Efficiency of bulky protic solvent for SN2 reaction

We calculate and compare the effects of aprotic vs protic solvent on the rate of SN2 reaction [F- + C3H7OMs--> C3H7F + OMs-]. We find that aprotic solvent acetonitrile is more efficient than a small protic solvent such as methanol. Bulky protic solvent (tert-butyl alcohol) is predicted to be quite efficient, giving the rate constant that is similar to that in CH3CN. Our calculated relative activation barriers of the SN2 reaction in methanol, tert-butyl alcohol, and CH3CN are in good agreement with experimental observations.     

Peptide chain dynamics in light and heavy water: zooming in on internal friction

Frictional effects due to the chain itself, rather than the solvent, may have a significant effect on protein dynamics. Experimentally, such "internal friction" has been investigated by studying folding or binding kinetics at varying solvent viscosity; however, the molecular origin of these effects is hard to pinpoint. We consider the kinetics of disordered glycine-serine and α-helix forming alanine peptides and a coarse-grained protein folding model in explicit-solvent molecular dynamics simulations. By varying the solvent mass over more than two orders of magnitude, we alter only the solvent viscosity and not the folding free energy. Folding dynamics at the near-vanishing solvent viscosities accessible by this approach suggests that solvent and internal friction effects are intrinsically entangled. This finding is rationalized by calculation of the polymer end-to-end distance dynamics from a Rouse model that includes internal friction. An analysis of the friction profile along different reaction coordinates, extracted from the simulation data, demonstrates that internal as well as solvent friction varies substantially along the folding pathways and furthermore suggests a connection between friction and the formation of hydrogen bonds upon folding.     

The role of solvent in some oxygen-transfer reactions of peroxy compounds

Solvent–solute interactions in the peroxyacid oxidations are believed to be specific rather than electrostatic in nature. The kinetic solvent effects reported for the oxidations of organic sulfides, olefins, acetylenes, nitrosobenzenes, thioketones, and aryl sulfines reveal that in each case the rates are fast in nonbasic solvents (e.g., benzene, nitrobenzene, and halogenated hydrocarbons) relative to those in basic solvents such as DMF, dioxane, and alcohols. The rates in CF₃CH₂OH and aqueous or partially aqueous media are again higher than those in the basic solvents. This remakably similar pattern of sensitivity of rates to changes in the solvent nature appears to be characteristic of these oxidations as demonstrated by the existence of linear free-energy relationship. The behavior is best understood in terms of cyclic transition states for these oxidations in which charge separation is avoided by intra- or intermolecular hydrogen bonding depending on the nature of the solvent. Solvent effects on sulfoxide oxidation and on oxidations by hydrogen peroxide and t-butylhydroperoxide are also briefly discussed.     

Resolution studies on counter-current chromatography using supercritical fluid carbon dioxide

Counter-current chromatography (CCC) is a form of liquid–liquid partition chromatography. It requires two immiscible solvent phases; the stationary phase is retained in the separation column, generally by centrifugal force, while the mobile phase is eluted. We recently replaced the mobile phase with supercritical fluid carbon dioxide (SF CO₂). Since the solvent strength of SF CO₂ can be varied by changing the temperature and pressure of the system, separation adjustments are thus more versatile. We investigated the pressure and temperature effects on resolution using water and low-carbon alcohol mixtures as the stationary phases. It was demonstrated that these special properties of SF CO₂ were indeed beneficial to the optimization of separations. In addition, the phase retention ratio was examined in terms of separation resolution. The results appeared very similar to those obtained from conventional traditional CCC. This study should be helpful for the future development of SF applications in CCC.     

Density functional theory of solvation and its relation to implicit solvent models

We describe a density functional theory approach to solvation in molecular solvents. The solvation free energy of a complex solute can be obtained by direct minimization of a density functional, instead of the thermodynamic integration scheme necessary when using atomistic simulations. In the homogeneous reference fluid approximation, the expression of the free-energy functional relies on the knowledge of the direct correlation function of the pure solvent. After discussing general molecular solvents, we present a generic density functional describing a dipolar solvent and we show how it can be reduced to the conventional implicit solvent models when the solvent microscopic structure is neglected. With respect to those models, the functional includes additional effects such as the microscopic structure of the solvent, the dipolar saturation effect, and the nonlocal character of the dielectric constant. We also show how this functional can be minimized numerically on a three-dimensional grid around a solute of complex shape to provide, in a single shot, both the average solvent structure and the absolute solvation free energy.     

On use of the Amber potential with the Langevin dipole method

Inclusion of solvent effects in biomolecular simulations is most ideally done using explicit methods, as they are able to capture the heterogeneous environment typical of biomolecules and systems involving them (e.g., proteins at solid interfaces). Common explicit methods based on molecular solvent models (e.g., TIP and SPC models) and molecular dynamic or Monte Carlo simulation are computationally expensive and are, therefore, not well-suited to situations where many simulations are required (e.g., in the ab initio structure prediction or design contexts). In such cases, more coarse-grained explicit approaches such as the Langevin dipole (LD) method of Warshel and co-workers are more appropriate. The recent incarnations of the LD method appear to produce good solvation free energy estimates. These incarnations use charges and solute structures obtained from high-level quantum mechanics simulations. As such an approach is clearly not possible for larger solutes or when many structures are to be considered, an alternative must be sought. One possibility is to use structures and charges derived from an existing analytical potential model-we report on such a coupling here with the Amber potential model. The accuracy and computational performance of this hybrid approach, which we term LD-Amber to distinguish it from previous incarnations of the LD method, was assessed by comparing results obtained from the approach with those from experiment and other theoretical methods for the solvation of 18 amino acid analogues and the alanine dipeptide. This comparison shows that the LD-Amber approach can yield results in line with experiment both qualitatively and quantitatively and is as accurate as other explicit methods while being computationally much cheaper.     

Incorporating solvent and ion screening into molecular dynamics using the finite-difference Poisson–Boltzmann method

The finite difference method for solving the Poisson–Boltzmann equation is used to calculate the reaction field acting on a macromolecular solute due to the surrounding water and ions. Comparisons with analytical test cases indicate that the solvation forces can be calculated rapidly and accurately with this method. These forces act to move charged solute atoms towards the solvent where they are better solvated, and to screen interactions between charges. A way of combining such calculations with conventional molecular dynamics force fields is proposed which requires little modification of existing molecular dynamics programs. Simulations on the alanine dipeptide show that solvent forces affect the conformational dynamics by reducing the preference for internal H-bonding forms, increasing the R-alpha helix preference and reducing transition barriers. These solvent effects are similar to previous explicit solvent simulations, but require little more computation than vacuum simulations. The method should scale up with little increase in computational cost to larger molecules such as proteins and nucleic acids.     

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.     

Volume-load capacity in fast-gradient liquid chromatography effect of sample solvent composition and injection volume on chromatographic performance

We studied the effects of sample solvent composition and injection volumes on the chromatographic performance of ODS-bonded silica columns under fast-gradient running conditions. Chromatographic performance is compromised as a function of both sample injection volume and sample solvent strength, with earlier-eluting analytes being much more affected than later-eluting ones. In general, when injecting samples dissolved in a strong solvent, performance was improved by diluting the strong injection solvent and injecting a proportionally larger volume. Volume loading capacity can be increased by using a longer column, or by using a column of equivalent length, but with a larger inner diameter. Data also suggest that sample solvent strength, not viscosity, is responsible for the noted effects.     

Broadening of peaks eluted before the solvent in capillary GC Part II: The role of phase soaking

Summary Phase soaking is a solvent effect which tends to reconcentrate peaks eluted after and to broaden peaks eluted before the solvent. The principles of the phase soaking effect on peaks eluted before the solvent are discussed. The broadening effect is distinguished from the broadening effect occurring in the flooded column inlet by partial solvent trapping. It was found that in most cases broadening by partial solvent trapping strongly predominated over broadening by phase soaking. Phase soaking was noticeable only in the neighbourhood of the solvent peak.Phase soaking does not broaden peaks eluted before the solvent as much as it re-concentrates those eluted after it. The two phase soaking effects on the front and the rear of the solvent band (that is, of the soaked zone) differ strongly from each other.Peak broadening by phase soaking is negligible for non-trapped components, because such solutes start their chromatography before a significant quantity of solvent enters the column. Phase soaking only broadens solute bands which were retained by the solvent in the column inlet, that is, bands already broadened by partial solvent trapping.     

Manipulation of separation selectivity in capillary zone electrophoresis of anionic solutes

This article discusses the main approaches to the manipulation of the separation selectivity of inorganic and low-molecular-mass anions in capillary zone electrophoresis (CZE). Physical or instrumental effects such as the detection mode, the sampling mode, the separation voltage, and the temperature are easy to control but their influence on selectivity is generally minimal, except for the use of selective detection. Selectivity effects arising from chemical parameters (i.e. effective size and charge, and structure of analyte; the pH, surfactant type and content, polyelectrolyte content, organic solvent content of the electrolyte; capillary treatment; and complexing agents) are much more significant than those resulting from physical effects. The effects on separation selectivity exerted by some of the above parameters can be complex, so that manipulation of selectivity in CZE of anionic solutes is often difficult. Nonetheless, many practical applications can be performed through the judicious control of parameters noted in this review. Some practical limitations to selectivity manipulation are highlighted and possible areas that can be studied in the future for selectivity control are noted.     

Solvatochromism of anthraquinone and symmetrical dihydroxy derivatives. Local interactions

The solvent effects on the electronic absorption spectra of 9,10-anthraquinone (AQ) and its symmetric dihydroxy derivatives namely 1,5-dihydroxyanthraquinone (1,5-DHAQ) and 2,6-dihydroxyanthraquinone (2,6-DHAQ) have been studied in pure solvents and some binary solvent mixtures. The frequencies of the absorption for AQ and 2,6-DHAQ are quite solvent sensitive while those for 1,5-DHAQ are not. Due to the intramolecular hydrogen bond between the CO and OH groups, no influence of solvent hydrogen bond acceptors is observed in 1,5-DHAQ. This hydrogen bond gives a stable six member cycle which is not broken even by the strongest hydrogen bond acceptor solvents used in this work, such as DMSO and DMF. The Taft and Kamlet's solvatochromic comparison method was applied for AQ and 2,6-DHAQ. Aromatic solvents and aliphatic amines were not included in the correlations since they strongly deviate suggesting another type of interactions. All the π→π^* bands of AQ and 2,6-DHAQ show strong influence of π^* despite the fact that their dipole moment is zero. Although it would be reasonable to expect that in the absence of a solute dipole moment there is not significant orientation of solvent molecules around the solute molecules, in this case dipolar interactions between solute and solvent due to local effects might be expected. AQ may be considered as formed by two carbonyl groups weakly interacting with the benzene rings; that means that the carbonyl group can behave as an isolated dipole and independently of the other. To detect possible specific interactions between the AQ and aliphatic amines and aromatic hydrocarbons, preferential solvation in mixed solvent was investigated. It is concluded that EDA interactions are important in the solvation of AQ with these compounds as solvents.     

Strong Short-Range Cooperativity in Hydrogen-Bond Chains

Chains of hydrogen bonds such as those found in water and proteins are often presumed to be more stable than the sum of the individual H bonds. However, the energetics of cooperativity are complicated by solvent effects and the dynamics of intermolecular interactions, meaning that information on cooperativity typically is derived from theory or indirect structural data. Herein, we present direct measurements of energetic cooperativity in an experimental system in which the geometry and the number of H bonds in a chain were systematically controlled. Strikingly, we found that adding a second H-bond donor to form a chain can almost double the strength of the terminal H bond, while further extensions have little effect. The experimental observations add weight to computations which have suggested that strong, but short-range cooperative effects may occur in H-bond chains.     

Analysis of environment response effects on excitation energies within subsystem-based time-dependent density-functional theory

We analyze the ability of subsystem time-dependent density-functional theory (sTDDFT) to describe environmental response effects. To this end, we utilize the recently proposed “exact” version of sTDDFT relying on projection-based embedding (PbE), which so far was applied only for the special case of two subsystems. We confirm that PbE-sTDDFT in combination with supersystem bases yields results equivalent to those of supermolecular TDDFT calculations for systems solvated by many solvent molecules, using the previously studied system of methylene-cyclopropene⋯(H₂O)₁₇ as an example. By means of this exact reference embedding framework, we are able to disentangle solvent effects introduced in terms of the embedding potential from those caused by solvent response couplings, both for the PbE variant and for sTDDFT with approximate non-additive kinetic energy functionals. Furthermore, we show that the use of a monomer basis introduces significant errors for the environmental response contribution. Employing a virtual-orbital localization strategy on top of PbE-sTDDFT, we can also directly assess the impact of inter-subsystem charge-transfer excitations on the entire solvent effect, which turn out to play a significant role for the environmental response. Finally, we analyze the response effects introduced by the individual solvent molecules and their interdependence, and show that a simple, pair-wise additive correction for solvent response yields excellent results in the present example.     

Solvatochromic studies of ionic liquid/organic mixtures

Room-temperature ionic liquids (ILs) have potential for many different applications, including catalysis and synthesis. Organics are often present during IL applications; therefore, a more fundamental understanding of the interactions between IL and organics is necessary. A systematic study of the effects of organic cosolvents, cations, and anions on the solvent strength of IL/organic mixtures will allow for a greater understanding and potential for tuning of ILs for specific purposes. Solvent strength is commonly quantified using spectroscopic probes. We report the solvent strength of IL/organic mixtures using Reichardt's dyes 30 and 33, Kamlet-Taft parameters, and phenol blue. The results show that the polarity of ILs is largely unaffected by the organic cosolvent; that is, the probes are preferentially solvated by the ILs. However, more specific solvation forces, such as hydrogen bonding, can be influenced indirectly by the strength of the anion/cation interaction, giving counterintuitive results.     

Size effect on the fluorescence properties of dansyl-doped silica nanoparticles

We present here the study of the photophysical properties of new dye-doped silica nanoparticles (DDNs) bearing dansyl fluorescent derivatives covalently linked to the silica matrix. The described experimental evidences show how the different location of the chromophores induces great changes in their photophysical behavior, suggesting that fluorophores located near the surface of the nanoparticles have a very different behavior with respect to the internal molecules. These latter ones, in fact, are shielded from the solvent and have a strong blue emission, while those at the periphery interact with the solvent and show a weaker red-shifted emission. As a consequence, the fluorescence properties of these nanoparticles are an average between the characteristics of the two different families of dyes. The relative amount of fluorophores located in the two compartments can be controlled simply by changing the size since, from our results, the thickness of the solvent permeable layer is not relevantly affected by the diameter of the nanoparticles. It is noteworthy that the fluorophores located in the outer shell exhibit very peculiar features: they are sensitive and interact with small molecules such as solvent molecules but, at the same time, they are not accessible to big receptor species such as beta-cyclodextrins. Such results indicate that most of the solvent-sensitive dansyl moieties are located within pores large enough to only accommodate solvent but not big molecules as cyclodextrins, giving precious insight on the morphology of the nanoparticles.     

Strong Short‐Range Cooperativity in Hydrogen‐Bond Chains

Chains of hydrogen bonds such as those found in water and proteins are often presumed to be more stable than the sum of the individual H bonds. However, the energetics of cooperativity are complicated by solvent effects and the dynamics of intermolecular interactions, meaning that information on cooperativity typically is derived from theory or indirect structural data. Herein, we present direct measurements of energetic cooperativity in an experimental system in which the geometry and the number of H bonds in a chain were systematically controlled. Strikingly, we found that adding a second H‐bond donor to form a chain can almost double the strength of the terminal H bond, while further extensions have little effect. The experimental observations add weight to computations which have suggested that strong, but short‐range cooperative effects may occur in H‐bond chains.     

Solvent effects in ligand substitutions of square planar complexes

Data on solvent effects in ligand substitution in square planar complexes are reviewed. In view of the fact that solvent effects for reactions of the planar complexes are quite different from those observed for saturated carbon substrates, it is felt that previous explanations for protic-dipolar aprotic solvent effects may have to be reconsidered.