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A Pohorille

Publications and source records attributed to A Pohorille.

50 records · Page 3Linked to original sources
PubMed1989

Interaction of a sodium ion with the water liquid-vapor interface.

Molecular dynamics results are presented for the density profile of a sodium ion near the water liquid-vapor interface at 320 K. These results are compared with the predictions of a simple dielectric model for the interaction of a monovalent ion with this interface. The interfacial region described by the model profile is too narrow and the profile decreases too abruptly near the solution interface. Thus, the simple model does not provide a satisfactory description of the molecular dynamics results for ion positions within two molecular diameters from the solution interface where appreciable ion concentrations are observed. These results suggest that surfaces associated with dielectric models of ionic processes at aqueous solution interfaces should be located at least two molecular diameters inside the liquid phase. A free energy expense of about 2 kcal/mol is required to move the ion within two molecular layers of the free water liquid-vapor interface.

Gases↗
PubMed1988

Surface potential of the water liquid-vapor interface.

The surface potential of the water liquid-vapor interface is studied by molecular dynamics using the TIP4P model. The surface potential predicted by this empirical model is -(130 +/- 50) mV. This value for the surface potential is of reasonable magnitude but of opposite sign to the expectations derived from laboratory experiments. The electrostatic potential displays a nonmonotonic variation with depth into the liquid. This nonmonotonic variation is explained on the basis of the nondipolar charge distribution of the H2O molecule and the observation that the more probable molecular orientations in the interfacial region place the molecular symmetry axis near the plane of the interface. It is shown that minor changes in the assumed molecular charge distribution can bring the computed surface potential into agreement with experimental expectations without qualitatively altering the nonmonotonic variation of the electrostatic potential through the interfacial region. Computed quantum mechanical descriptions of the electron distribution of the isolated H2O molecule are not compatible with the surface structure predicted by the TIP4P model and the experimental expectation that the surface potential of the water liquid-vapor interface is small, roughly of the of order of 10-100 mV. The surface potential is sensitive to details in the large distance wings of the molecular electron distribution. It is hypothesized that the surface environment qualitatively alters the wings of the distribution from the result obtained by a superposition of the isolated molecule electron densities.

Gases↗
PubMed1988

A molecular dynamics study of chloride binding by the cryptand SC24.

The capture of chloride from water by the tetraprotonated form of the spherical macrotricyclic molecule SC24 was studied using molecular dynamics simulation methods. This model ionophore represents a broad class of molecules which remove ions from water. Two binding sites for the chloride were found, one inside and one outside the ligand. These sites are separated by a potential energy barrier of approximately 20 kcal mol-1. The major contribution to this barrier comes from dehydration of the chloride. The large, unfavorable dehydration effect is compensated for by an increase in electrostatic attraction between the oppositely charged chloride and cryptand, and by energetically favorable rearrangements of water structure. Additional assistance in crossing the barrier and completing the dehydration of the ion is provided by the shift of three positively charged hydrogen atoms of the cryptand towards the chloride. This structural rigidity is partially responsible for its selectivity.

Chelating Agents↗
PubMed1988

Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24.

A molecular dynamics study of chloride capture from water by the tetraprotonated cryptand SC24 is presented. The system under study consisted of a cryptand molecule, chloride ion, and 319 water molecules. Calculations were performed for 19 distances between the cryptand and the chloride. For each distance a trajectory of at least 60 ps was obtained. Two anion binding sites of comparable energy were found. The chloride can bind either inside the cryptand cavity or more loosely outside of the ligand. The binding sites are separated by an energy barrier of 20 kcal/mol. Chloride movement toward the cryptand is accompanied by stepwise dehydration of the anion. The energy loss due to this dehydration is offset by the electrostatic attraction between the anion and the ligand and by an increase in favorable water-water interactions. The most striking feature of chloride capture is a rapid cooperative change in the conformation of the cryptand when the Cl- starts to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, so that they point toward the chloride. The shift provides electrostatic stabilization, which compensates for the loss of the remaining three water molecules from the hydration shell of the anion. The N-H bonds remain directed toward the anion during its further movement into the ligand and guide chloride into a stable position inside the cryptand cavity. The flexibility of the receptor, the stepwise dehydration of an ionic substrate, and the characteristic balance between different energy components in the system all may be features of ion binding common to a wide range of abiotic and biological ionophores.

Anions↗
PubMed1987

Comparison of the structure of harmonic aqueous glasses and liquid water.

Glassy structures of water were generated by rapidly quenching configurations of 64 and 343 molecules of liquid water. The potential energy was then expanded through quadratic order around local minima generated this way and properties of the resulting harmonic system were calculated. The results were used to test the extent to which the structure of liquid water is similar to that of a harmonic aqueous glass. The radial distribution functions for the glass are remarkably similar to those of the liquid. The vibrational density of states for the glassy water exhibits a gap between 300 and 400 cm-1. The normal modes below 300 cm-1 correspond to molecular translations while the modes above 400 cm-1 are ascribed to molecular librations. Translational modes are almost entirely responsible for the broadening of oxygen-oxygen radial distribution function of the quenched configuration. They are also primarily responsible for the broadening of other radial distribution functions. Vibrational density of states leads to classical and quantum free energies for the harmonic system equal -9.62 +/- 0.12 and -8.89 +/- 0.12 kcal/mol, respectively, at T = 300 K. Both free energies were found to be insensitive to sample size and to the configurational differences between the quenched structures.

Computer Simulation↗
PubMed1987

Molecular dynamics of the water liquid-vapor interface.

The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.

Chemical Phenomena↗
PubMed1985

Base-pairing properties of O-methylated bases of nucleic acids. Energetic and steric considerations.

Base-pairing properties of O-methylated nucleic-acid bases have been systematically investigated using both semi-empirical quantum-mechanical methods and a second-order perturbation formalism. The energetic, steric and electronic properties of (a) the individual methylated bases, (b) possible base-pairs formed between O-methylated and normal bases, and (c) mini-helices incorporating O-methylated bases were calculated. Two types of base-paired complexes were obtained: Those involving classical linear hydrogen bonds, and those involving bifurcated hydrogen-donor-hydrogen-acceptor interactions. In most complexes the presence of mispairs in the helical structure of nucleic acids is expected to create a local perturbation in the structure of the helix. Even though the most stable planar configurations of the mispairs may deviate markedly from those in the regular double helix, the induced deformations in the structure of the backbone are relatively small. Internal energies and geometries of mispairs are strongly affected by the conformation of the exocyclic group of the methylated bases. Another important contribution to the stability of various base-pairing schemes comes from stacking interactions.

Allosteric Site↗
PubMed1984

Monte Carlo simulation of the influence of solvent on nucleic acid base associations.

The results of Monte Carlo calculations of the association between nucleic acid bases in a nonpolar solvent (CCl4) are described. The influence of the solvent on planar and stacked associations of bases was examined by analyzing the total energy of the system, including solute-solute, solute-solvent, and solvent-solvent contributions. Good quantitative agreement with the available experimental data was obtained. Solute-solvent interactions are primarily determined by dispersion forces; consequently, solute-solvent interactions vertical to the solute plane that maximize dispersion interactions are most favored, and a rough proportionally between solute-solvent energy and the surface of the solute was observed. Analysis of solvent-solvent energy is not necessarily reduced when surface area decreases, contrary to the simple cavity concept. "Single molecule probe" calculations were performed to explain the differences in base associations in H2O and CCl4. In CCl4 dispersion forces dominate and planar complexes are stabilized by maximum exposure of molecular planes to the solvent. In H2O electrostatic forces dominate so that the most stable structures are stacked association that allow the maximum number of hydrophilic centers to be exposed to the solvent.

Adenine↗
PubMed1984

Solution influence on biomolecular equilibria: nucleic acid base associations.

This paper consists of two parts. In the first part, the general problem of biomolecular equilibria in solution is considered, stressing that molecular interactions ultimately determine the answer to this problem. It is discussed how computer simulation techniques can reliably treat the problem and several pitfalls of computer simulation to be avoided are pointed out. Other approaches based on modeling and conceptual simplifications such as perturbative methods, long-range interaction approximations, surface thermodynamic approaches, and hydration shell models are discussed. In the second part, the results of Monte Carlo calculations on the associations of nucleic acid bases in water and carbon tetrachloride are presented. Stacked self-associations are found to be preferred in water and hydrogen-bonded complexes are favored in nonpolar solutions, in agreement with experimental data. The influence of the solvent on base associations is explained in terms of solute-solvent and solvent-solvent contributions to the total energy. No enthalpic stabilization of the complexes by the solvent was found. The results are used to examine the validity of various approximations discussed in the first part of the paper.

Base Composition↗
PubMed1980

Comparison of theoretical and experimental approaches to determination of conformation of nucleosides about the glycosidic bond.

A study has been made by means of 1H-NMR spectroscopy of the syn in equilibrium anti dynamic equilibrium about the glycosidic bond for 5'-deoxyadenosine and some 8-substituted analogues, in different solvents. The results are compared with those previously obtained for the parent adenosine and its 8-substituted analogues. Quantum chemical calculations, with the aid of the Classical Potential and PCILO procedures, were applied to obtain the energies for different conformations of the base in adenosine and 5'-deoxyadenosine, and their 8-methyl and 8-halogeno derivatives. Good agreement was found between experimentally determined conformations in solution and those corresponding theoretically to the energy minima, particularly those calculated by the PCILO method. Comparison of the quantitative experimental data with the theoretical results was used to evaluate the validity of the latter and their applicability to studies of nucleoside conformation. The experimental and theoretical findings pointed to the existence of a marked flexibility about the glycosidic bond of the parent nucleosides and their 8-substituted analogues, when the 8-substituents were not too bulky, such as methyl or bromine. Considerations is given to possible correlations between conformational parameters in nucleosides and their 5'-deoxy analogues. It is shown that the proposed stabilization of the conformation syn by intramolecular hydrogen bonding, 5'-OH...N(3), is not in accord with the results of the present study.

Adenosine↗
PubMed1978

Molecular orbital studies on the conformations of 8-amino- and 8-dimethylaminoadenosine 5'-monophosphate.

The quantum mechanical PCILO method has been applied for the determination of conformational properties of 8-amino- and 8-dimethylaminoadenosine 5'-monophosphate. Contrary to other 8-substituted nucleotides the amino derivative shows a preference for an anti arrangement about the glycosidic bond. This conformation is stabilized by an intramolecular hydrogen bond between the purine and the exocyclic group. 8-dimethylamino-adenosine-5'-monophosphate adopts the syn conformation with slightly rotated dimethylamino group. There is, however, a local minimum for the anti form associated with the unusual value of chiCN = 300 degrees. This minimum is probably populated when the nucleotide is bound to lactate dehydrogenase apoenzyme. No particularly strong interactions are necessary for the stabilization of the anti form. The computations account satisfactorily for the available experimental data.

Adenosine↗
PubMedDate not supplied

Revising regulatory networks: from expression data to linear causal models.

Discovering the complex regulatory networks that govern mRNA expression is an important but difficult problem. Many current approaches use only expression data from microarrays to infer the likely network structure. However, this ignores much existing knowledge because for a given organism and system under study, a biologist may already have a partial model of gene regulation. We propose a method for revising and improving these initial models, which may be incomplete or partially incorrect, with expression data. We demonstrate our approach by revising a model of photosynthesis regulation proposed by a biologist for Cyanobacteria. Applied to wild type expression data, our system suggested several modifications consistent with biological knowledge. Applied to a mutant strain, our system correctly modified the disabled gene. Power experiments with synthetic data that indicate that reliable revision is feasible even with a small number of samples.

Gene Expression Profiling↗