Parametrizing PCM to obtain solvation free energies from group contributions

A parametrization methodology for evaluating the solvation free energy, using the polarizable continuum model implemented in Gamess software, is presented in a formulation which makes use of a group contribution conception to construct the cavities. The systems studied include alkanes, alcohols, aldehydes and ketones embeded in a continuous medium simulating the water as the solvent. For each family, the CH2, OH, and C=O moieties of atoms are put together in single spheres forming a group. The cavities are constructed in two different ways, one for the electrostatic component and the other for nonelectrostatic contributions, i.e., the cavitation, dispersion, and repulsion components of free energy of solvation. A multivariate analysis is performed to obtain an assembly of variables, for each homologous series, able to give the results which are close to experiment. The analysis is addressed in order to (i) compare the theoretical free energy of solvation with the experimental trends of the solutes in aqueous media, when the chain is increased, (ii) compare the behavior of each component of free energy with the increasing CH2 number, (iii) investigate the influence of the oxygen atom on the components, and (iv) quantify the relative contribution of each component to the final free energy of solvation for some homologous series.     

A quantum mechanical strategy to investigate the structure of liquids: the cases of acetonitrile, formamide, and their mixture

A computational strategy based on quantum mechanical (QM) calculations and continuum solvation models is used to investigate the structure of liquids (either neat liquids or mixtures). The strategy is based on the comparison of calculated and experimental spectroscopic properties (IR-Raman vibrational frequencies and Raman intensities). In particular, neat formamide, neat acetonitrile, and their equimolar mixture are studied comparing isolated and solvated clusters of different nature and size. In all cases, the study seems to indicate that liquids, even when strongly associated, can be effectively modeled in terms of a shell-like system in which clusters of strongly interacting molecules (the microenvironments) are solvated by a polarizable macroenvironment represented by the rest of the molecules. Only taking into proper account both these effects can a correct picture of the liquid structure be achieved.     

Complexation behavior of alpha-, beta-, and gamma-cyclodextrin in modulating and constructing polymer networks

A systematic study of the host-guest complexation by alpha-, beta-, and gamma-cyclodextrin (CD) in either the free state or as substituents of poly(acrylic acid) (PAA) with the hydrophobic n-octadecyl groups, C18, substituted onto PAA (HMPAA) and its effect on polymer aggregation and network formation is reported. Free alpha-CD, beta-CD, and gamma-CD mask hydrophobic associations between the C18 substituent of HMPAA in aqueous solution and form host-guest complexes with a 1:1 or CD:C18 substituent stoichiometry at 0.5 wt % polymer concentration. For alpha-CD this host-guest stoichiometry changes to 2:1 or 2alpha-CD:C18 at > or =1 wt % polymer concentrations but not for beta-CD and gamma-CD. Shear-thickening occurs when gamma-CD complexes C18 HMPAA substituents. Upon addition of sodium dodecyl sulfate, SDS (SDS:CD = 1:1), the hydrophobic associations between C18 diminished by alpha-CD masking were fully restored, were only partly restored in the case of beta-CD, and not restored for gamma-CD. When alpha- and beta-CD substituted PAA (alpha-CDPAA and beta-CDPAA) were mixed with HMPAA polymer, networks formed. As for free beta-CD, the beta-CD substituents of beta-CDPAA also formed 1:1 or beta-CD:C18 stoichiometry host-guest complexes with the C18 substituents of HMPAA. The alpha-CD substituents of alpha-CDPAA also formed 1:1 or alpha-CD:C18 stoichiometry host-guest complexes with some indication of the formation of 2:1 or 2alpha-CD:C18 stoichiometry host-guest complexes at polymer concentrations > or =1 wt %. The polymer networks formed by beta-CDPAA with HMPAA are less viscous than those formed by alpha-CDPAA, for which shear-thickening occurs at polymer concentrations > or =2 wt %. It is evident that the difference in CD annular size and its match with the C18 of HMPAA control the diversity of the interactions of alpha-CD, beta-CD, gamma-CD, alpha-CDPAA, and beta-CDPAA with HMPAA.     

Kinetic characterization of an extremely slow DNA binding equilibrium

We here exploit the recently reported thermodynamic preference for poly(dAdT)(2) over mixed-sequence calf thymus (ct) DNA of two binuclear ruthenium complexes, DeltaDelta-[mu-bidppz(bipy)4Ru2](4+) (B) and DeltaDelta-[mu-bidppz(phen)(4)Ru(2)](4+) (P), that bind to DNA by threading intercalation, to determine their intrinsic dissociation rates. After adding poly(dAdT)(2) as a sequestering agent to B or P bound to ct-DNA, the observed rate of change in luminescence upon binding to the polynucleotide reflects the rate of dissociation from the mixed sequence. The activation parameters for the threading and dissociation rate constants allow us for the first time to characterize the thermodynamics of the exceedingly slow threading intercalation equilibrium of B and P with ct-DNA. The equilibrium is found to be endothermic by 33 and 76 kJ/mol, respectively, and the largest part of the enthalpy difference between the complexes originates from the forward threading step. At physiological temperature (37 degrees C) B and P have dissociation half-lives of 18 and 38 h, respectively. This is to our knowledge the slowest dissociating noncovalently bound DNA-drug reported. SDS sequestration is the traditional method for determination of rate constants for cationic drugs dissociating from DNA. However, the rates may be severely overestimated for slowly dissociating molecules due to unwanted catalysis by the SDS monomers and micelles. Having determined the intrinsic dissociation rates with poly(dAdT)(2) as sequestering agent, we find that the catalytic effect of SDS on the dissociation rate may be up to a factor of 60, and that the catalysis is entropy driven. A simple kinetic model for the SDS concentration dependence of the apparent dissociation rate suggests an intermediate that involves both micelles and DNA-threaded complex.     

Distinguishing and quantification of the human visual pathways using high-spatial-resolution diffusion tensor tractography

Quantification of the living human visual system using MRI methods has been challenging, but several applications demand a reliable and time-efficient data acquisition protocol. In this study, we demonstrate the utility of high-spatial-resolution diffusion tensor fiber tractography (DTT) in reconstructing and quantifying the human visual pathways. Five healthy males, age range 24–37 years, were studied after approval of the institutional review board (IRB) at The University of Texas Health Science Center at Houston. We acquired diffusion tensor imaging (DTI) data with 1-mm slice thickness on a 3.0-Tesla clinical MRI scanner and analyzed the data using DTT with the fiber assignment by continuous tractography (FACT) algorithm. By utilizing the high-spatial-resolution DTI protocol with FACT algorithm, we were able to reconstruct and quantify bilateral optic pathways including the optic chiasm, optic tract, optic radiations free of contamination from neighboring white matter tracts.     

Characterization of PDMS-modified glass from cast-and-peel fabrication

In glass/poly(dimethylsiloxane) (PDMS) hybrid microfluidic chips, two different fabrication approaches are used: photolithographic or solid ink molds, or cast-and-peel methods. In the latter, a thin slab of PDMS is laid down and fluid channels are cut manually or by machine. The cast-and-peel approach has been used successfully for low-shear culture devices, among other applications. The main drawback, not reported to date, of cast-and-peel methods is that removal of PDMS (exposing the glass substrate) results in nanoscopic domains of PDMS still attached to the surface. This residual PDMS is not observable by eye, but affects the hydrophobicity of the device. Using contact angle measurement, atomic force and fluorescence microscopy, the changes in glass surfaces from the cast-and-peel technique were elucidated. This study demonstrates the enhanced protein (NeutrAvidin) adsorption on PDMS treated glass surfaces, and the potential influence of altered glass properties on microfluidic applications has been discussed as well.     

Thermosolvatochromism of merocyanine polarity indicators in pure and aqueous solvents: relevance of solvent lipophilicity

The following novel solvatochromic probes were synthesized: 2,6-dibromo-4-[(E)-2-(1-alkylpyridinium-4-yl)ethenyl] phenolate, where the alkyl groups are methyl, n-butyl, n-hexyl, and n-octyl, respectively. Solvatochromism of three of these probes (C(1), C(4), and C(8)) was studied in 36 protic and aprotic solvents. A modified linear solvation energy relationship has been applied to the data obtained at 25 degrees C. Correlation of (empirical) polarities with other solvent properties showed more dependence on lipophilicity than on basicity. A similar conclusion has been reached for a series of other solvatochromic indicators. Exceptions are those that carry acidic hydrogens, being biased toward solvent basicity. Thermosolvatochromism has been studied in mixtures of water with methanol, 1-propanol, acetonitrile, and DMSO. Thermosolvatochromic data have been treated according to a model that explicitly considers the presence in bulk solution of three "species": water, organic component, and solvent-water hydrogen-bonded aggregate. Solvation by the latter is favored over solvation by either of the two precursor solvents (aqueous DMSO is an exception). Temperature increase resulted in desolvation of the probes, due to concomitant decrease of the structures of the component solvents. The above-mentioned modified solvation equation has been successfully applied to solvatochromism in aqueous methanol and aqueous 1-propanol.