Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution

Unrestrained molecular dynamics (MD) simulations have been carried out to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA conformational transitions in aqueous RbCl solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbCl concentration on the dynamics of the A→B conformational transition in the DNA duplex d(CGCGAATTCGCG)2 . Canonical Aand B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was monitored for 3.0 ns and the distances between the C5′ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simulations. In addition, increasing the RbCl concentration in aqueous solution hindered the A→B conformational transition and the transition in aqueous RbCl solution was faster than that in aqueous NaCl solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A→B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The rubidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help explain the effect of RbCl concentration on the dynamics of the A→B conformational transition.     

Free energy landscape of receptor-mediated cell adhesion

Receptor-mediated cell adhesion plays a critical role in cell migration, proliferation, signaling, and survival. A number of diseases, including cancer, show a strong correlation between integrin activation and metastasis. A better understanding of cell adhesion is highly desirable for not only therapeutic but also a number of tissue engineering applications. While a number of computational models and experimental studies have addressed the issue of cell adhesion to surfaces, no model or theory has adequately addressed cell adhesion at the molecular level. In this paper, the authors present a thermodynamic model that addresses receptor-mediated cell adhesion at the molecular level. By incorporating the entropic, conformational, solvation, and long- and short-range interactive components of receptors and the extracellular matrix molecules, they are able to predict adhesive free energy as a function of a number of key variables such as surface coverage, interaction distance, molecule size, and solvent conditions. Their method allows them to compute the free energy of adhesion in a multicomponent system where they can simultaneously study adhesion receptors and ligands of different sizes, chemical identities, and conformational properties. The authors' results not only provide a fundamental understanding of adhesion at the molecular level but also suggest possible strategies for designing novel biomaterials.     

Free energy of interaction of sodium dodecyl sulfate in aqueous solution with carbon black surfaces

The free energy of the adsorption process of an ionic surfactant from aqueous solutions onto a set of carbon blacks in the range of low concentrations was evaluated using the model proposed by van Oss and co-workers. The obtained results indicated that the free energy of interaction between adsorbent and adsorbate through water results mainly from Lifshitz-van der Waals and electrostatic interactions, and its value showed a good correspondence with that previously found from a combination of the classical measurements of adsorption isotherms and the Langmuir model.     

Free energy surfaces for the interaction of D-glucose with planar aromatic groups in aqueous solution

Multidimensional potentials of mean force for the interactions in aqueous solution of both anomers of D-glucopyranose with two planar aromatic molecules, indole and para-methyl-phenol, have been calculated using molecular dynamics simulations with umbrella sampling and were subsequently used to estimate binding free energies. Indole and para-methyl-phenol serve as models for the side chains of the amino acids tryptophan and tyrosine, respectively. In all cases, a weak affinity between the glucose molecules and the flat aromatic surfaces was found. The global minimum for these interactions was found to be for the case when the pseudoplanar face of β-D-glucopyranose is stacked against the planar surfaces of the aromatic residues. The calculated binding free energies are in good agreement with both experiment and previous simulations. The multidimensional free energy maps suggest a mechanism that could lend kinetic stability to the complexes formed by sugars bound to sugar-binding proteins.     

Free energy landscape for glucose condensation reactions

Ab initio molecular dynamics and metadynamics simulations were used to determine the free energy surfaces (FES) for the acid catalyzed β-D-glucose condensation reaction. Protonation of C1-OH on the β-D-glucose, breakage of the C1-O1 bond, and the formation of C1 carbocation is the rate-limiting step. The effects of solvent on the reaction were investigated by determining the FES both in the absence and presence of solvent water. It was found that water played a critical role in these reactions. The reaction barrier for the proton-catalyzed glucose condensation reaction is solvent induced because of proton's high affinity for water. During these simulations, β-D-glucose conversion to α-d-glucose process via the C1 carbocation was also observed. The associated free energy change and activation barrier for this reaction were determined.     

Cellulose conversion to polyols on supported Ru catalysts in aqueous basic solution

It is of great significance and challenge to achieve direct conversion of cellulose to specific polyols, e.g., ethylene glycol and propylene glycol. For such selective conversion, a novel one-pot approach was studied by combination of alkaline hydrolysis and hydrogenation on supported Ru catalysts. A wide range of bases including solid bases, e.g., Ca(OH)₂ and La₂O₃, and phosphate buffers were examined in the cellulose reaction in water, and the cellulose conversions and polyol products depended largely on the basicity or pH values in the aqueous solutions. Ethylene glycol, 1,2-propanediol, and especially 1,2,5-pentanetriol were obtained with selectivities of 15%, 14% and 22%, respectively, at 38% cellulose conversion at pH 8 in phosphate buffer solution. These preliminary results provide potentials for efficient conversion of cellulose to targeted polyols by using the advantages of bases.     

Free radical-induced oxidative degradation of polyacrylamide in aqueous solution

The oxidative main chain degradation of polyacrylamide initiated by ^·OH radicals attacking the polymer in aqueous solution was studied. ^·OH radicals were produced by irradiating dilute polymer solutions with high energy radiation. A bimolecular process (combination of PO₂ radicals) was found to be the rate determining step in the series of consecutive reactions leading to main-chain rupture. This was revealed from results obtained in pulse radiolysis studies using the light scattering detection method. Under the given experimental conditions, the number of radical sites per initial macromolecule exceeded unity with the consequence that intramolecular reactions of PO₂ radicals dominated intermolecular combinations. From both pulse radiolysis and continuous irradiations it was inferred that only a small fraction (about 1%) of the attacking ^·OH radicals initiated main-chain scission.     

MD simulation of the transitions between B-DNA and A-DNA in the framework of a coarse-grained model

Transitions between the B and A forms of a short DNA double helix (12 base pairs) at different salt concentrations in an aqueous solution have been studied by the molecular dynamics method in the framework of a coarse-grained model with explicit ions but without friction. It has been shown that the A-DNA, stable at high salt concentrations, is a dynamic conglomerate of the molecule and the ions coming from the solution into the deep major groove and then leaving it. In such a short helix, in the model without friction, even at low salt concentrations, transitions from B-DNA to A-DNA and back are frequent and fast. Stable ADNA (without transitions to B-DNA) forms at salt concentrations greater than 0.45 mol/L.     

Free energy landscape of protein-like chains with discontinuous potentials

In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond interactions, electrostatic repulsion, and covalent bond vibrations are modeled by discontinuous step, shoulder, and square-well potentials, respectively. The protein-like chains exhibit a secondary alpha helix structure in their folded states at low temperatures, and allow a natural definition of a configuration by considering which beads are bonded. Free energies and entropies of configurations are computed using the parallel tempering method in combination with hybrid Monte Carlo sampling of the canonical ensemble of the discontinuous potential system. The probability of observing the most common configuration is used to analyze the nature of the free energy landscape, and it is found that the model with the least number of possible bonds exhibits a funnel-like free energy landscape at low enough temperature for chains with fewer than 30 beads. For longer proteins, the free landscape consists of several minima, where the configuration with the lowest free energy changes significantly by lowering the temperature and the probability of observing the most common configuration never approaches one due to the degeneracy of the lowest accessible potential energy.     

Free energy decomposition analysis of bonding and nonbonding interactions in solution

A free energy decomposition analysis algorithm for bonding and nonbonding interactions in various solvated environments, named energy decomposition analysis-polarizable continuum model (EDA-PCM), is implemented based on the localized molecular orbital-energy decomposition analysis (LMO-EDA) method, which is recently developed for interaction analysis in gas phase [P. F. Su and H. Li, J. Chem. Phys. 130, 074109 (2009)]. For single determinant wave functions, the EDA-PCM method divides the interaction energy into electrostatic, exchange, repulsion, polarization, desolvation, and dispersion terms. In the EDA-PCM scheme, the homogeneous solvated environment can be treated by the integral equation formulation of PCM (IEFPCM) or conductor-like polarizable continuum model (CPCM) method, while the heterogeneous solvated environment is handled by the Het-CPCM method. The EDA-PCM is able to obtain physically meaningful interaction analysis in different dielectric environments along the whole potential energy surfaces. Test calculations by MP2 and DFT functionals with homogeneous and heterogeneous solvation, involving hydrogen bonding, vdW interaction, metal-ligand binding, cation-π, and ionic interaction, show the robustness and adaptability of the EDA-PCM method. The computational results stress the importance of solvation effects to the intermolecular interactions in solvated environments.     

Electrochemical conversion of aqueous ethanol solution in an electrolyzer with a solid polymer electrolyte

Russian Journal of Applied Chemistry - The electrochemical conversion of an aqueous ethanol solution (40 vol %) in an electrolysis cell with a solid polymer electrolyte in the presence of various...     

Multivariate analysis of a data matrix containing A-DNA and B-DNA dinucleoside monophosphate steps: Multidimensional Ramachandran plots for nucleic acids

A method to construct the equivalent of multidimensional Ramachandran plots for nucleic acids on the basis of singular value decomposition (SVD) is presented. For this purpose, a data matrix containing 244 DNA dinucleoside monophosphate steps, represented by nine torsion angles, was decomposed into a score and loading matrix. It is shown that biplots, containing both score points and loading vectors, provide a simple tool to interpret the principles of DNA class separation. Scores separate the data matrix into one A-DNA class, two different B-DNA classes, and one so-called crankshaft class. Loading vectors correlate torsion angles. The projections of scores on loading vectors indicate which torsion angles play a dominant role in DNA class separation. The results of the biplots are supported by (simple) physical interpretations. From a three-dimensional score space the nine original torsion angles can be reconstructed. Hence, the potential to create the multidimensional equivalent of a Ramachandran plot is available; that is, forbidden and accessible regions in the reduced space reflect these same regions in the nine-dimensional original space. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 695–715, 1998     

Free energy relationships in aqueous amino acid and peptide solutions containing sodium chloride

Three systems of the type amino acid or peptide-sodium chloride-water have been investigated over wide solute molality ranges using the isopiestic vapor pressure method. The amino acid employed was L--alanine, while the peptides were diglycine and triglycine. Equations were obtained for the activity coefficients of these compounds in the salt solutions in terms of the molalities of the solutes. The trace activity coefficients of the peptides were negative at low salt molality and became positive as the salt molality was increased. The limiting interaction parameters were calculated for the systems using the Kirkwood ion-dipole expression and empirical quantities derived from previous work to obtain the salt effect on the nonpolar and amide portion of the molecule. Good agreement was obtained between the calculated values and the experimental results in the case of diglycine, but they diverged in the case of triglycine. The calculated value for L--alanine is in poorer agreement with the experimental value than for the other amino acids studied previously.Presented in part at the Second International Conference on Calorimetry and Thermodynamics, Orono, Maine, July 1971.     

Free enthalpy landscape of SrO

Trying to predict thermodynamically stable and metastable solid compounds as function of pressure and temperature requires the global exploration of the enthalpy landscapes of chemical systems and the subsequent construction of their free enthalpy landscapes. In this work, we present a general approach to the determination of a free energy landscape. As an example, we construct the free enthalpy landscape of SrO for two different pressures on the empirical potential level and also compute various thermodynamic and elastic properties of SrO in the NaCl-, CsCl-, NiAs-, NbS-, TiP-, beta-BeO, sphalerite-, and wurtzite-structure type on an ab initio level. We employ density functional theory within the hybrid B3LYP approximation. The results show good agreement with experimental and theoretical data.     

Modelling of phenol removal in aqueous solution depending on the electron beam energy

This paper deals with the influence of the electron beam energy (E=1.2–3 MeV; I=20–125 μA; D_R=1.3–8.3 kGy s⁻¹) on the degradation of phenol in aqueous solution. The decomposition of phenol and the concentration of its principal by-products are significantly influenced by the energy of the electron beam. The degradation yield increases with the electron energy. A simplified phenomenologic model of the reactor was proposed to describe the results.