, unmodified silica as the stationary phase, and a set of four polycyclic hydrocarbons as the test mixture. Temperature and pressure ranges were from 25 to 300°C and from 30 to 75 bar, respectively. The plots for α and N are found to resemble those for capacity ratio, k′, and resolution, R, studied earlier with the same system [1]. A distinct maximum is observed for N in the supercritical region, as found earlier for k′ and R. This applies also to α for the homologous substrate pair naphthalene/anthracene, while the resemblance for α is less pronounced for the pair anthracene/pyrene.     

Molecular Dynamics Studies of the Kinetics of Phase Changes in Clusters IV： Crystal Nucleation from Molten （NaCl）256 and （NaCl）500 Clusters

Molecular dynamics computer simulation based on the Born-Mayer-Huggins potential function has been carried out to study the effects of duster size and temperature on the nucleation rate of sodium chloride dusters in the temperature range of 580 K to 630 K. Clusters with 256 and 500 NaCl molecules have been studied and the results have been compared with those obtained from 108 molecule dusters. The melting point (MP) of the clusters were observed to increase with the size of the clusters and can be well described by a linear equation MP =1107(37)-1229(23)N^-1/3(N is the number of molecules in the duster).The nucleation rate was found to decrease with increasing the duster size or temperature. Various nucleation theories have been used to interpret the nucleation rates obtained from this molecular dynamics simulation. It is possible to use a constant diffuse interface thickness to interpret the nucleation rate from the diffuse interface theory in the temperature range of this study. However, the interfacinl free energy estimated from classical nucleation theory and diffuse interface theory increases too fast with increasing the temperature while that from Gran-Gunton theory does not change with changing temperatures.The sizes of critical nuclei estimated from all the theories are smaller than those estimated from our simulations.     

Description of core excitations by time-dependent density functional theory with local density approximation, generalized gradient approximation, meta-generalized gradient approximation, and hybrid functionals

Time-dependent density functional theory (TDDFT) is employed to investigate exchange-correlation-functional dependence of the vertical core-excitation energies of several molecules including H, C, N, O, and F atoms. For the local density approximation (LDA), generalized gradient approximation (GGA), and meta-GGA, the calculated X1s-->pi* excitation energies (X = C, N, O, and F) are severely underestimated by more than 13 eV. On the other hand, time-dependent Hartree-Fock (TDHF) overestimates the excitation energies by more than 6 eV. The hybrid functionals perform better than pure TDDFT because HF exchange remedies the underestimation of pure TDDFT. Among these hybrid functionals, the Becke-Half-and-Half-Lee-Yang-Parr (BHHLYP) functional including 50% HF exchange provides the smallest error for core excitations. We have also discovered the systematic trend that the deviations of TDHF and TDDFT with the LDA, GGA, and meta-GGA functionals show a strong atom-dependence. Namely, their deviations become larger for heavier atoms, while the hybrid functionals are significantly less atom-dependent.     

Where are the angles? Angular dependence (and independence) of orbitals and functions

Certain conditions under which a collection of atomic orbitals becomes angularly independent are considered. The results are applied to molecules of chemical interest. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Molecular Dynamics Studies of the Kinetics of Phase Changes in Clusters II: Crystal Nucleation from Molten (RbCl)256 and (RbCl)500 Clusters

Molecular dynamics computer simulations have been carried out to study the effects of cluster size and temperature on the nucleation rate of rubidium chloride clusters in the temperature range of 500-650 K. Clusters with 256 and 500 RbCl molecules have been studied and the results are compared with those obtained from 108 molecule clusters. The melting point (MP) of the clusters was observed to increase with the size of the clusters and can be described by a linear equation MP=997-405 N^−1/3, where N is the number of molecules in the cluster. The nucleation rate is found to decrease with increasing cluster size or increasing nucleation temperature. Both classical nucleation theory and diffuse interface theory are used to interpret our observed results.     

Phase behavior of pseudo-IPN's of polycarbonate-urethane and polystyrene

The pseudo-IPN's of PCU/PS with different M_n and narrow MWD of the linear PS have been synthesized and characterized. The effect of M_n and composition on the phase morphology of the pseudo-IPN's of PCU/PS has been studied by DSC and SEM. The pseudo-IPN's with ultra-high M_n of the linear PS appeared to possess a single T_g and no SEM-resolvable domains at 35 wt % PS and below. This metastable state may reflect the result of a high extent of entanglement of the linear PS chains with the PCU network and the limited molecular mobility of the linear PS chains with high M_n. © 1993 John Wiley & Sons, Inc.     

Compressibilities of cyclohexane and toluene mixtures at various temperatures

The isothermal compressibilities _T for cyclohexane+toluene mixtures at 25, 35, 45 and 60°C have been determined by direct piezometric measurement. By combining our results with supplementary literature data, we have calculated the isentropic compressibility _S. Values of the excess functions (V^E/_p)_T, _T ^E and _S ^E were also calculated at four temperatures and their behavior as a function of mole fraction and temperature was studied.     

Dosimetric properties of commercial grade plexiglas as a possible routine dosimeter for radiation processing

Dyed and undyed polymethylmethacrylate (PMMA) are commercially available for high dose dosimetry in radiation processing applications. In order to investigate the properties of the locally available clear perspex as a subsitute routine dosimeter, we have looked into the optical and dosimetric properties of clear perspex sheets with a thickness of 2 mm.

The selected wavelength used for read out was 314 nm. Absorption spectra obtained showed a sharp cutoff at 260 nm wavelength. Post-irradiation studies at different doses indicate that the optical density decrease with storage time. No significant dose rate dependence in the range of 1.1 to 11 kGy/hr has been observed. The temperature response of the said clear perspex in the range of 0–30°C during irradiation has also been determined.

Comparison of the optical density versus dose for the local clear perspex against that of red perspex from Harwell, at an absorbed dose of 25 kGy, as obtained in our gamma irradiator, IR-136, showed a difference of 3%. The reproducibility of the local clear PMMA has been observed to be also less than 3% in an absorbed dose range of 5 to 50 kGy.     

Critical Evaluation of Protonation Constants. Literature Analysis and Experimental Potentiometric and Calorimetric Data for the Thermodynamics of Phthalate Protonation in Different Ionic Media

The protonation constants of phthalate were determined in aqueous NaCl (0.1 ≤ I ≤ 5,mol⋅L⁻¹) and in aqueous Me₄NCl (0.1 mol⋅L⁻¹ ≤ I ≤ 3,mol⋅L⁻¹) at t = 25,^∘C. Experimental data were employed in conjunction with literature data from studies in different ionic media (Et₄NI: 0 ≤ I ≤ 1,mol⋅L⁻¹; NaClO₄: 0.05 mol⋅L⁻¹ ≤ I ≤ 2,mol⋅L⁻¹)to study the dependence on ionic strength using different models, such as the SIT and Pitzer equations, and an Extended Debye-Hückel type equation. Experimental calorimetric data in NaCl and protonation constants at different temperatures in Et₄NI (5 ≤ t ≤ 45^∘C) and in NaClO₄ (15 ≤ t ≤ 35 ^∘C) were also used to study their dependence on temperature. Recommended equilibrium data are reported together with a short discussion of a prospective protocol for drawing these data.     

Effects of stress ratio on fatigue crack growth of thermoset epoxy resin

The influences of stress ratio (R) on fatigue crack growth (FCG) of thermoset epoxy resin with polyamine hardener were investigated. The FCG growth rates (da/dN) have been correlated by the linear-elastic fracture mechanics parameters (ΔK and K_max), and nonlinear-elastic fracture mechanics parameter (ΔJ). The effects of R on FCG were observed when the ΔK and ΔJ were used as fracture mechanics parameters for FCG. However, the K_max successfully characterized FCG under cyclic-dependent condition (FCGs at R = 0.1 and 0.4); but it failed to characterize the FCG under time-dependent condition (FCG at R = 0.7). As a time-dependent fracture mechanics parameter, C* was applied to correlate the time-dependent FCG rate (da/dt). A reasonable agreement was obtained between time-dependent FCG (R = 0.7) and creep crack growth (CCG) results.     

Partial molar enthalpies of solution as indicators of interactions in mixtures of 2-butoxyethanol and 2-butanol with water

Calorimetric measurements have been made of differential enthalpies of solution of both components in the binary system 2-butoxyethanol-water and of 2-butanol in the system 2-butanol-water as a function of composition at three different temperatures. The heat capacity changes for dissolution were calculated from the temperature variation of the solution enthalpies. Drastic changes of the solution properties are seen with increasing solute concentration in water-rich solutions. In the 2-butoxyethanol-water system, which could be studied over the whole composition range, four different regions can be identified. At extreme dilution in water, the solute is fully hydrated with a primary hydration layer of monolayer thickness involved in long-range secondary hydration. In dilute solutions the primary hydration layer is unchanged but the secondary hydration diminishes with increasing solute concentration. In semi-dilute solution the primary hydration layer breaks down and the particular hydrophobic characteristics of hydrocarbon groups in aqueous solution disappear. At higher solute content the mixtures show no hydrophobic character but the behavior of regular mixtures of polar solutes.     

Unexpected proton spin‐lattice relaxation in the solutions of polyolefin and tetrachloroethane

‘Unexpected’ proton spin‐lattice relaxation (T₁) times are reported for the solutions of poly(ethylene‐co‐1‐octene) and tetrachloroethane‐d₂. For the residual protons of the deuterated solvent and the methyl and vinyl protons at the polymer chain ends, their T₁ relaxation times vary significantly with both the polymer concentration and molecular weight over a wide range. The T₁s also decrease with increasing temperature at relative high temperatures. Such behaviors are in contrast to most reported polymer solutions in which the T₁ has nearly no concentration or molecular weight dependence in the dilute and semi‐dilute regime, and normal dependence on temperature. Further investigation revealed that the paramagnetic oxygen effect did shorten the measured proton T₁s, but cannot account for the unexpected T₁ dependences. Spin rotation is proposed to provide a reasonable explanation. Copyright © 2010 John Wiley & Sons, Ltd.     

Modelling of proton and metal exchange in the alginate biopolymer

Acid–base behaviour of a commercial sodium alginate extracted from brown seaweed (Macrocystis pyrifera) has been investigated at different ionic strengths (0.1≤I/mol l^?1≤1.0) and in different supporting electrolytes (Et₄NI, NaCl, KCl, LiCl, NaCl+MgCl₂), with the aim of examining the influence of ionic medium on the proton-binding capacity and of quantifying the strength of interaction with light metal ions in the perspective of speciation studies in natural aqueous systems. Potentiometric ([H⁺]-glass electrode) and titration calorimetric data were expressed as a function of the dissociation degree (α) using different models (Henderson–Hasselbalch modified, Högfeldt three parameters and linear equations). The dependence on ionic strength of the protonation constants was taken into account by a modified specific interaction theory model. Differences among different media were explained in terms of the interaction between polyanion and metal cations of the supporting electrolytes. Quantitative information on the proton-binding capacity, together with the stabilities of different species formed, is reported. Protonation thermodynamic parameters, at α=0.5, are log K ^H=3.686±0.005, ΔG ⁰=?21.04±0.03 kJ mol^?1, ΔH ⁰=4.8±0.2 kJ mol^?1 and TΔS ⁰=35.7±0.3 kJ mol^?1, at infinite dilution. Protonation enthalpies indicate that the main contribution to proton binding arises from the entropy term. A strict correlation between ΔG and TΔS was found, TΔS=?9.5–1.73 ΔG. Results are reported in light of building up a chemical complexation model of general validity to explain the binding ability of naturally occurring polycarboxylate polymers and biopolymers. Speciation profiles of alginate in the presence of sodium and magnesium ions, naturally occurring cations in natural waters, are also reported.     

Computational linear dependence in molecular electronic structure calculations using universal basis sets

Distributed universal even‐tempered basis sets have been developed over recent years that are capable of supporting Hartree–Fock energies to an accuracy approaching the sub‐μHartree level. These basis sets have also been exploited in correlation studies, in applications to polyatomic molecules, and in the calculation of electric properties, such as multipole moments, polarizabilities, and hyperpolarizabilities. Jorge and coworkers have also developed universal basis sets and have recently reported applications to diatomic molecular systems. In this article, we compare the molecular calculations reported by Jorge and coworkers with our previous studies. Particular attention is given to the degree of computational linear dependence associated with the various basis sets employed and the consequential effects of the accuracy of the calculated energies. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005