Solute Molecules In Water Research Articles

Theoretical Study of the Thermodynamics of a Solvated Peptide: Contryphan Vn

In recent papers we combined molecular dynamics (MD) simulations with the quasi Gaussian entropy (QGE) theory, in order to model the statistical mechanics and thermodynamics of simple solute molecules in water. In this paper we apply this approach to a more complex solute in water: a 9 residues peptide, Contryphan Vn. Results show that this approach can provide an accurate theoretical description of this complex solute-solvent system over a wide range of temperature.

Preparation and characterization of ZnS nanoparticles synthesized from chitosan laurate micellar solution

Synthesis of ZnS nanostructured materials has been performed in the micellar solution system, containing chitosan laurate as the surfactant. The self-assembling of the surfactant molecules in water solution can form unique architecture that can be adopted as the reaction template for the formation of nanomaterials. The synthesized nanomaterials have been characterized by energy filter transmission electron microscopy (EFTEM), Energy Dispersive X-ray Analysis (EDAX), X-ray diffractometry (XRD) and UV–Visible absorption measurement in order to determine the size, morphology, composition, crystal structure and optical behavior of the products. The spectroscopic results showed that the synthesized nanoparticles exhibited strong quantum confinement effect as the optical band gap increased significantly as compared to the bulk materials. In addition, the size of the resulting nanoparticles is greatly affected by the surfactant concentration and range from 2 to 10 nm. It was found that the nanomaterials obtained existed in face-centered cubic structure and exhibited the characteristic line broadening feature in the XRD patterns.

Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: a case study of a glutamate molecule in water solution and in a protein-bound form.

We propose a hierarchical approach to model vibrational frequencies of a ligand in a strongly fluctuating inhomogeneous environment such as a liquid solution or when bound to a macromolecule, e.g., a protein. Vibrational frequencies typically measured experimentally are ensemble averaged quantities which result (in part) from the influence of the strongly fluctuating solvent. Solvent fluctuations can be sampled effectively by a classical molecular simulation, which in our model serves as the first, low level of the hierarchy. At the second high level of the hierarchy a small subset of system coordinates is used to construct a patch of the potential surface (ab initio) relevant to the vibration in question. This subset of coordinates is under the influence of an instantaneous external force exerted by the environment. The force is calculated at the lower level of the hierarchy. The proposed methodology is applied to model vibrational frequencies of a glutamate in water and when bound to the Glutamate receptor protein and its mutant. Our results are in close agreement with the experimental values and frequency shifts measured by the Jayaraman group by the Fourier transform infrared spectroscopy [Q. Cheng et al., Biochem. 41, 1602 (2002)]. Our methodology proved useful in successfully reproducing vibrational frequencies of a ligand in such a soft, flexible, and strongly inhomogeneous protein as the Glutamate receptor.

Two-photon absorption investigation in reduced and oxidized cytochrome c solutions

Here we present, a two-photon absorption (2PA) study in Fe 2+ and Fe 3+ oxidation states of cytochrome c molecule in water solution, using the femtosecond Z-scan technique with pulses from 560 to 850 nm. No qualitative difference was observed in the 2PA process for the two Fe oxidation states. The 2PA cross-sections, for both samples, increase as the wavelength approaches the absorption band, in agreement with the resonant denominator in the sum-over states model, presenting a maximum value of approximately 1000 GM at about 600 nm.

On the use of the quasi-Gaussian entropy theory in the study of simulated dilute solutions.

In a recent paper [M. D'Alessandro, M. D'Abramo, G. Brancato, A. Di Nola, and A. Amadei, J. Phys. Chem. B 106, 11843 (2002)] we showed how to combine molecular dynamics simulations with the quasi-Gaussian entropy theory, in order to model the statistical mechanics and thermodynamics of ionic (water) solutions. In this paper we extend the method to treat nonspherical solutes, describe more thoroughly its theoretical basis and apply it to a set of more complex solute molecules in water (i.e., water, methane, ethane, methanol, and ethanol). Results show that this approach can really provide an excellent theoretical description of solute-solvent systems over a wide range of temperatures.

Supramolecular Guanosine 5‘-Monophosphate Structures in Solution. Light Scattering Study

During the past decade, from the vast evidence it became clear that DNA oligomers rich in guanine stretches can form in solution highly ordered forms called G-quadruplexes and G-wires. G-quadruplexes are present in many sites of the human genome, can inhibit telomerase, and can be used as drug delivery supramolecules. G-wires and related structures seem to be an excellent material of biological origin for nanostructures. Therefore, in this paper we have studied the structures formed by specific association of guanosine 5′-monophosphate (GMP) nucleotide molecules in water solutions by photon correlation spectroscopy and depolarized Rayleigh light scattering. One relaxation process with distinct amplitude was observed, as a function of temperature and sample concentration. It was attributed to the translational diffusion coefficient of the stacks of G-quartets in a range of high concentration and to the stacks of GMP monomer associates for low concentration (less than 40 mg/mL). From the measurements the hydrodynamic radius of GMP molecule has been estimated as rH = 5.4 A. The bead modeling of the hydrodynamic parameters allowed us to distinguish the wide spectrum of structures formed in solution: from single GMP nucleotides to stacks of multiassociates of G-quartets of GMP.

Impact of Radiation Damage on DNA Determined by Computational Simulation

Review of molecular dynamics (MD) studies of several radiation-originated lesions on DNA molecules is presented. Main focus is to describe structural and energy changes in DNA molecule with the respect to proper recognition of the lesion by respective repair enzyme. Pyrimidine lesions (cytosinyl radical, thymine glycol) and purine lesion (8-oxoguanine) were subjected to MD simulations for several hundreds picosecond (ps), (200ps for cytosinyl radical, 2 nanosecond for thymine glycol and 8-oxoguanine) using MD simulation code AMBER 5.0 (4.0) and its respective force field modified for each lesion. Simulations were performed as all atoms simulations for fully solvated solute molecules in water. Negative charges of DNA phosphates were neutralized by sodium counterions Na+ that are essential for its double helical structure. In most cases the significant structural changes in DNA are observed: a) breaking of hydrogen bonds network between complementary bases and resulting opening of the double helix (cytosinyl radical, 8-oxoguanine); b) sharp bending of the DNA helix centered at the lesion site (thymine glycol); and c) flipped-out base (8-oxoguanine). These changes are related to overall collapsing of the double helical structure around the lesion and are considered to facilitate docking of the repair enzyme into the DNA and formation of DNA-enzyme complex. Stable DNA-enzyme complex is necessary condition for the onset of entire enzymatic repair process. In addition to the structural changes, specific values of electrostatic interaction energy are detected at several lesion sites (thymine glycol, 8-oxoguanine). The specific electrostatic energy is considered as a factor that enables repair enzyme to discriminate lesion from native, non-damaged site.

Spectroscopic and semiempirical studies of the phototropic species of 8-amino-5,8′-azo-bis-naphthalene-2-sulphonic acid

Structural study of the azo compound obtained as a result of diazotization and coupling of 8-amino-naphthalene-2-sulfonic acid (Cleve's acid), has been performed by the spectroscopic methods 1H NMR and FTIR. UV–vis spectra of 8-amino-5,8′-azo-bis-naphthalene-2-sulphonic acid (CA-CA) were measured in water environment at different pH values and at a constant ionic strength. On the basis of the NMR, FTIR as well as on the grounds of a comparison of the experimental UV–vis spectra with those obtained by the MM/ PM5 in water followed by ZINDO method calculation, geometry of the CA-CA molecule in water solution has been proposed. Moreover, the value of the first dissociation constant of the dye has been determined (2.75×10 −2).

Computational determination of radiation damage effects on DNA structure

AbstractMolecular dynamics (MD) studies of several radiation originated lesions on the DNA molecules are presented. The pyrimidine lesions (cytosinyl radical, thymine dimer, thymine glycol) and purine lesion (8-oxoguanine) were subjected to the MD simulations for several hundred picoseconds using MD simulation code AMBER 5.0 (4.0). The simulations were performed for fully dissolved solute molecules in water. Significant structural changes in the DNA double helical structure were observed in all cases which may be categorized as: a) the breaking of hydrogen bonds network between complementary bases and resulted opening of the double helix (cytosinyl, radical, 8-oxoguanine); b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and c) the flippingout of adenine on the strand complementary to the lesion (8-oxoguanine). These changes related to the overall collapsing of the double helical structure around the lesion, are expected to facilitate the docking of the repair enzyme into the DNA in the formation of DNA-enzyme complex. The stable DNA-enzyme complex is a necessary condition for the onset of the enzymatic repair process. In addition to structural changes, specific values of electrostatic interaction energy were determined at several lesion sites (thymine dimer, thymine glycol and 8-oxoguanine). This lesion-specific electrostatic energy is a factor that enables repair enzyme to discriminate lesion from the native site during the scanning of the DNA surface.

Molecular organization and electrochemical reduction of a Ni(II)Porphyrin complex in LB films

In this work, mixed films of a tetra-cationic porphyrin, Ni(II)TMPyP, and an anionic phospholipid, DMPA, in molar ratio of 1:4, were formed at the air–water interface and transferred onto glass and optically transparent indium tin oxide (ITO) electrodes. Transmission spectroscopy (on glass and ITO) and cyclic voltammetry (on ITO) were used to infer the molecular organization and the electrochemical reduction of these LB films. Likewise, we compare the electrochemical reduction of the Ni(II)TMPyP in water solution with that in LB films. The porphyrin molecules in water solution show three two-electron reduction waves, which are related to the two-electron reduction of the central ring of the porphyrin and to the one-electron reductions of the four methyl–pyridyl groups of the molecule, respectively, while only two reversible one-electron reduction waves are observed in LB films corresponding to the reduction of the central ring of the porphyrin and to the Ni(II) to Ni(I) reduction, respectively.

Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules.

We propose a framework to describe the cooperative orientational motions of water molecules in liquid water and around solute molecules in water solutions. From molecular dynamics (MD) simulation a new quantity "site-dipole field" is defined as the averaged orientation of water molecules that pass through each spatial position. In the site-dipole field of bulk water we found large vortex-like structures of more than 10 A in size. Such coherent patterns persist more than 300 ps although the orientational memory of individual molecules is quickly lost. A 1-ns MD simulation of systems consisting of two amino acids shows that the fluctuations of site-dipole field of solvent are pinned around the amino acids, resulting in a stable dipole-bridge between side-chains of amino acids. The dipole-bridge is significantly formed even for the side-chain separation of 14 A, which corresponds to five layers of water. The way that dipole-bridge forms sensitively depends on the side-chain orientations and thereby explains the specificity in the solvent-mediated interactions between biomolecules.

Some physicochemical properties of 7-oxoacyl- l-alanyl- d-isoglutamines

N-(7-Oxoacyl)- l-alanyl- d-isoglutamines are substances with similar effects on immune system as N-acetylmuramyldipeptide (MDP). They were synthesized to eliminate some side effects of MDP: pyrogenicity, leucopenia, hypertension and fast elimination from the body. The aim of our work was to determine some physicochemical properties of a series of N-(7-oxoacyl)- l-alanyl- d-isoglutamines, that have zero to six methylene groups between terminal methyl and 7-oxo group. The following properties were examined: water solubility, lipophilicity, thermal behaviour and true density. The results were compared and it was established that the lipophilic parameter determined by high-performance liquid chromatography is increasing by the increase of alkyl chain while the water solubility is decreasing at the same time. In both cases the substance with the longest chain ( N-(7-tetrakanoyl)- l-alanyl- d-isoglutamine) is an exception. The lipophilic parameter of this substance is lower and water solubility higher than with the substances with three, four and five methylene groups between terminal methyl and 7-oxo group. These results can be explained by the twisted conformation of N-(7-tetrakanoyl)- l-alanyl- d-isoglutamine molecule in water solution. By means of thermal analysis it was discovered that the melting point is decreasing with the increase of alkyl chain. From the true density and melting enthalpy measurements it is evident that with the increase of alkyl chain the arrangement of molecules in solid state is increasing up to the molecule with four methylene groups between terminal methyl and 7-oxo group. Substances with longer chains have lower true density and melting enthalpy because of the different arrangements of the molecules.

Solution properties and sweetness response of selected bulk and intense sweeteners.

Two bulk sweeteners (sucrose and maltitol) and four intense sweeteners (acesulfame K, aspartame, sodium cyclamate, and sodium saccharin) are used in this study. Densities and sound velocity values of the sweeteners in solution are measured at 20 degrees C, and their apparent molar and specific volumes, their isentropic apparent molar and specific compressibilities, as well as their compressibility hydration numbers are calculated and reported. The introduction of solute molecules in water results in a volume change of the solvent as a result of attractive forces exerted by the solute molecules; such forces are in the form of electrostrictive or hydrogen-bonding forces, or charge-dipole attraction. Changes of molar volumes with increasing concentration give an indication of the extent of solute-solute interaction, whereas isentropic compressibilities give a direct measurement of the state of hydration of the solute molecules. The compressibility hydration numbers reported give an indication of the number of water molecules disturbed by the presence of each solute molecule in solution. Isentropic compressibilities seem to be a more sensitive parameter for distinguishing the bulk sweeteners from the artificial sweeteners. The sweetness response of the sweeteners is then explained in terms of their solution behaviors.

Potential of mean force calculation of solute molecules in water by a modified solvent-accessible surface method

We propose an empirical method for evaluating the potential of . mean force pmf of solute molecules in water by modifying the solvent- . accessible surface SAS method described by Eisenberg et al. We re-evaluated the SAS energy for each united atom composing the solute. We took into account the energy required to generate a void between adjacent solute molecules and the Coulombic interactions between atom-centered point charges of solute molecules containing C, O, P, K q ,N a q , and Cl y atoms in water. The modified SAS method well reproduced the various pmfs given by MD calculations or the integral equation method. The large activation energy of K q )18-crown-6 complexation can be explained mostly by the void energy. The computational time required for the modified SAS method is approximately three to four orders of magnitude less than that by MD calculations. Q 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1656)1663, 1997

A cellular automata model of the hydrophobic effect.

Dynamic simulations of solute molecules in water are made using cellular automata. By varying the parameter governing the breaking probability of water-solute tesselated pairs, sets of configurations were modeled of solutions ranging from polar to non-polar solutes. The emergent behavior of the non-polar solute models leads us to believe that this is a possible model of the hydrophobic effect.

The dynamics of some metal-organic and organic molecules in water solution studied by molecular mechanical and molecular dynamical methods

A force field is developed to reproduce geometries and vibration spectra of rutheniumhexaamine(III) and rutheniumhexamine(II) complexes. The force constants for ruthenium were then used in molecular dynamics simulation of a Ru 2+ ion, a Ru 3+ ion and Ru(NH 3) 5-pyrazine 2+ in water solution. Simulations of pyrazine and 1,3-dimethyluracile in water solution were also performed. A comparison of different ways of how to include solvation effects in quantum chemical calculations is discussed using the results from the simulations. The MD simulations show that the solvent surrounding a small charged ion, such as a Ru 2+ ion, have a pronounced shell structure and the first layer of solvent molecules is stable during a 61 ps simulation. For a metal-organic molecule as Ru(NH 3) 5-pyrazine the solvent shows shell structure, but the water molecules are exchanged frequently. In the relatively charge-symmetric pyrazine the solvent is not polarized around the molecule. In a molecule like 1,3-dimethyluracile, which is non-symmetric in the charge distribution, the water is strongly polarized.

Aggregation of amphiphilic molecules in water. I. α‐phenylethylamine: 1H and 13C NMR study

AbstractThe concentration dependence of the 1H and 13C NMR chemical shifts in D2O and in CDCl3 solutions were determined for (±)‐α‐phenylethylamine (I). Aqueous solutions of (−)‐I and (+)‐I, 50% enantiomerically enriched in (−)‐ and (±)‐2, 2, 2,‐trifluoro‐1‐phenylethanol and the (+)‐ and (−)‐N‐formyl derivatives of I, were also studied. 1H nuclear Overhauser enhancements were used to check the conformations of the solutes at various concentrations and 1H T1 values were used to monitor the changes in molecular tumbling in solutions. The results are interpreted in terms of a spontaneous aggregation of solute molecules in water, with the possible determination of the critical micelle concentration. The time‐dependent splittings in the 1H NMR spectra suggest further, more detailed, studies of the structures of the aggregates and the possibility of chiral recognition in water.

An insoluble chromolytic substrate for the determination of proteolytic activity

A new insoluble chromolytic substrate for the determination of proteolytic activity was prepared by immobilization of dyed casein into the structure of polyacrylamide gel. The prepared substrate could detect approximately 0.1 μg of trypsin per ml. The spontaneous leakage of dyed casein molecules in water solutions was negligible.

Measurement of the hydrophobic interaction between two hydrophobic surfaces in aqueous electrolyte solutions

The attractive force-law between two hydrophobic (hydrocarbon) surfaces in aqueous solutions has been derived from total force measurements on monolayer coated mica surfaces. This “hydrophobic interaction” is much stronger than the expected van der Waals interaction at distances below 8 nm and decays exponentially with distance. The results highlight the long-range nature of hydrophobic (solvation) forces and indicate that these forces may determine the magnitude of the energy barriers between interacting charged particles and hence the stability of hydrophobic colloids. The results are also consistent with previous experimental and theoretical estimates of the hydrophobic interaction between contacting nonpolar solute molecules in water.

Exit Rates of Micellar Radicals Measured

A nuclear magnetic resonance (NMR) method to measure rates of migration of free radicals out of micelles has been developed by organic chemistry professor Nicholas J. Turro of Columbia University. Because Turro's is an NMR method, it yields detailed structural information on the particular species being investigated. Micelles are assemblies of detergent molecules in water solutions that entrap small, hydrophobic molecules in their interiors. Turro's accomplishment may lead to studies of dynamics of small molecules or reactive intermediates of low concentrations and/or short lifetimes in biological systems. Examples include determining migration rates of intermediates during photoaffinity labeling of biological macromolecules and measuring association and dissociation rates of drug molecules and proteins during transport. Industrial chemists also might use the technique. (For more details on the use of micelles as models of biological systems, see the special report on membrane mimetic chemistry beginning ...