Volumetric and optical study of molecular association in binary mixtures of dimethyl sulphoxide with carboxylic acid

Density and refractive index have been measured for the binary mixture of dimethyl sulphoxide (DMSO) with propanoic acid and n-butyric acid at three temperatures, 293, 303 and 313 K, over the entire composition range. Excess parameters such as excess molar volume (V ^E) and molar refraction deviation (ΔR _m) have been calculated from the measured density and refractive index to study the molecular association between the component molecules. The V ^E and ΔR _m values of these mixtures were fitted to the Redlich–Kister polynomial equation. Both excess parameters were plotted against the mole fraction of DMSO over the whole composition range. The values of V ^E and ΔR _m have been found to be negative for both mixtures over the entire composition range, which suggests the presence of strong intermolecular interaction. The experimental refractive data of these mixtures were also used to test the validity of the empirical relations for the refractive index.     

Phase behaviors of nematic liquid crystal/linear polymer systems: Effect of specific interactions

A new model has been proposed that takes into account the specific interaction between nematic liquid crystal and polymer. A generalized lattice fluid model was employed to describe the specific interaction between liquid crystal and polymer. The proposed model postulates that a specific interaction between dissimilar components in a mixture has both an energetic and an entropic component. A degeneracy parameter and an interaction parameter are also discussed, followed by a comparison of the experimental data to the model. The results show that that a specific interaction plays an important role in the phase behaviors of the given systems. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 4128–4136, 2000     

Semi-empirical relation between freezing point and critical point properties of a wide variety of molecular liquids

Based on experimental data for some 28 freezing liquids, we define a semi-empirical relation connecting surface tension and molar volume with the molar critical volume. It is shown that the semi-empirical equation deduced by means of this relation allows one to calculate the given critical property for various molecular liquids with high accuracy.     

Partial Molar Volumes and Refractions of Cobalt(III) Complexes, Part 1: Homologous Series of Hexaaminecobalt(III) Complexes

Both the partial molar volumes (V∘_solute) and refractions (R∘_solute) of the solute at infinite dilution have been determined for a series of four octahedral N₆-coordinated cobalt(III) species with increasing ligand size (ammonia, ethylenediamine, sepulchrate, and 1,2-diaminocyclohexane). The experimental values for V∘ _solute are consistent with the relative sizes of the ligands but show larger values than those generated by computer modeling as the size of the cation increases. This suggests that the void space of the cation increases with the size of the cation. It is proposed that increasing hydrophobicity of the alkane ligand frameworks contributes to larger volumes.     

Study of the molecular configuration and the dipole moment in fluorinated liquid crystals

We have investigated the relationship between the molecular configuration and dipole moment of some fluorinated liquid crystals (LCs). The geometries of the molecules were preliminarily optimized at empirical AM1 and then were further optimized at B3LYP/6‐31G(d) level. The dipole moment has been calculated. It is strongly influenced by the position and number of fluorine substituents in the benzene ring of the molecule. The polarizability, mean polarizabilities, and anisotropic polarizability of the phenylbicyclohexane (PBC) fluorine substituents are also given and discussed. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Interactions between chlorinated dioxins and a positively charged molecular probe: New molecular interaction potential

Interaction with the ligand binding domain of receptors for natural chemicals present one potential mechanism for the biological effects of environmental chemicals. Evidence suggests that the electrostatic interaction between the ligand and the receptor is an important component for binding to some of the relevant receptors. The presence of charged residues near the binding site suggests that the charge distribution of the free ligand may be different from the charge distribution of the ligand as it approaches the binding domain of the protein. In this study a new type of potential is computed for a series of dibenzo-p-dioxin (dioxin) ligands. This quantum mechanically computed potential results from interaction between the ligand and a trimethyl ammonium probe at a set of grid points. This interaction potential is compared with the molecular electrostatic potential computed from the wave function of the isolated ligands. Three types of local minima are found: (1) above the oxygen; (2) above the conjugated ring; and (3) above the chlorine(s). The molecular electrostatic potential emphasizes the minima associated with the chlorine atoms and, in that potential, the minima associated with the oxygen atoms disappear with chlorination. In the new potential, the minima over the oxygen atoms are maintained even in tetrachlorodioxin. As chlorination is increased the differences between the two potentials increases. The new potential shows the influence of the π-cation interaction, which is largest when there is little substitution on the ring. The presence of the probe induces a dipole component of 1 debye perpendicular to the plane of the ligand. Local minima in the interaction potential are then used as starting structures for the determination of the most stable ligand–probe complexes. The most stable structures are obtained from the minima associated with the oxygen atoms. These structures are stabilized by a hydrogen bond formation between the probe and the oxygen and the molecule is bent by 30° about the O(SINGLE BOND)O axis. For this series of molecules, the new potential retains some of the features that determine the hydrogen bond whereas the molecular electrostatic potential does not. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 673–684, 1998     

Structural determinants for the efficient and specific interaction of thioredoxin with 2-oxoacid dehydrogenase complexes

Specificity and efficiency of thiored oxin action upon the 2-oxoacid dehydrogenase complexes are studied by using a number of thiored oxins and complexes. Bacterial and mammalian pyruvate and 2-oxoglutarate dehydrogenase systems display similar row of preference to thioredoxins that may result from thioredoxin binding to the homologous or common dihydrolipoamide dehydrogenase components of the complexes. The most sensitive tothioredoxin is the complex whose component exhibits the highest sequence similarity to eukaryotic thioredoxin reductase. Hence, thioredoxin binding to the complexes may be related to that in the thioredoxin reductase, a dihydrolipoamide dehydrogenase homolog. The highest potency of mitochondrial thioredoxin to affect the mitochondiral complexes is revealed. A 96–100% conservation of the mitochondrial thioredoxin structure is shown within the four known sequences and the N-terminus of the pigheart protein determined. Eleven thioredoxins tested biochemically are analyzed by multiple sequence alignment and homology modeling. Their effects correlate with the residues at the contact between the α 3/3₁₀ and α 1 helices, the length of the α 1 helix and charges in the α2–β3 and β4–β5 linkers. Polarization of the thioredoxin molecule and its active site surroundings are characterized. Thioredoxins with a highly polarized surface around the essential disulfide bridge (mitochondiral, pea f, and Arabidopsis thaliana h3) show low cross-reactivity as compared to the species with a decreased polarization of this area (e.g., from Escherichia coli). The strongest polarization of the whole molecule results in the highest magnitude of the electrostatic dipole vector of mitochondrial thioredoxin. Thiored oxins with the dipole orientation similar to that of the latter have the affinities for the 2-oxoacid dehydrogenase complexes, proportional to the dipole magnitudes. Thioredoxin with an opposite dipole orientation shows no effect. Activating and inhibitory thioredoxin disulfides are distinguished by the charges of the residues 13/14 (α1 helix(, 51 (α2–β3 linker), and 83/85 (β4–β5 linker), changing the dipole direction. The results show that the thioredoxin-target interplay may be controlled by the long-range interactions between the electrostatic dipole vectors of the proteins and the degree of their interface polarization.     

The influence of universal and specific interactions on structural properties of liquid formamide

Monte Carlo simulation of the structure of liquid formamide at 298 K was carried out. Intermolecular interactions were calculated using five different potentials. No essential changes in the spatial structure and topological properties of the network of hydrogen bonds of liquid formamide occur upon varying the electrostatic intermolecular interactions, strength of H-bonds, and temperature. Fragments of crystal structure are partly retained in liquid formamide. It was found that the network of H-bonds is structurally inhomogeneous and contains long-lived associates of closed cycles of H-bonds as well as tree-like and chain-like structures. The energy, topological, and statistical characteristics of closed cycles of H-bonds were determined. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2227–2236, December, 1999.     

Experimental verification of an equivalent circuit for the characterization of electrothermal micropumps: High pumping velocities induced by the external inductance at driving voltages below 5 V

Electrothermal micropumps (ETμPs) use local heating to create conductivity and permittivity gradients in the pump medium. In the presence of such gradients, an external AC electric field influences smeared spatial charges in the bulk of the medium. When there is also a symmetry break, the field‐charge interaction results in an effective volumetric force resulting in medium pumping. The advantages of the ETμP principle are the absence of moving parts, the opportunity to passivate all the pump structures, homogeneous pump‐channel cross‐sections, as well as force plateaus in broad frequency ranges. The ETμPs consisted of a DC‐heating element and AC field electrodes arranged in a 1000 μm × 250 μm × 60 μm (length × width × height) channel. They were processed as platinum structures on glass carriers. An equivalent‐circuit diagram allowed us to model the frequency‐dependent pumping velocities of passivated and nonpassivated ETμPs, which were measured at medium conductivities up to 1.0 S/m in the 300 kHz to 52 MHz frequency range. The temperature distributions within the pumps were controlled by thermochromic beads. Under resonance conditions, an additional inductance induced a tenfold pump‐velocity increase to more than 50 μm/s at driving voltages of 5 V_rms. A further miniaturization of the pumps is viewed as quite feasible.     

Partial Molar Volumes and Refractions of Cobalt(III) Complexes, Part 2: Homologous Series of Nitrilopentaamminecobalt(III) Complexes

Both the partial molar volumes (V° _2m refractions (R° _2m ) of the solutes at infinite dilution have been determined at 20 °C for a series of six octahedral N₆-coordinated cobalt(III) species featuring five coordinated ammonia ligands along with a sixth N-coordinated organonitrile of increasing ligand size (from acetonitrile to sebaconitrile). The experimental values for V° _2m are consistent with the relative sizes of the ligands but show larger values than those generated by computer modeling as the size of the cation increases, presumably due to the void space of the cation which increases with the size of the nitrile ligand.     

Excess molar enthalpies of the binary systems: (Dibutyl ether + isomers of pentanol) at T = (298.15 and 308.15) K

In this work, we present the experimental measurements of excess molar enthalpies for the binary systems of dibutyl ether with different isomers of pentanol: 1-pentanol, 2-pentanol, 3-pentanol, 3-methyl-2-butanol, 2-methyl-1-butanol, 3-methyl-1-butanol and 2-methyl-2-butanol; all of them at T = (298.15 and 308.15) K and atmospheric pressure. Our goal was to determine the influence of the OH-group position on the different isomers of pentanol in the excess molar enthalpies of the binary systems studied. For this purpose we have analysed their experimental effective-reduced dipole moments. All values of excess molar enthalpies for the mixtures studied are positive whereas the results obtained for the effective-reduced dipole moments of the isomers of pentanol are similar.     

Solvent Effects on the Absorption and Emission Spectra of Some Nematic Liquid Crystals: Determination of Dipole Moment and First-Order Hyperpolarizability

The effect of solvent on the absorption and fluorescence spectra of two liquidcrystalline molecules LC1 and LC2 were studied. These data were used to evaluatethe values of the change in the dipole moment between the ground and excitedstate and the first-order hyperpolarizability in each solvent. The values of gives an indication of how these liquid crystalline samples can find applicationsas nonlinear materials. The values are in the range 1–1.9 × 10²⁹ esu for LC1and LC2. The values of indicate that these compounds can be used as goodnonlinear materials. Here solvatochromism has been used as an effective tool toestimate the hyperpolarizability in solution.     

Study of intermolecular interactions through dielectric properties of the mixtures consisting of 1,4-butanediol,primary amyl alcohols and 1,4-dioxane at various temperatures

This paper presents relative permittivities, excess permittivities, effective dipole moments, and excess Kirkwood correlation factors of binary mixtures of 1,4-butanediol with two primary pentanol isomers [1-pentanol (amyl alcohol) + 3-methyl-1-butanol (isoamyl alcohol)] from T = (298.15 to 318.15) K at p = 101.3 kPa over the entire composition range. Experimental permittivity values for polar–non-polar binary systems of (1,4-dioxane + amyl alcohol or isoamyl alcohol) were also obtained as a function of composition at the same range of temperatures. The experimental permittivity data were fitted using Redlich–Kister equation to evaluate the adjustable parameters and the standard errors. From the experimental data, the excess parameters were calculated. In this work, variations of effective dipole moment and correlation factor were investigated using Kirkwood−Frohlich equation. The experimental data of measurements were used in the analysis of the homo- and hetero interactions occurring in these binary solutions.     

Quantitative evaluation of specific and nonspecific interactions in radical exchange between phenyllithium and bromobenzene

The results of kinetic studies on the exchange of radicals between PhLi and PhBr in variuos binary pentane-ether mixtures in the presence of alkaline metal halides were discussed. The nucleophilicity of the ethers and metal halides, which is a quantitative measure of their influence on the exchange reaction, was determined. The specific and nonspecific components of coordination were identified and quantitatively evaluated for some parameters of the exchange reaction.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 272–275, February, 1995.     

Estimation of pure component properties. Part 4: Estimation of the saturated liquid viscosity of non-electrolyte organic compounds via group contributions and group interactions

A new group contribution method for the prediction of pure component saturated liquid viscosity has been developed. The method is an extension of the pure component property estimation techniques that we have developed for normal boiling points, critical property data, and vapour pressures. Predictions can be made from simply having knowledge of the molecular structure of the compound. In addition, the structural group definitions for the method are identical to those proposed for estimation of saturated vapour pressures. Structural groups were defined in a standardized form and fragmentation of the molecular structures was performed by an automatic procedure to eliminate any arbitrary assumptions. The new method is based on liquid viscosity data for more than 1600 components. Results of the new method are compared to several other estimation methods published in literature and are found to be significantly better. A relative mean deviation in viscosity of 15.3% was observed for 813 components (12,139 data points). By comparison, the Van Velzen method, the best literature method in our benchmarking exercise produced a relative mean deviation of 92.8% for 670 components (11,115 data points). Estimation results at the normal boiling temperature were also tested against an empirical rule for more than 4000 components. The range of the method is usually from the triple or melting point to a reduced temperature of 0.75–0.8. Larger than average deviations were observed in the case of molecules with higher rotational symmetry, but no specific correction of this effect was included in this method.     

Specific interactions and binding free energies between thermolysin and dipeptides: molecular simulations combined with ab initio molecular orbital and classical vibrational analysis

Thermolysin (TLN) is a metalloprotease widely used as a nonspecific protease for sequencing peptide and synthesizing many useful chemical compounds by the chemical industry. It was experimentally shown that the activity and functions of TLN are inhibited by the binding of many types of amino acid dipeptides. However, the binding mechanisms between TLN and dipeptides have not been clarified at the atomic and electronic levels. In this study, we investigated the binding mechanisms between TLN and four dipeptides. Specific interactions and binding free energies (BFEs) between TLN and the dipeptides were calculated using molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital (FMO) methods. The molecular systems were embedded in solvating water molecules during calculations. The calculated BFEs were qualitatively consistent with the trend of the experimentally observed inhibition of TLN activity by binding of the dipeptides. In addition, the specific interactions between the dipeptides and each amino acid residue of TLN or solvating water molecules were elucidated by the FMO calculations.     

Development of hardware accelerator for molecular dynamics simulations: a computation board that calculates nonbonded interactions in cooperation with fast multipole method

Evaluation of long-range Coulombic interactions still represents a bottleneck in the molecular dynamics (MD) simulations of biological macromolecules. Despite the advent of sophisticated fast algorithms, such as the fast multipole method (FMM), accurate simulations still demand a great amount of computation time due to the accuracy/speed trade-off inherently involved in these algorithms. Unless higher order multipole expansions, which are extremely expensive to evaluate, are employed, a large amount of the execution time is still spent in directly calculating particle-particle interactions within the nearby region of each particle. To reduce this execution time for pair interactions, we developed a computation unit (board), called MD-Engine II, that calculates nonbonded pairwise interactions using a specially designed hardware. Four custom arithmetic-processors and a processor for memory manipulation ("particle processor") are mounted on the computation board. The arithmetic processors are responsible for calculation of the pair interactions. The particle processor plays a central role in realizing efficient cooperation with the FMM. The results of a series of 50-ps MD simulations of a protein-water system (50,764 atoms) indicated that a more stringent setting of accuracy in FMM computation, compared with those previously reported, was required for accurate simulations over long time periods. Such a level of accuracy was efficiently achieved using the cooperative calculations of the FMM and MD-Engine II. On an Alpha 21264 PC, the FMM computation at a moderate but tolerable level of accuracy was accelerated by a factor of 16.0 using three boards. At a high level of accuracy, the cooperative calculation achieved a 22.7-fold acceleration over the corresponding conventional FMM calculation. In the cooperative calculations of the FMM and MD-Engine II, it was possible to achieve more accurate computation at a comparable execution time by incorporating larger nearby regions.