Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides

DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to be considered mostly electrostatics in origin and to be calculated with DelPhi assigning residue-specific value of the internal dielectric constant of protein. The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations. The best fit between experimental values and predicted changes is used to find out the effective value of the internal dielectric constant for each type of amino acid. The predicted folding free energy changes with the optimal, amino acid specific, dielectric constants are within RMSD=0.86 kcal/mol from experimentally measured changes.

DelPhi: a comprehensive suite for DelPhi software and associated resources

Background

Accurate modeling of electrostatic potential and corresponding energies becomes increasingly important for understanding properties of biological macromolecules and their complexes. However, this is not an easy task due to the irregular shape of biological entities and the presence of water and mobile ions.

Results

Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi, enriched with additional features to facilitate DelPhi usage. The suite allows for easy download of both DelPhi executable files and source code along with a makefile for local installations. The users can obtain the DelPhi manual and parameter files required for the corresponding investigation. Non-experienced researchers can download examples containing all necessary data to carry out DelPhi runs on a set of selected examples illustrating various DelPhi features and demonstrating DelPhi’s accuracy against analytical solutions.

Conclusions

DelPhi suite offers not only the DelPhi executable and sources files, examples and parameter files, but also provides links to third party developed resources either utilizing DelPhi or providing plugins for DelPhi. In addition, the users and developers are offered a forum to share ideas, resolve issues, report bugs and seek help with respect to the DelPhi package. The resource is available free of charge for academic users from URL: http://compbio.clemson.edu/DelPhi.php.

Specific counter-ion and co-ion effects revealed in mixing of aqueous solutions of 3,3 and 6,6-ionenes with solutions of low molecular weight salts

Enthalpies of mixing of aliphatic 3,3 and 6,6-ionene fluorides with low molecular weight salts (sodium formate, acetate, nitrate, chlorate(v), and thiocyanate), all dissolved in water, were determined. In addition, to complement our previous study (Lukšičet al., Phys. Chem. Chem. Phys., 2012, 14, 2024), new measurements were performed where aqueous solutions of 3,3 and 6,6-ionene bromides were mixed with solutions of sodium fluoride, chloride, bromide, and iodide. Electrostatic theory, based on Manning's limiting law or the Poisson-Boltzmann equation, predicted the enthalpy of mixing to be endothermic in all the cases, while experiments showed that this is not always true. When an aqueous solution of 3,3-ionene fluoride was mixed with a solution of sodium fluoride (or formate and acetate) in water, the effect was indeed endothermic. For all other salts, i.e. sodium chlorate, nitrate, and thiocyanate, heat was released upon mixing. The situation was similar for 6,6-ionene fluoride solutions with an exception of mixing with sodium chlorate, where the effect was endothermic. The enthalpy of mixing was strongly correlated with the enthalpy of hydration of the counterion of the low molecular weight salt. A lyotropic series, similar to that of Hofmeister, was obtained. To examine also the effect of co-ions, ionene bromides were titrated with tetramethyl-, tetraethyl-, or tetrapropylammonium bromides. The enthalpy was exothermic for all mixtures while, somewhat unexpectedly, the co-ion specific effect was quite strong.

Isothermal titration calorimetry and molecular dynamics study of ion-selectivity in mixtures of hydrophobic polyelectrolytes with sodium halides in water

Aliphatic x,y-ionenes are polyelectrolytes in which x and y denote the numbers of methylene groups separating quaternary ammonium ions. They represent useful model substances for studying hydrophobic and charge effects in aqueous solutions. We used isothermal titration calorimetry to measure the enthalpies of mixing, ΔH(mix), of 3,3- and 6,6-ionene fluorides and bromides with low molecular weight salts (NaF, NaCl, NaBr, and NaI) at 298 K in water. The signs and magnitudes of the measured enthalpies depend on the hydrophobicity of the ionene and on the nature of the added salt. For example, addition of sodium fluoride to solutions of 3,3- and 6,6-ionene fluorides produced endothermic effects, while addition of sodium bromide to 3,3-ionene bromide resulted in a strong exothermic effect. Interestingly, mixing of 6,6-ionene bromide and NaBr solutions in water gave a small exothermic heat effect. Polyelectrolyte theories, based on continuum-solvent models, predict enthalpies of mixing to be positive (endothermic) for all the solutions examined in this work. The ion-specific effect is more strongly expressed in ionene solutions with higher charge density (3,3-ionene). The most important result of this work is the finding that the enthalpy of mixing of 3,3- (and of 6,6-ionene) fluorides with sodium halides can be expressed as a linear function of the enthalpy of hydration of the halide counterions. The experimental results were complemented with an explicit water molecular dynamics simulation of solutions of oligoions modelling 3,3- and 6,6-ionenes. The computer simulation results for various nitrogen-counterion pair distribution functions were in most cases consistent with the enthalpy measurements.

Interplay of ion-specific and charge-density effects in aqueous solutions of weakly charged ionenes as revealed by electric-transport measurements

In 3,3-ionenes, one quaternary nitrogen is bonded to a chain of three methylene groups on each side, and in 6,9-ionene, it is bonded to a chain of six on one side and nine on the other. We examined how the solution properties of several ionenes changed with increased hydrophobicity of the polyion, depending on the nature of the counterion. We determined the electrical conductivities of aqueous solutions of 3,3-, 4,5-, 6,6-, and 6,9-ionene fluorides and bromides in the range of concentrations from 5 x 10(-3) to 1 x 10(-1) M and for the temperature interval 5-35 degrees C. Over these ranges, the conductivities of the ionenes were found to decrease with increasing concentration and increase with increasing temperature. The conductivity of 3,3-ionene bromide was lower than that of its fluoride analogue throughout the whole range of concentrations, whereas for the 6,9-ionenes, the trend was reversed. For 4,5- and 6,6-ionene, we observed a crossover in the concentration dependence of conductivity. The conductivity data were compared with the predictions of Manning's theory and scaling theory. Separately determined transport-number values were combined with the conductivity data to obtain the fractions of so-called "free" counterions, f. For bromide samples, f increased from 3,3- to 6,9-ionene. In the case of fluoride counterions, the fraction of free counterions was the lowest for 3,3-ionene and, within the experimental uncertainty, approximately constant for the other less charged ionenes.