Nonuniform charge scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins

In molecular mechanics calculations, electrostatic interactions between chemical groups are usually represented by a Coulomb potential between the partial atomic charges of the groups. In aqueous solution these interactions are modified by the polarizable solvent. Although the electrostatic effects of the polarized solvent on the protein are well described by the Poisson--Boltzmann equation, its numerical solution is computationally expensive for large molecules such as proteins. The procedure of nonuniform charge scaling (NUCS) is a pragmatic approach to implicit solvation that approximates the solvent screening effect by individually scaling the partial charges on the explicit atoms of the macromolecule so as to reproduce electrostatic interaction energies obtained from an initial Poisson--Boltzmann analysis. Once the screening factors have been determined for a protein the scaled charges can be easily used in any molecular mechanics program that implements a Coulomb term. The approach is particularly suitable for minimization-based simulations, such as normal mode analysis, certain conformational reaction path or ligand binding techniques for which bulk solvent cannot be included explicitly, and for combined quantum mechanical/molecular mechanical calculations when the interface to more elaborate continuum solvent models is lacking. The method is illustrated using reaction path calculations of the Tyr 35 ring flip in the bovine pancreatic trypsin inhibitor.     

Solution properties of phosphonitrilic fluoroelastomers

A series of phosphonitrilic fluoroelastomers which have excellent solvent resistance and low temperature flexibility, and which perform well under a broad range of service conditions, have been developed. The solution properties of one of these polymers were studied more extensively in order to develop suitable quality control procedures and to gain a better understanding of the polymer structure. Solvents for these procedures were established, fractionation procedures were developed, and intrinsic viscosity, osmotic pressure, and light-scattering measurements were conducted. We found this polymer to have a very broad molecular weight distribution. And, although fractionation by molecular weight was effected, the fractions retained a broad molecular weight distribution. Our data do not indicate significant branching for this polymer. As a result of our studies, we have theorized that a supermolecular structure may be present in this polymer.     

Structure and properties of polyimide films during a far‐infrared‐induced imidization process

The conversion of poly(amic acid) into polyimide (PI) was achieved with far‐infrared radiation (FIR) and conventional thermal treatments. The structure and properties of PI films during different stages of imidization were studied with Fourier transform infrared spectroscopy, weight‐loss analysis during imidization, tensile property measurements, and dynamic mechanical thermal analysis. The effects of the imidization degree, postimidization, and solvent on the thermal and mechanical properties of PI films were quantitatively investigated. The corresponding structural changes were also examined. The experimental results showed that the imidization process proceeded more quickly and more completely in an FIR oven than in a conventional oven. A prolonged FIR treatment at a lower temperature (25–100 °C) accelerated the imidization process. The tensile stress–strain curves had a fanlike distribution with the development of the FIR imidization process and a fishtail distribution with conventional thermal imidization. During FIR imidization, the best tensile properties were obtained at 340 °C, and thermooxidative degradation occurred at about 420 °C. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 2490–2501, 2004     

Physical and chemical evolution of PMDA-ODA during thermal imidization

The processing of poly(imide) films from poly(amic acid) solutions involves the simultaneous loss of solvent and chemical conversion, and may involve structural reorganization such as orientation or crystallization. Here, we describe weight loss, solvent sorption. Fourier transform infrared (FTIR), and wide-angle x-ray scattering (WAXS) studies during thermal imidization of the commercially important poly(imide) PMDA-ODA. The results indicate that imidization proceeds nearly to completion before significant crystallization occurs. The experimental data are interpreted in terms of a triangular phase diagram that makes it possible to plot the processing pathway during the conversion from poly(amic acid) solution to solid poly(imide). In constructing this triangular phase diagram the extent of imidization (i.e., the composition of the poly(amic acid-co-imide) copolymers during conversion) is treated as an independent thermodynamic variable. The form of the triangular phase diagram can be predicted from the Flory-Huggins lattice theory of mixing. There is inevitably a two-phase region present due to the relatively poor solubility of the poly(imide) in the poly(amic acid) solvent (NMP). The specific processing pathway taken depends on the relative amount of solvent loss and imidization during conversion. Further details about the triangular phase diagrams of poly(imides) will require such studies as solvent swelling at intermediate stages of conversion. © 1995 John Wiley & Sons, Inc.     

A Study of the Molecular Weight and Chain Length Distribution of Cyclocopolymers of Divinyl Ether and Maleic Anhydride

Some physical properties of a cyclocopolymer formed by an intra-inter-molecular polymerization mechanism were studied. The cyclic copolymer of divinyl ether and maleic anhydride was chosen for study. Intrinsic viscosities were determined in two solvents. The weight-average molecular weight was determined by light-scattering measurements and the number-average molecular weight was determined by osmometry. Results from a sedimentation velocity pattern indicated that the chain length distribution is much broader than random, which is in agreement with the ratio of the two molecular weight determinations. The polymer was fractionated by precipitation from acetone with hexane as precipitant. Addition of sodium tetraphenyl boron was necessary to obtain separation. Correlation of intrinsic viscosity and weight-average molecular weights was not obtained because of anomalous solubility effects preventing light-scattering determinations.     

Aggregates of polymer-substituted fullerenes

We analyzed the self-organized supermolecular architectures observed in solutions of singly polymer-substituted fullerenes by light-scattering and fluorescence spectroscopy, as well as the surface pattern obtained from spraying the solution by atomic force microscopy. We found that the concentration dependence on aggregate size and fluorescence intensity can be explained quantitatively using a scaling argument, assuming that the aggregates in solution are self-emulsified micelles. Our results indicate that the core of the structure is unreacted fullerenes. Based on our scaling arguments, we predict that there is a critical molecular weight that allows for a narrow distribution of the self-assembled structures in solution.     

Solution properties of ion-containing polymers in polar solvents

The placement of ionic groups within the molecular structure of a polymer produces marked modification in physical properties. A large number of studies have been performed on these ion-containing polymers, but few have focused on the effects of anion–cation interactions (i.e., counterion binding or ionization) on hydrodynamic volume, especially as the molecular structure of the solvent and nature of counterion are varied. In this study changes in hydrodynamic volume are followed through reduced viscosity measurements as a function of the abovementioned molecular parameters. The dilute solution properties of various polyelectrolytes that contain sulfonate and carboxylate groups were investigated as a function of the counterion structure, charge density, molecular weight, and solvent structure. The polymeric materials were selected because of their specific chemical structure and physical properties. In the first instance a (2-acrylamide-2 methylpropanesulfonic acid)-acrylamide-sodium vinyl sulfonate terpolymer was synthesized and subsequently neutralized with a series of bases. Viscometric measurements on these materials indicate that the nature of the cation affects the ability of the polyelectrolyte to expand its hydrodynamic volume at low polymer levels. The magnitude of the molecular expansion is shown to be due in part to the ability of the counterion to dissociate from the backbone chain, which, in turn, is directly related to the solvent structure. The changes in solution behaviour of these inomers lend support for the existence of ion pairs (i.e., site binding) and ionized moieties on the polymer chains. Measurements performed in a variety of solvent systems further confirm this interpretation. In addition, and acrylamide-sodium vinyl sulfonate copolymer was partially hydrolyzed with sodium hydroxide to study the effect of varying the charge density at a constant degree of polymerization and counterion structure. The results show that the charge density has a significant effect on the magnitude of the reduced viscosity and dilute solution behaviour. These observations, made in aqueous and nonaqueous solvents, are related to the interrelation of hydrodynamic volume, counterion concentration, and site binding. Again the controlling factor is the degree of site binding of the counterion onto the polymer backbone. Finally, we observe that the increased hydrodynamic volume affects viscosity behavior beyond the polyelectrolyte effect regime. If the average charge density on the macromolecule is relative high and/or the molecular weight is large (≥ 10⁶) sufficient intermolecular interactions will occur to produce rapid changes in reduced viscosity.     

Transport properties in concentrated polymer solutions

Transport properties of polymer solutions at finite concentration are derived in the partial draining case by formulating a static version of the theory given by Freed and Edwards (FE) for unentangled concentrated polymer solution. The method follows the Kirkwood—Riseman theory for infinitely dilute solutions: the dynamics of the polymer are ignored apart from the overall rotation or translation of the chain and the solvent velocity is given by the Navier—Stokes equations perturbed by point friction forces. The concentration dependence of viscosity and translational friction coefficient of finite chains obtained by numerical calculations are compared with the results of the FE closed-form solution. It is shown that the screening of the hydrodynamic interaction approximately follows Debye-like behavior in the entire range of concentration. The progressive balancing of the increasing intramolecular hydrodynamic interaction with its reduction due to the screening effects, as the molecular weight increases, is well evidenced by comparing results obtained at constant number concentration for different chain lengths.     

Molecular structure of synthetic rubber. I. Light-scattering properties of styrene–butadiene copolymers

The discrepancy between the values reported for the weight-average molecular weight and molecular weight distribution of cold-type styrene-butadiene rubber is examined. The results obtained indicate that aggregation of the rubber due to hydrogen bonding or cluster formation is not a contributing factor to the high weight-average molecular weights obtained. The very broad molecular weight distributions, the M?_w/M?_n of the order of 10–20, are attributable to the presence of a few per cent of very high molecular weight fraction microgel in samples polymerized to moderate conversions. This microgel has been removed to various degrees by several methods: (1) mastication, (2) treatment with CaSO₄, (3) ultracentrifugation, and (4) ultrafiltration. The nature of this microgel is examined in terms of its light-scattering property, intrinsic viscosity, and concentrated solution viscosity. The weight-average molecular weight obtained by light scattering on these samples after removal of microgel are lower by as much as an order of magnitude. The operational definition of the weight-average molecular weight, M?′_w, is therefore introduced, corresponding to the one obtained after removal of the microgel. It is suggested that the actual and the operational weight-average molecular weights be used in conjunction in the characterization of these copolymers.     

Solution properties of poly(methyl acrylate) and (1:1) poly(styrene-co-methyl acrylate)

Poly(methyl acrylate) (PMA) and 1:1 poly(styrene-co-methyl acrylate) (PSMA) were prepared by solution and bulk polymerization, respectively. The copolymer was analyzed with NMR to ascertain its composition and microstructure. The solution properties of unfractionated PMA and fractionated PSMA in ethyl acetate were investigated by light-scattering and viscosity techniques at 35°C. Narrow composition heterogeneity as revealed from the light-scattering measurements in different solvents justified the use of a single solvent for the copolymer characterization. The equations relating the limiting viscosity number to molecular weight, the molecular dimension to molecular weight, etc., were found for homopolymer and copolymers in ethyl acetate at 35°C. In the evaluation of the Flory constant K for the unperturbed state by methods based on Flory-Fox-Schaefgen, Kurata-Stockmayer, and Stockmayer-Fixman expressions, only the first method gave a value for PMA in ethyl acetate, consistent with that obtained in other solvents, whereas similar values of K were obtained by the three methods for PSMA in ethyl acetate. The studies indicate reduced thermodynamic interaction for PSMA–ethyl acetate compared to PMA–ethyl acetate, but increased steric effect in the copolymer compared with the homopolymer.     

Light-scattering studies on solutions of cellulose in the ammonia/ammonium thiocyanate solvent system. I. Classical light-scattering

This article reports the use of classical light scattering to study cellulose in the NH3/NH4SCN solvent system. Three solvent compositions were used, 27.01 73.0,25.5/ 74.5, and 24.51 75.5 weight ammonia/weight ammonium thiocyanate. The coefficient, (dn/dc)_υ, was determined by back calculating using the molecular weight determined by solution viscometry in the solvent system cupriethylenediamine and the classical light-scattering results. Second virial coefficients were found to be similar to those values measured for cellulose in the FeTNa and LiCl/DMAC solvent systems. The characteristic ratios were found to vary with solvent composition with the highest values being at a composition of 25.5/74.5 weight ammonia/ weight ammonium thiocyanate. Persistence lengths were also found to vary with solvent composition with the highest value being 264 × 10^?8 cm at solvent composition 25.5/74.5.     

Steric desolation enhances the effective molarities of intramolecular H-bonding interactions

Free energy contributions due to intramolecular phosphonate diester-phenol H-bonds have been measured for 20 different supramolecular architectures in cyclohexanone solution. High throughput UV/Vis titrations were used in combination with chemical double mutant cycles to dissect out the contributions of different functional group interactions to the stabilities of over 100 different zinc porphyrin-pyridine ligand complexes. These complexes have previously been characterised in toluene and in 1,1,2,2-tetrachloroethane (TCE) solution. Intramolecular ester-phenol H-bonds that were measured in these less polar solvents are too weak to be detected in cyclohexanone, which is a more competitive solvent. The stability of the intermolecular phosphonate diester-phenol H-bond in cyclohexanone is an order of magnitude lower than in TCE and two orders of magnitude lower than in toluene. As a consequence, only seven of the twenty intramolecular phosphonate diester-phenol interactions that were previously measured in toluene and TCE could be detected in cyclohexanone. The effective molarities (EM) for these intramolecular interactions are different in all three solvents. Determination of the EM accounts for solvent effects on the strengths of the individual H-bonding interactions and the zinc porphyrin-pyridine coordination bond, so the variation in EM with solvent implies that differences in the solvation shells make significant contributions to the overall stabilities of the complexes. The results suggest that steric effects lead to desolvation of bulky polar ligands. This increases the EM values measured in TCE, because ligands that fail to replace the strong interactions made with this solvent are unusually weakly bound compared with ligands that make intramolecular H-bonds.     

Computer simulation of dissociative equilibrium in aqueous NaCl electrolyte with account for polarization and ion recharging. Model of interactions

Comparative analysis of different models applied in theoretical studies of electrolytes points to the considerable role of polarization interactions. In order to study aqueous electrolytes on the molecular level, a detailed model is presented of intermolecular interactions that accounts in explicit form, apart from Coulombic, exchange, and dispersion interactions, also many-body interactions caused by polarization of solvent molecules in the field of ions and ion polarization in the field of solvent molecules, and also many-body covalent interactions, effects of excess charge transfer and effects of partial counterion recharging. Numeric values of parameters for an aqueous NaCl solution are obtained by correlation of the calculated values of free energies and entropy of the first reactions of vapor molecule addition to hydrate ion shells with the corresponding experimental values and also from the experimental data on the dissociation energy and IR vibration frequencies of the ion pair and quantum-chemical calculation of the energy of stable configurations of a hydrated ion pair. A special form of describing many-body interactions allows by more than an order of magnitudes reducing the extent of the required calculations and makes it possible to apply the developed model for computer simulation of aqueous electrolytes at the room temperatures.     

Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

Solute–solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical–physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute–solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.     

The Study on Pervaporation Behaviors of Dilute Organic Solution Through PDMS/PTFE Composite Membrane

As an energy-efficient alternative to distillation, pervaporation has been widely combined with fermentation to remove organic compounds from their dilute solutions in a fermentation broth. In this work, the organic permselective composite membrane is prepared by coating polydimethylsiloxane (PDMS) cross-linked with n-heptane on the substrate of polytetrafluoroethylene(PTFE) membrane. The separation behavior is studied in different dilute organic solutions, which include acetone dilute solution, butanone dilute solution, cyclohexanone dilute solution, ethanol dilute solution, isopropanol dilute solution, n-butyl alcohol dilute solution, acetic acid dilute solution, and ethyl acetate dilute solution. Most of these solutions are main reaction products or by-products from fermentation process. The effects of solubility of organics in the membrane, molecular weight, and polarity of the organics on the pervaporation performance are investigated. The effects of operating temperature and organic concentration in the feed solutions on the performance of composite membrane are studied as well. The experimental results show that molecular volume has less influence than solubility and molecular polarity for these organic solvent. The selectivity of PDMS membrane to ethyl acetate is relative high due to good solubility and diffusion of ethyl acetate molecules in polymer.     

An explicit quantum chemical method for modeling large solvation shells applied to aminocoumarin C151

The absorption spectra of aminocoumarin C151 in water and n-hexane solution are investigated by an explicit quantum chemical solvent model. We improved the efficiency of the frozen-density embedding scheme, as used in a former study on solvatochromism (J. Chem. Phys. 2005, 122, 094115) to describe very large solvent shells. The computer time used in this new implementation scales approximately linearly (with a low prefactor) with the number of solvent molecules. We test the ability of the frozen-density embedding to describe specific solvent effects due to hydrogen bonding for a small example system, as well as the convergence of the excitation energy with the number of solvent molecules considered in the solvation shell. Calculations with up to 500 water molecules (1500 atoms) in the solvent system are carried out. The absorption spectra are studied for C151 in aqueous or n-hexane solution for direct comparison with experimental data. To obtain snapshots of the dye molecule in solution, for which subsequent excitation energies are calculated, we use a classical molecular dynamics (MD) simulation with a force field adapted to first-principles calculations. In the calculation of solvatochromic shifts between solvents of different polarity, the vertical excitation energy obtained at the equilibrium structure of the isolated chromophore is sometimes taken as a guess for the excitation energy in a nonpolar solvent. Our results show that this is, in general, not an appropriate assumption. This is mainly due to the fact that the solute dynamics is neglected. The experimental shift between n-hexane and water as solvents is qualitatively reproduced, even by the simplest embedding approximation, and the results can be improved by a partial polarization of the frozen density. It is shown that the shift is mainly due to the electronic effect of the water molecules, and the structural effects are similar in n-hexane and water. By including water molecules, which might be directly involved in the excitation, in the embedded region, an agreement with experimental values within 0.05 eV is achieved.     

Employment of detergent-tag/solute interactions in capillary electrophoresis of neutral polysaccharides

Neutral and inherently immobile polysaccharides are induced to migrate in an electric field through interactions with a detergent added to the electrophoretic electrolyte buffer. Before analysis the polysaccharides are converted to fluorescent derivatives to enable detection, but choice of a tag can also be utilized for modulation of the electrophoretic mobility. Three cases are discussed and exemplified, namely detergent-solute, detergent-solute+tag, and detergent-tag interactions. Anionic as well as cationic surfactants were exploited along with different derivatization reagents. Depending on the approach chosen, different kinds of information about sample composition and distribution(s) can be obtained, including degree of substitution, distribution of molecular weight (obtained in free solution without sieving media) and polymer conformation. A shift in polymer conformation upon a change in solvent composition can be monitored.     

Mutual selective exclusion of unlike polymers in dilute solution and its measurement by light scattering

The interaction of unlike polymer molecules (components 2 and 4) in a ternary solution can be regarded as selective exclusion or desorption of one polymer by another. A relation is derived between the coefficient of selective sorption and the interaction parameters A₂₄ and A₂₄₄ which are analogs of the second and third virial coefficients. The ratio between the apparent light-scattering molecular weight and the true value for a polymer solute in a ternary system with one component of a binary solvent polymeric is more involved than in a ternary system in which both solvent components are of low molecular weight. Under certain conditions, the introduction of polymer component 2 into a dilute solution of polymer component 4 may lead to a decrease in the total intensity of scattered light.     

Quasiliving Carbocationic Polymerization. XI. An Interpretation of Solvent Effects by Donor and Acceptor Numbers

Counteranion/solvent interactions (counteranion solvation) profoundly influence each and every elementary step of carbocationic polymerizations and are just as important as the commonly emphasized cation/solvent interactions (cation solvation). Counteranion solvation and carbocation solvation have been characterized by Gutmann' s acceptor number AN and donor number DN, respectively. Analysis of earlier data leads to the conclusion that the effect of monomer concentration on the rate, molecular weight, and molecular weight distribution obtained in cationic olefin polymerizations in “polar” solvents are in fact due to subtle changes in solvent concentration. Indeed, olefin monomers behave as “nonpolar” solvents and by changing the monomer concentration the character of the medium may profoundly change. It is further concluded that quasiliving polymerizations cannot be achieved in batch operations because the conditions that prevail in the initial charge, although possibly suitable for quasiliving polymerizations, must continuously change with the diminishing monomer concentration, i.e., by continuously changing the solvent character of the system. In contrast, in continuous systems initial conditions in the charge suitable for the attainment of living or quasiliving conditions can be maintained even for long periods of time by continuously replenishing the consumed monomer. By the use of these concepts, heretofore unexplained observations made in the course of quasiliving polymerization studies have been accounted for and, beyond this, new insight into solvation phenomena in cationic polymerizations is generated.     

Molecular dynamics calculation of molecular volumes and volumes of activation

Experimentally, the effects of pressure on reaction rates are described by their pressure derivatives, known as volumes of activation. Transition state theory directly links activation volumes to partial molar volumes of reactants and transition states. We discuss a molecular dynamics method for the accurate calculation of molecular volumes, within which the volumes of molecular species are obtained as a difference between the volumes of pure solvent and solvent with a single molecule inserted. The volumes thus obtained depend on the molecular geometry, the strength and type of the solute-solvent interactions, as well as temperature and pressure. The partial molar volumes calculated using this approach agree well with experimental data. Since this method can also be applied to transition state species, it allows for quantitative analysis of experimental volumes of activation in terms of structural parameters of the corresponding transition states. The efficiency of the approach is illustrated by calculation of volumes of activation for three nonpolar reactions in nonpolar solvents. The results agree well with the experimental data.