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Solute Molecules (solute + molecule)
Selected AbstractsSynthesis and Chemical Properties of Diacetylenes with Pyridinium and 4,4,-Bipyridinium GroupsHELVETICA CHIMICA ACTA, Issue 5 2010Isao Yamaguchi Abstract Diacetylenes (DAs) having a dipolar D- , -A structure (D=donor: amino group; ,=, -conjugation core; A=acceptor: pyridinium (Py) and bipyridinium (BPy) groups), i.e., 4 (APBPyDA) and 5 (APPyPyDA), or an A- , -A structure, i.e., 7 (DBPyDA) and 8 (PyDA(Cl)), were obtained by 1,:,1 and 1,:,2 reactions of 4,4,-(buta-1,3-diyne-1,4-diyl)bis[benzenamine] (APDA; 3) with 1-(2,4-dinitrophenyl)-1,-hexyl-4,4,-bipyridinium bromide chloride (1,:,1,:,1) (1), 1-(2,4-dinitrophenyl)-4-(pyridin-4-yl)pyridinium chloride (2), or 1-(2,4-dinitrophenyl)pyridinium chloride (6) (Schemes 1 and 2). The anion-exchange reactions of 8 with NaI and Li(TCNQ) (TCNQ,=2,2,-(cyclohexa-2,5-diene-1,4-diylidene)bis[propanedinitrile] radical ion (1,)) yielded the corresponding I, and TCNQ, salts 9 (PyDA(I)) and 10 (PyDA(TCNQ)). Compounds 10 and 4 exhibited a UV/VIS absorption due to a charge transfer between the TCNQ, and the pyridinium groups and a strong solute,solvent interaction of a dipolar solute molecule in the polar environment, respectively. Compounds 8,10 exhibited photoluminescence in solution, whereas 4 and 7 did not because of the presence of the 4,4,-bipyridinium quenching groups. Differential-scanning-calorimetry (DSC) measurements suggested that the DAs obtained in this study can be converted into poly(diacetylenes) by thermal polymerization. [source] A new method to locate saddle points for reactions in solution by using the free-energy gradient method and the mean field approximationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2004I. Fdez. Abstract A new method for calculating saddle points of reactions in solution is presented. The main characteristics of the method are: (1) the solute,solvent system is described by the averaged solvent electrostatic potential/molecular dynamics method (ASEP/MD). This is a quantum mechanics/molecular mechanics method (QM/MM) that makes use of the mean field approximation (MFA) and that permits one to simultaneously optimize the electronic structure and geometry of the solute molecule and the solvent structure around it. (2) The transition state is located by the joint use of the free-energy gradient method and the mean field approximation. An application to the study of the Menshutkin reaction between NH3 and CH3Cl in aqueous solution is discussed. The accuracy and usefulness of the proposed method is checked through comparison with other methods. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1227,1233, 2004 [source] Prediction of the Solubility, Activity Coefficient and Liquid/Liquid Partition Coefficient of Organic CompoundsMOLECULAR INFORMATICS, Issue 9 2004H. Hilal Abstract Solvation models, based on fundamental chemical structure theory, were developed in the SPARC mechanistic tool box to predict a large array of physical properties of organic compounds in water and in non-aqueous solvents strictly from molecular structure. The SPARC self-interaction solvation models that describe the intermolecular interaction between like molecules (solute-solute or solvent-solvent) were extended to quantify solute-solvent interaction energy in order to estimate the activity coefficient in almost any solvent. Solvation models that include dispersion, induction, dipole-dipole and hydrogen bonding interactions are used to describe the intermolecular interaction upon placing an organic solute molecule in any single or mixed solvent system. In addition to estimation of the activity coefficient for 2674 organic compounds, these solvation models were validated on solubility and liquid/liquid distribution coefficient in more than 163 solvents including water. The RMS deviations of the calculated versus observed activity coefficients, solubilities and liquid/liquid distribution coefficients were 0.272,log mole fraction, 0.487,log mole fraction and 0.44,log units, respectively. [source] Computational screening of biomolecular adsorption and self-assembly on nanoscale surfacesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2010Hendrik Heinz Abstract The quantification of binding properties of ions, surfactants, biopolymers, and other macromolecules to nanometer-scale surfaces is often difficult experimentally and a recurring challenge in molecular simulation. A simple and computationally efficient method is introduced to compute quantitatively the energy of adsorption of solute molecules on a given surface. Highly accurate summation of Coulomb energies as well as precise control of temperature and pressure is required to extract the small energy differences in complex environments characterized by a large total energy. The method involves the simulation of four systems, the surface-solute,solvent system, the solute,solvent system, the solvent system, and the surface-solvent system under consideration of equal molecular volumes of each component under NVT conditions using standard molecular dynamics or Monte Carlo algorithms. Particularly in chemically detailed systems including thousands of explicit solvent molecules and specific concentrations of ions and organic solutes, the method takes into account the effect of complex nonbond interactions and rotational isomeric states on the adsorption behavior on surfaces. As a numerical example, the adsorption of a dodecapeptide on the Au {111} and mica {001} surfaces is described in aqueous solution. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Strategies to model the near-solute solvent molecular density/polarizationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2009Pei-Kun Yang Abstract The solvent molecular distribution significantly affects the behavior of the solute molecules and is thus important in studying many biological phenomena. It can be described by the solvent molecular density distribution, g, and the solvent electric dipole distribution, p. The g and p can be computed directly by counting the number of solvent molecules/dipoles in a microscopic volume centered at r during a simulation or indirectly from the mean force F and electrostatic field E acting on the solvent molecule at r, respectively. However, it is not clear how the g and p derived from simulations depend on the solvent molecular center or the solute charge and if the gF and pE computed from the mean force and electric field acting on the solvent molecule, respectively, could reproduce the corresponding g and p obtained by direct counting. Hence, we have computed g,p,gF, and pE using different water centers from simulations of a solute atom of varying charge solvated in TIP3P water. The results show that gF and pE can reproduce the g and p obtained using a given count center. This implies that rather than solving the coordinates of each water molecule by MD simulations, the distribution of water molecules could be indirectly obtained from analytical formulas for the mean force F and electrostatic field E acting on the solvent molecule at r. Furthermore, the dependence of the g and p distributions on the solute charge revealed provides an estimate of the change in g and p surrounding a biomolecule upon a change in its conformation. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Application of the frozen atom approximation to the GB/SA continuum model for solvation free energyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2002Olgun Guvench Abstract The generalized Born/surface area (GB/SA) continuum model for solvation free energy is a fast and accurate alternative to using discrete water molecules in molecular simulations of solvated systems. However, computational studies of large solvated molecular systems such as enzyme,ligand complexes can still be computationally expensive even with continuum solvation methods simply because of the large number of atoms in the solute molecules. Because in such systems often only a relatively small portion of the system such as the ligand binding site is under study, it becomes less attractive to calculate energies and derivatives for all atoms in the system. To curtail computation while still maintaining high energetic accuracy, atoms distant from the site of interest are often frozen; that is, their coordinates are made invariant. Such frozen atoms do not require energetic and derivative updates during the course of a simulation. Herein we describe methodology and results for applying the frozen atom approach to both the generalized Born (GB) and the solvent accessible surface area (SASA) parts of the GB/SA continuum model for solvation free energy. For strictly pairwise energetic terms, such as the Coulombic and van-der-Waals energies, contributions from pairs of frozen atoms can be ignored. This leaves energetic differences unaffected for conformations that vary only in the positions of nonfrozen atoms. Due to the nonlocal nature of the GB analytical form, however, excluding such pairs from a GB calculation leads to unacceptable inaccuracies. To apply a frozen-atom scheme to GB calculations, a buffer region within the frozen-atom zone is generated based on a user-definable cutoff distance from the nonfrozen atoms. Certain pairwise interactions between frozen atoms in the buffer region are retained in the GB computation. This allows high accuracy in conformational GB comparisons to be maintained while achieving significant savings in computational time compared to the full (nonfrozen) calculation. A similar approach for using a buffer region of frozen atoms is taken for the SASA calculation. The SASA calculation is local in nature, and thus exact SASA energies are maintained. With a buffer region of 8 Å for the frozen-atom cases, excellent agreement in differences in energies for three different conformations of cytochrome P450 with a bound camphor ligand are obtained with respect to the nonfrozen cases. For various minimization protocols, simulations run 2 to 10.5 times faster and memory usage is reduced by a factor of 1.5 to 5. Application of the frozen atom method for GB/SA calculations thus can render computationally tractable biologically and medically important simulations such as those used to study ligand,receptor binding conformations and energies in a solvated environment. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 214,221, 2002 [source] Analyses of the partition coefficient, log P, using ab initio MO parameter and accessible surface area of solute moleculesJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2004Hiroshi Chuman Abstract To analyze the log Psol/w values (sol: n -octanol or chloroform, w: water) in the framework of the molecular orbital (MO) procedure, we selected solute descriptors such as the solvation energy difference between aqueous and organic solvent phases and the "surface" area of solute molecules to which water molecules are accessible. The solvation energy of solute molecules in their minimum free-energy conformation was calculated using the ab initio self-consistent reaction field-MO method with the conductor-like screening model. The experimentally measured log Psol/w value of various solutes except for those of amphiprotics was shown to be analyzable reasonably well by the MO model with additional descriptors for the hydrogen-bonding patterns in the solute,solvent interactions. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:2681,2697, 2004 [source] Investigation of solute permeation across hydrogels composed of poly(methyl vinyl ether- co -maleic acid) and poly(ethylene glycol)JOURNAL OF PHARMACY AND PHARMACOLOGY: AN INTERNATI ONAL JOURNAL OF PHARMACEUTICAL SCIENCE, Issue 7 2010Thakur Raghu Raj Singh Abstract Objectives, Swelling kinetics and solute permeation (theophylline, vitamin B12 and fluorescein sodium) of hydrogels composed of poly(methyl vinyl ether- co -maleic acid) (PMVE/MA) and poly(ethylene glycol) (PEG) are presented. Methods, The effects of PMVE/MA and PEG 10 000 content on swelling behaviour (percentage swelling, the type of diffusion and swelling rate constant) were investigated in 0.1 m phosphate buffer. Network parameters, such as average molecular weight between crosslinks (Mc) and crosslink density, were evaluated. Key findings, The percentage swelling and Mc of hydrogels increased with decrease in PMVE/MA content, where the water diffusion mechanism into the hydrogels was Class-II type. In contrast, increase in PMVE/MA content caused an increase in the crosslink density. Permeation of theophylline, vitamin B12 and fluorescein sodium, with increasing hydrodynamic radii, was studied through the equilibrium swollen hydrogels composed of PMVE/MA and PEG. In general, the permeability and diffusion coefficients of all three solutes decreased with increase in the PMVE/MA content. In addition, permeability and diffusion coefficient values increased with decreases in the hydrodynamic radii of the solute molecules. Conclusions, The hydrogels have shown a change in swelling behaviour, crosslink density, Mc and solute permeation with change in PMVE/MA content, thus suggesting a potential application in controlled drug-delivery systems. [source] Solvent dependent study of carbonyl vibrations of 3-phenoxybenzaldehyde and 4-ethoxybenzaldehyde by Raman spectroscopy and ab initio calculationsJOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2009Veerabahu Ramakrishnan Abstract A Raman spectroscopy investigation of the carbonyl stretching vibrations of 3-phenoxybenzaldehye (3Phbz) and 4-ethoxybenzaldeheyde (4Etob) was carried out in binary mixtures with different polar and nonpolar solvents. The purpose of this study was twofold: firstly, to describe the interaction of the carbonyl groups of two solute molecules in terms of a splitting in the isotropic and anisotropic components and secondly, to analyze their spectroscopic signatures in a binary mixture. Changes in wavenumber position, variation in the anisotropic shift and full width half maximum were investigated for binary mixtures with different mole fractions of the reference systems. In binary mixtures, the observed increase in wavenumber with solvent concentration does not show linearity, indicating the significant role of molecular interactions on the occurrence of breaking of the self-association of the solute. In all the solvents, a gradual decrease in the anisotropic shift reflects the progressive separation of the coupled oscillators with dilution. ,i(,c), 3Phbz,solvent mixtures, exhibit a gradual decrease with decrease in the concentration of the solute which is an evidence on the influence of micro viscosity on linewidth. For 4Etob, the carbonyl stretching vibration shows two well-resolved components in the Raman spectra, attributed to the presence of two distinct carbonyl groups: hydrogen-bonded and free carbonyl groups. The intensity ratio of the carbonyl stretching vibration of these two types of carbonyl groups is studied to understand the dynamics of solute/solvent molecules owing to hydrogen bond interactions. Ab initio calculations were employed for predicting relevant molecular structures in the binary mixtures arising from intermolecular interactions, and are related to the experimental results. Copyright © 2009 John Wiley & Sons, Ltd. [source] Small molecule adsorption on to polyester capillary-channeled polymer fibers: Frontal analysis of naphthalene and naphthol (naphthalene and naphthol adsorption on capillary-channeled polymer fibers)JOURNAL OF SEPARATION SCIENCE, JSS, Issue 1 2010Christine M. Straut Abstract Frontal analysis was carried out employing poly(ethylene-terephthalate) capillary-channeled polymer fibers as the stationary phase for the immobilization of low-molecular-weight polycyclic aromatic hydrocarbon compounds (naphthol and naphthalene) from 2% methanol/water solutions. The effects of several experimental parameters on the frontal profile, the breakthrough volume, and the equilibrium parameters were determined for each solute. The amount adsorbed at exhaustion of naphthalene and naphthol was also compared. The kinetics and thermodynamics were maintained at relatively fast flow rates/linear velocities (,6,18,mm/s). Comparisons of dynamic capacity revealed that naphthalene was more retained than naphthol, in most situations more than five times that of the naphthol adsorption. This increase in capacity is most likely due to the multilayering of naphthalene on the surface of the fibers through ,,, interactions between the solute and the fiber surface and successive layering of solute molecules. The extent of layering is a function of the flow, with faster flow rates (and subsequent shear forces) reducing the extent of adsorbate,adsorbate interactions. Although the overall loading capacity of the capillary-channeled polymer fibers is far below porous phases, there are a number of attractive attributes that support further development. [source] Relationship between ice recrystallisation rates and the glass transition in frozen sugar solutionsJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 15 2002Steve Ablett Abstract The increase in ice crystal size that occurs through recrystallisation when many frozen products such as ice cream and frozen desserts are stored is one of the major factors contributing to the perceived deterioration of the product by the consumer. In order to reduce the rate of deterioration, a detailed understanding of the fundamental mechanism is needed. This study demonstrates that ice recrystallisation rates in a series of frozen sugar solutions are strongly correlated with the molecular mobilities of the water and solute molecules as measured by time domain nuclear magnetic resonance. The study also demonstrates that the proximity to the glass transition temperature as described by state diagrams correlates well with the measured ice recrystallisation rates. The temperature dependence in these systems is described by Williams, Landel and Ferry theory. © 2002 Society of Chemical Industry [source] Liposome/water lipophilicity: Methods, information content, and pharmaceutical applicationsMEDICINAL RESEARCH REVIEWS, Issue 3 2004Georgette Plemper van Balen Abstract This review discusses liposome/water lipophilicity in terms of the structure of liposomes, experimental methods, and information content. In a first part, the structural properties of the hydrophobic core and polar surface of liposomes are examined in the light of potential interactions with solute molecules. Particular emphasis is placed on the physicochemical properties of polar headgroups of lipids in liposomes. A second part is dedicated to three useful methods to study liposome/water partitioning, namely potentiometry, equilibrium dialysis, and 1H-NMR relaxation rates. In each case, the principle and limitations of the method are discussed. The next part presents the structural information encoded in liposome/water lipophilicity, in other words the solutes' structural and physicochemical properties that determine their behavior and hence their partitioning in such systems. This presentation is based on a comparison between isotropic (i.e., solvent/water) and anisotropic (e.g., liposome/water) systems. An important factor to be considered is whether the anisotropic lipid phase is ionized or not. Three examples taken from the authors' laboratories are discussed to illustrate the factors or combinations thereof that govern liposome/water lipophilicity, namely (a) hydrophobic interactions alone, (b) hydrophobic and polar interactions, and (c) conformational effects plus hydrophobic and ionic interactions. The next part presents two studies taken from the field of QSAR to exemplify the use of liposome/water lipophilicity in structure,disposition and structure,activity relationships. In the conclusion, we summarize the interests and limitations of this technology and point to promising developments. © 2004 Wiley Periodicals, Inc. Med Res Rev, 24, No. 3, 299,324, 2004 [source] | ||||||||||