Excited state calculations on fluorene-based polymer blends: effect of stacking orientation and solvation

Polyfluorene-based polymer blends have been utilized in the development of optoelectronic devices. The constituent copolymers are chemically designed to facilitate more efficient electron/hole mobility, thereby enhancing control over exciton formation and dissociation. When appropriate pairs of these are blended together, intermolecular charged-particle localizations are induced, leading to significant intermolecular charge-transfer character and luminescence that exhibit some sensitivity to their interfacial orientation. The authors report on a time-dependent density functional theory quantum chemical investigation of the relevant excited states of the polymer blend poly[9,9-dioctylfluorene-co-N-(4-butylphenyl)diphenylamine]/poly(9,9-dioctylfluorene-co-benzothiadiazole. They show that the calculated excited states generally agree with experimental observations although there is a consistent underestimation of the charge-transfer states. Further, they show sensitivity to lateral shifts in interfacial stacking. Finally, solvation with a low dielectric solvent greatly stabilizes the charge-transfer states.     

Thermodynamics of solvation and solvophobic effect in formamide

Using semi-adiabatic calorimetry, we measured the enthalpies of solution for various low-polar compounds including alkanes, aromatic hydrocarbons and their halogenated derivatives in formamide at temperature of 298 K. For the same compounds, the values of limiting activity coefficients in formamide were determined using GC headspace analysis at 298 K, and Gibbs free energies of solution and solvation were calculated. Based on these data and the available literature values of the Gibbs free energy of solvation in formamide for a number of other low-polar solutes, a study of the solvophobic effect in this solvent is performed, and its resemblance to the hydrophobic effect in aqueous solutions is demonstrated. It is shown that the contribution of the solvophobic effect into the solvation Gibbs free energy in formamide is much higher than that in aliphatic alcohols, but lower than that in water. Like in water, the magnitude of this contribution for different solutes linearly increases with the solute molecular volume. Solvophobic effect also significantly affects the enthalpies of dissolution in formamide, causing them to be more negative in the case of alkanes and more positive in the case of arenes.     

Modeling the effect of solvation on solute retention in reversed-phase liquid chromatography

The retention of a homologous series of alkylbenzenes was determined on octyl and octadecyl reversed-phase columns in several polar organic liquids. Free energies of transfer were calculated by the SM5.0R classical solvation model for each organic liquid tested and for several alkanes. The relationships between the measured retention factors and the calculated free energies of transfer were then investigated. Although the natural logarithms of the retention factor and the calculated free energies of transfer were linearly correlated, the obtained free energies of transfer of the solutes did not completely explain the retention behavior of the solutes. Nonetheless, even in these pure organic liquids, the energetics of RPLC retention behaved very similarly to those of partitioning.     

DNA base stacking involving adenine and 2-aminopurine

The potential energy surfaces of stacked structures consisting of adenine (A) and 2-aminopurine (2AP) have been investigated in the gas phase. Both face-to-back (the double-ring system of one base exactly on top of that of the other one) and face-to-face (one base flipped by 180°) A/A, 2AP/2AP and A/2AP stacks were considered. Minima and transition states were optimised at the counterpoise-corrected M06-2X/6-31+G(d) level of theory. For each type of stack, between five and nine minima were located, usually connected by low barriers of 1–2 kcal/mol. This shows the large conformational flexibility of these stacked base pairs. The double-ring system in A and 2AP affords multiple minima with similar twist angles, making the potential energy surface of stacks comprising of purine bases more complex than those of pyrimidine stacks. The locations of the stationary points on the potential energy surface differ for the three different systems; thus, the replacement of A by 2AP in a base stack changes its potential energy landscape.     

Studies on the effect of ethanol on the solvation behaviour of thiamine hydrochloride in water

The specific conductance of Thiamine hydrochloride in water and water-ethanol mixtures was measured at different temperatures 283, 293, 303 and 313 K. Kraus-Bray and Shedlovsky models of conductivity were used for analyzing conductance data. The limiting molar conductance, association constant K _a, energy of activation of the rate process E _a, and related thermodynamic parameters have been determined. Based on viscosity of the solvent, Walden product and Stokes molecular radius were also been determined. Born model of ion solvation was proved. Standard thermodynamic parameters of association (G _a, H _a and S _a) were calculated and discussed. The results show the decrease in limiting molar conductance and increase in K _a with decrease in relative permittivity. Such computed values have been used to discuss the solvation behaviour of Thiamine hydrochloride in water-ethanol mixtures.     

An improved coarse-grained model of solvation and the hydrophobic effect

We present a coarse-grained lattice model of solvation thermodynamics and the hydrophobic effect that implements the ideas of Lum-Chandler-Weeks theory [J. Phys. Chem. B 134, 4570 (1999)] and improves upon previous lattice models based on it. Through comparison with molecular simulation, we show that our model captures the length-scale and curvature dependence of solvation free energies with near-quantitative accuracy and 2-3 orders of magnitude less computational effort, and further, correctly describes the large but rare solvent fluctuations that are involved in dewetting, vapor tube formation, and hydrophobic assembly. Our model is intermediate in detail and complexity between implicit-solvent models and explicit-water simulations.     

Power-law solvation dynamics in DNA over six decades in time

Time-resolved Stokes shifts in a dye-containing oligonucleotide have been observed over the entire time range from 40 fs to 40 ns. The dynamics fit to a power law with a small exponent of 0.15. Similar relaxation has been seen in proteins but has not been anticipated in DNA. Distinct relaxation components due to specific subcomponents of the system, bulk water, bound water, counterions, backbone, bases, and so on, are not found. The various subcomponents may be so strongly coupled that their motions cannot be treated separately.     

The effect of methylation on the hydrogen-bonding and stacking interaction of nucleic acid bases

Methylated nucleosides play an important role in DNA/RNA function, and may affect republication by interrupting the base-pairing and base-stacking. In order to investigate the effect of methylation on the interaction between nucleic acid bases, this work presents the hydrogen-bonding and stacking interactions between 5-methylcytosine and guanine (G), cytosine (C) and G, 1-methyladenine and thymine (T), as well as adenine and T. Geometry optimization and potential energy surface scan have been performed for the involved complexes by MP2 calculations. The interaction energies, which were corrected for the basis-set superposition error by the full Boys–Bernardi counterpoise correction scheme, were used to evaluate the interaction intensity of these nucleic acid bases. The atoms in molecules theory and natural bond orbital analysis have been performed to study the hydrogen bonds in these complexes. The result shows that the methyl substitute contributes the stability to these complexes because it enhances either the hydrogen bonding or the staking interaction between nucleic acid bases studied.     

Preferential solvation within hydrophilic nanocavities and its effect on the folding of cholate foldamers

The conformations of three cholate foldamers and one molecular basket were studied by fluorescence and NMR spectroscopy. In nonpolar solvents (e.g., hexane/ethyl acetate or ethyl acetate) mixed with a small amount of a polar solvent (e.g., alcohol or DMSO), the cholate oligomer folded into a helix with the hydrophilic faces of the cholates turned inward. Folding created a hydrophilic nanocavity preferentially solvated by the entrapped polar solvent concentrated from the bulk. This microphase separation of the polar solvent was critical to the folding process. Folding was favored by larger-sized polar solvent molecules, as fewer such molecules could occupy and solvate the nanocavity, thus requiring a smaller extent of phase separation during folding. Folding was also favored by smaller/acyclic nonpolar solvent molecules, probably because they could avoid contact with the OH/NH groups within the nanocavity better than larger/cyclic nonpolar solvent molecules.     

Counterintuitive solvation effect of ionic-liquid/DMSO solvents on acidic C–H dissociation and insight into respective solvation

How would acidic bond dissociation be affected by adding a small quantity of a weakly polar ionic liquid IL (the “apparent” or “measured” dielectric constant ε of the IL is around 10–15) into a strongly polar molecular solvent (e.g., ε of DMSO: 46.5), or vice versa? The answer is blurred, because no previous investigation was reported in this regard. Toward this, we, taking various IL/DMSO mixtures as representatives, have thoroughly investigated the effects of the respective solvent in ionic–molecular binary systems on self-dissociation of C–H acid phenylmalononitrile PhCH(CN)₂via pK_a determination. As disclosed, in this category of binary media, (1) no linear correspondence exists between pK_a and molar fractions of the respective solvent components; (2) only ∼1–2 mol% of weakly polar ILs in strongly polar DMSO make C–H bonds even more dissociative than in neat DMSO; (3) a small fraction of DMSO in ILs (<10 mol%) can dramatically ease acidic C–H-dissociation; and (4) while the DMSO fraction further increases, its acidifying effect becomes much attenuated. These findings, though maybe counterintuitive, have been rationalized on the basis of the precise pK_a measurement of this work in relation to the respective roles of each solvent component in solvation.

The dependence of PhCH(CN)₂ pK_a on the molar fraction of ionic liquids in ionic–molecular binary mixtures showed a nonlinear three-fragment plot, which was rationalized for the first time by the respective roles of each solvent component for solvation.     

Excited-state solvation and proton transfer dynamics of DAPI in biomimetics and genomic DNA

The fluorescent probe DAPI (4',6-diamidino-2-phenylindole) is an efficient DNA binder. Studies on the DAPI-DNA complexes show that the probe exhibits a wide variety of interactions of different strengths and specificities with DNA. Recently the probe has been used to report the environmental dynamics of a DNA minor groove. However, the use of the probe as a solvation reporter in restricted environments is not straightforward. This is due to the presence of two competing relaxation processes (intramolecular proton transfer and solvation stabilization) in the excited state, which can lead to erroneous interpretation of the observed excited-state dynamics. In this study, the possibility of using DAPI to unambiguously report the environmental dynamics in restricted environments including DNA is explored. The dynamics of the probe is studied in bulk solvents, biomimetics like micelles and reverse micelles, and genomic DNA using steady-state and picosecond-resolved fluorescence spectroscopies.     

Exceptional thermodynamic stability of DNA duplexes modified by nonpolar base analogues is due to increased stacking interactions and favorable solvation: Correlated ab initio calculations and molecular dynamics simulations

The geometries of DNA hexamer (5'-GGAACC-3') and DNA 13-mer (5'-GCGTACACATGCG-3') have been determined by molecular dynamics (MD) simulations using an empirical force field. The central canonical base pair was replaced by a pair of nonpolar base analogues, 2,2'-bipyridyl and 3-methylisocarbostyril. The stabilization energy of the model system (model A) consisting of a central base pair (base-analogue pair) and two neighboring base pairs was determined by the RI-MP2 method using an extended aug-cc-pVDZ basis set. The geometry of the model was averaged from structures determined by MD simulations. The role of the solvent was covered by the COSMO continuum solvent model and calculations were performed for a larger model system (model B) which also contained a sugar-phosphate backbone. The total stabilization energies of the unperturbed system and the system perturbed by a base-analogue pair (model A) were comparable to the stability of both duplexes experimentally determined. This is due to large stacking interaction energy of the base-analogue self-pair which compensates for the missing hydrogen-bonding energy of the replaced adenine...thymine base pair. The selectivity of the base-analogue pair was reproduced (model B) when their desolvation energy was included with the interaction energy of both strands determined by the approximate SCC-DFTB-D method.     

The effect of preferential solvation on the kinetic order of alkyl methacrylate polymerization in benzene

The kinetic order of the polymerization of n-alkylmethacrylates with respect to monomer in benzene (fractional and greater than one) has been interpreted as due to concentration changes of a monomer at the site of reaction caused by preferential solvation of the growing macromolecule by benzene. Correlation of the rates of polymerization at 30° with determined monomer concentrations in the close vicinity of the polymer chain gives kinetic orders of 1±0.05 for both n-butyl- and n-dodecyl-methacrylates. The coefficient of preferential solvation at 30° for the polymers investigated is between 0.1 and 0.4 [cm³ g^?1] depending on the composition of the mixture of benzene and monomer. The coordination numbers 3 and 4 needed for calculation of the composition of the solvent in the solvating layer correspond to theoretical views on polymer solutions.     

Numerical model for DNA loading in microdevices: stacking and autogating effects

Many electrophoresis-based DNA sequencing and genotyping microdevices rely on field-driven effects to load and preconcentrate the sample. A quantitative model is developed for a broad class of electrophoresis-based microfabricated sample injectors. Quantitative predictions of DNA preconcentration are compared with experimental data and are shown to qualitatively reproduce the detailed time-evolving sample distribution in the injector. The model provides practical guidance on device and protocol design, in order to optimize this critical aspect of microfluidic devices.     

A breathing wormlike chain model on DNA denaturation and bubble: effects of stacking interactions

DNA stably exists as a double-stranded structure due to hydrogen-bonding and stacking interactions between bases. The stacking interactions are strengthened when DNA is paired, which results in great enhancement of bending rigidity. We study the effects of this stacking-induced stiffness difference on DNA denaturation and bubble formations. To this end, we model double-stranded DNA as a duplex of two semiflexible chains whose persistence length varies depending on the base-pair distance. Using this model, we perform the Langevin dynamics simulation to examine the characteristics of the denaturation transition and the statistics of the bubbles. We find that the inclusion of the stacking interactions causes the denaturation transition to be much sharper than otherwise. At physiological temperature, the stacking interactions prohibit the initiation of bubble formation but promote bubbles, once grown, to retain the large size.     

Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides

Continuous stacking hybridization of oligodeoxyribonucleotides with the stem of a preformed minihairpin structure of a DNA template was studied by thermal denaturation in solution. The thermodynamic parameters (H°, S°, and G°₃₇) were determined for the formation of all 16 possible types of coaxial stackings (or cooperative interactions) ^5" X*pY ^3"/^5" ZZ"3" (an asterisk stands for a nick) between the terminal complementary base pairs of two adjacent duplexes formed on a common DNA template. The maximum efficacy G°₃₇ of coaxial stacking (1 M NaCl, pH 7.4) was observed for the G*pC/GC interaction (–2.76 kcal mol^–1), whereas the minimum efficacy was observed for the T*pA/TA interaction (–0.85 kcal mol^–1). In the general case, the efficacy of the cooperative interaction at the X*pY/ZZ" junction does not correlate with the energy of formation of the corresponding unified XY/ZZ" dinucleotide pair in the structure of native DNA. The formation of a stack by the terminal oligonucleotide bases upon their continuous stacking hybridization makes the major and governing contribution to the energy of cooperative interaction.