Incorporating the excluded solvent volume and surface charges for computing solvation free energy

Gauss's law or Poisson's equation is conventionally used to calculate solvation free energy. However, the near‐solute dielectric polarization from Gauss's law or Poisson's equation differs from that obtained from molecular dynamics (MD) simulations. To mimic the near‐solute dielectric polarization from MD simulations, the first‐shell water was treated as two layers of surface charges, the densities of which are proportional to the electric field at the solvent molecule that is modeled as a hard sphere. The intermediate water was treated as a bulk solvent. An equation describing the solvation free energy of ions using this solvent scheme was derived using the TIP3P water model. © 2013 Wiley Periodicals, Inc.     

Maintaining solvent accessible surface area under rotamer substitution for protein design

Although quantities derived from solvent accessible surface areas (SASA) are useful in many applications in protein design and structural biology, the computational cost of accurate SASA calculation makes SASA-based scores difficult to integrate into commonly used protein design methodologies. We demonstrate a method for maintaining accurate SASA during a Monte Carlo search of sequence and rotamer space for a fixed protein backbone. We extend the fast Le Grand and Merz algorithm (Le Grand and Merz, J Comput Chem, 14, 349), which discretizes the solvent accessible surface for each atom by placing dots on a sphere and combines Boolean masks to determine which dots are exposed. By replacing semigroup operations with group operations (from Boolean logic to counting dot coverage) we support SASA updates. Our algorithm takes time proportional to the number of atoms affected by rotamer substitution, rather than the number of atoms in the protein. For design simulations with a one hundred residue protein our approach is approximately 145 times faster than performing a Le Grand and Merz SASA calculation from scratch following each rotamer substitution. To demonstrate practical effectiveness, we optimize a SASA-based measure of protein packing in the complete redesign of a large set of proteins and protein-protein interfaces.     

Joint neighbors approximation of macromolecular solvent accessible surface area

A new method for approximate analytical calculations of solvent accessible surface area (SASA) for arbitrary molecules and their gradients with respect to their atomic coordinates was developed. This method is based on the recursive procedure of pairwise joining of neighboring atoms. Unlike other available methods of approximate SASA calculations, the method has no empirical parameters, and therefore can be used with comparable accuracy in calculations of SASA in folded and unfolded conformations of macromolecules of any chemical nature. As shown by tests with globular proteins in folded conformations, average errors in absolute atomic surface area is around 1 A2, while for unfolded protein conformations it varies from 1.65 to 1.87 A2. Computational times of the method are comparable with those by GETAREA, one of the fastest exact analytical methods available today.     

Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations

Continuing advances in computer hardware and software are permitting atomic-resolution molecular simulations for longer time scales and on larger systems. Despite these advances, routinely performing atomistic simulations with explicit water for even small proteins, which reach the folding time of such proteins, remains intractable for the foreseeable future. An implicit approximation of the solvent environment using a solvent accessible surface area (SASA) term in a molecular mechanics potential function allows exclusion of the explicit water molecules in protein simulations. This reduces the number of particles by approximately an order of magnitude. We present a fast and acceptably accurate approximate all-atom SASA method parameterized using a set of folded and heat-denatured conformations of globular proteins. The parameters are shown to be transferable to folded and heat-denatured conformations for another set of proteins. Calculation of the approximate SASA and the associated derivatives with respect to atomic positions for a 4644 atom protein requires only 1/11th the CPU time required for calculation of the nonbonded interactions for this system. On a per atom basis, this algorithm is three times faster than the fastest previously published approximate SASA method and achieves the same level of accuracy.     

Qualitative and quantitative topographical surface investigation and solvent effects on internal surface of polypropylene tubes

An alternative way for plastic tubes surface analysis was presented, and the time course of the effects of solvent exposure was evaluated. Atomic force microscopy was used to qualitatively and quantitatively analyze internal tubes topography. Differences in nanoroughness parameters were shown as potential markers for quality control check to detect differences among brands and areas along each tube. Mass spectrometry analysis was carried out to evaluate the effects of some solvents after the intrinsic contact with the polymer. The obtained spectra did not allow the visualization of any leaching component, suggesting a low rate of some possible reaction or dissociative interaction caused by polymer and tested solvent interactions that were in concordance with principal component analysis. The use of these techniques as tools for quality control evaluation, or search for new support to biomolecules immobilization can be seen as important innovations and can be applied in several other investigative and developmental approaches. Copyright © 2011 John Wiley & Sons, Ltd.     

The surface potential of solvent and the intraphase pre-existing potential

Using own and literature data, the differences of real solvation energy for ferricenium and ferrocene in six solvents are found. These quantities are confronted with the calculated difference of the dielectric response energies plus nonelectrostatic energies for the redox couple. Such a comparison allows determining the sum of the surface and intraphase potentials. The comparison of these sums with the experimental values of the surface potential differences obtained by the measuring of Volta potentials allowed determining the differences of pre-existing intraphase potentials formed by solvent molecules on the ferrocene molecule. Thus, the intraphase potentials are evaluated for the first time, using an approach not based on the molecular-dynamic modeling. Using some approximations, the surface potentials of the studied solvents are found.     

混合极性溶剂乙二醇／水中正负离子表面活性剂SDS／CTAB的界面性质研究

正负离子混合表面活性剂由于其特异的自组织行为及良好的稳定性,已成为研究生物膜和用于生物活性物质分离分析的理想模型[1-2],近年来,该体系在界面化学性质中得到了广泛的研究,但是由于正负电性中和,其水溶液很不稳定,一旦超过临界胶束浓度(CMC),极易发生沉淀,从而失去表面活性,使其应用受到限制.     

GC/FT-IR: A unique choice for solvent analysis

The analysis of solvents for both purity and component identifications is routinely performed by gas chromatography (GC). Coupling it with the latest FT-IR systems results in a technique which yields ppm sensitivity and excellent library search results.     

Solvent models for protein–ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations

Solvent effects play a crucial role in mediating the interactions between proteins and their ligands. Implicit solvent models offer some advantages for modeling these interactions, but they have not been parameterized on such complex problems, and therefore, it is not clear how reliable they are. We have studied the binding of an octapeptide ligand to the murine MHC class I protein using both explicit solvent and implicit solvent models. The solvation free energy calculations are more than 10³ faster using the Surface Generalized Born implicit solvent model compared to FEP simulations with explicit solvent. For some of the electrostatic calculations needed to estimate the binding free energy, there is near quantitative agreement between the explicit and implicit solvent model results; overall, the qualitative trends in the binding predicted by the explicit solvent FEP simulations are reproduced by the implicit solvent model. With an appropriate choice of reference system based on the binding of the discharged ligand, electrostatic interactions are found to enhance the binding affinity because the favorable Coulomb interaction energy between the ligand and protein more than compensates for the unfavorable free energy cost of partially desolvating the ligand upon binding. Some of the effects of protein flexibility and thermal motions on charging the peptide in the solvated complex are also considered. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 591–607, 2001     

Molecular mechanics and dynamics of biomolecules using a solvent continuum model

An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson-Boltzmann equation (polar contribution) and the solvent-accessible surface area approach (nonpolar contribution). The feasibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simulations. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1830-1842, 2001     

Derivatives of molecular surface area and volume: simple and exact analytical formulas

The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy-to-use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear-scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header-only template library.     

Choline chloride based deep eutectic solvent as an efficient solvent for the benzylation of phenols

Deep eutectic solvents (such as the combination of urea and choline chloride) are found to be promising solvent and phase-transfer-media for benzylation of phenol. These methods avoided the complexity of multiple alkylations giving selectively O-alkylated aromatic products. Good to excellent yields of the corresponding benzyl phenyl ether were obtained. The non-toxic, biodegradable, inexpensive, and recyclable nature of DES make this protocol green and cost-effective.     

Polarity Control at Interfaces: Quantifying Pseudo‐solvent Effects in Nano‐confined Systems

Surface functionalization controls local environments and induces solvent‐like effects at liquid–solid interfaces. We explored structure–property relationships between organic groups bound to pore surfaces of mesoporous silica nanoparticles and Stokes shifts of the adsorbed solvatochromic dye Prodan. Correlating shifts of the dye on the surfaces with its shifts in solvents resulted in a local polarity scale for functionalized pores. The scale was validated by studying the effects of pore polarity on quenching of Nile Red fluorescence and on the vibronic band structure of pyrene. Measurements were done in aqueous suspensions of porous particles, proving that the dielectric properties in the pores are different from the bulk solvent. The precise control of pore polarity was used to enhance the catalytic activity of TEMPO in the aerobic oxidation of furfuryl alcohol in water. An inverse relationship was found between pore polarity and activity of TEMPO in the pores, demonstrating that controlling the local polarity around an active site allows modulating the activity of nanoconfined catalysts.     

A study of solvent effects on the stereoselectivity of Diels-Alder reactions through molecular surface electrostatic potentials

Statistical models for the study of solvent effects on the endo/exo selectivity of Diels-Alder reactions using molecular surface electrostatic potentials was obtained. The models show that hydrogen bond interactions of solvent molecules favor the predominance of the endo isomer for the reaction of methyl acrylate, methyl methacrylate and methyl trans-crotonate with cyclopentadiene whereas the effect of solvophobicity seems to be negligible.     

Formamide as solvent for capillary zone electrophoresis

A comprehensive investigation of a number of aspects when using formamide as background electrolyte solvent in capillary zone electrophoresis was presented. It included (i) the change of the ion mobility with ionic strength, (ii) the influence of the ionic strength on diffusion coefficients, and (iii) on the separation efficiency expressed by the maximum reachable plate numbers (when only longitudinal diffusion contributed to zone broadening), (iv) the effect of the solvent on pKa values (taken from the literature) of neutral and cation acids, (v) the establishment of the a pH scale in formamide by dissolving acids with known pKa values and their salts at defined proportion (thus circumventing the problem of calibrating the pH meter), (vi) the agreement between the experimentally derived and the theoretical dependence of the effective mobility on pH, (vii) the uptake of water of this hygroscopic solvent from the humidity of the environment and its consequence to the ion mobilities, pKa values, and the chemical stability of the solvent (e.g., hydrolysis), and finally (viii) the use of conductivity and indirect UV absorption to enable detection of analytes below the optical cutoff of formamide.     

Pressurised solvent extraction for organotin speciation in vegetable matrices

Because organotin compounds (OTC) are widely used in many fields of activity, they have become an ubiquitous environmental presence. The presence of organotins in the environment impacts upon food safety, making it important to monitor the levels of organotin pesticides in fruits and vegetables. Nevertheless, only a few studies have been published on organotin speciation in plants. The objective of the present study was to evaluate and optimise a specific procedure based on pressurised solvent extraction (PSE) that is suitable for monitoring organotin content in vegetables. In ASE, solvents are used at elevated temperatures and pressures to increase the rate and efficiency of the extraction process. The results from this procedure were compared to those from the technique usually employed, solid/liquid extraction (SLE) performed in an acidic solvent by mechanical shaking. Three extracting solutions were tested—methanol, ethyl acetate and a mixture of methanol and ethyl acetate—and the mixture was found to give the most quantitative results while preserving the speciation. French bean and lettuce leaves as well as potato tubers were used as the plant materials. These vegetables were considered because they are the vegatables consumed in the most quantities in Europe. The study focuses on trisubstituted OTCs, which are the most toxic tin species. The samples were spiked with four trisubstituted organotins: tributyltin (TBT), triphenyltin (TPhT), tricyclohexyltin (TcHexT) and trioctyltin (TOcT). The influence of the pressure and the temperature of the PSE on the quantitativity of the process and on species preservation was evaluated using the experimental design methodology. The optimised PSE allowed detection limits down to 1–2 ng (Sn) g^–1 to be reached. These are higher than those obtained by SLE (0.1–1 ng (Sn) g^–1). Although the repeatability is similar for both PSE and SLE (2–12% for triorganotin compounds), this appears to be highly time-dependent in the case of SLE. Comparison with SLE confirms that PSE is an interesting tool for vegetable analysis considering the satisfactory OTC preservation and repeatability obtained for a relatively short extraction duration (only 15 min against 2–12 h for SLE).     

Nanocomposite membranes for organic solvent nanofiltration

Organic solvent nanofiltration (OSN) is a molecular separation method which offers a sustainable and reliable solution compared to the conventional energy-intensive separation processes. OSN can be successfully applied to several applications, such as food, pharmaceutical, petrochemical and fine-chemical industries. Current research on OSN membranes mainly focuses on polymeric materials due to the ease of processing, controlled formation of pores, lower fabrication costs and higher flexibility as compared with inorganic materials. However, there are some limitations for the polymeric membranes which can be partially surmounted by adding nanoscale fillers into the polymeric matrix to make nanocomposite membranes. This review aims to comprehensively evaluate and report the advances in nanocomposite membranes prepared by using either different nanoscale fillers or various fabrication methods for OSN applications. Nanoparticles that will be discussed include metal-organic framework, graphene oxide, carbon nanotubes, silica, titanium, gold, zeolite and other fillers. The incorporation of these nanoscale fillers into the polymeric membranes can positively influence the mechanical strength, chemical and thermal stability, hydrophilicity, solute selectivity and solvent permeance. This study may provide helpful insights to develop next-generation of OSN membranes for years to come.     

Sulpholane--A new solvent for the Baylis-Hillman reaction

Sulpholane, a commercially available solvent, is used for the first time as a new solvent for the Baylis-Hillman reaction under ambient conditions; a wide variety of olefins as well as aldehydes participate very efficiently resulting in good to excellent yields of products. Acrylamide also underwent the Baylis-Hillman reaction with 4-nitrobenzaldehyde under these reaction conditions.     

Concurrent solvent evaporation for on-line coupled HPLC-HRGC

A technique is proposed which allows introduction of very large volumes of liquid (10 ml were tested) into capillary columns equipped with short (1–2 m long) retention gaps. It is based on concurrent solvent evaporation, i.e. evaporation of the solvent during introduction of the sample. The technique presupposes high carrier gas flow rates (at least during sample introduction) and column temperatures near the solvent boiling point. The major limitation of the method is the occurrence of peak broadening for solutes eluted up to 30°, in some cases up to 100°, above the injection temperature. This is due to the absence of solvent trapping and a reduced efficiency of phase soaking. Therefore, use of volatile solvents is often advantageous. Application of the concurrent solvent evaporation technique allows introduction of liquids which do not wet the retention gap surface. However, the method is still not very attractive for analysis of aqueous or water-containing solutions (reversed phase HPLC).