Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “electrostatics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,639 records · Page 91Linked to original sources
PubMed2001

Correlation between molecular structure and helicity of induced chiral nematics in terms of short-range and electrostatic-induction interactions. The case of chiral biphenyls.

The helical structure of the chiral nematic phases induced by chiral dopants in nematic solvents provides a macroscopic image of the molecular chirality of the dopant promoted by the orientational order. Chiral biphenyls are challenging systems because their twisting ability shows a strong dependence on the molecular structure, which does not conform to empirical correlation rules. This points out the need for adequate interpretative tools, able to establish a link between molecular properties and macroscopic response. In this paper the twisting ability of chiral biphenyls is reviewed, by reporting examples taken from the literature together with some new experimental results. The microscopic origin of the observed behavior is explained in terms of chirality and anisotropy of short-range and electrostatic-induction interactions. These are described, respectively, by a shape model and a reaction field method, having the common characteristics of a realistic representation of the structure and properties of the chiral dopants in terms of molecular surface, atom charges, and distributed polarizabilities.

Journal Article↗
PubMed2002

A structural model for the high-valent intermediate Q of methane monooxygenase from broken-symmetry density functional and electrostatics calculations.

A combined broken-symmetry density functional and electrostatics approach has been used to construct a model for the high-valent diiron intermediate Q of methane monooxygenase. The presence of high-spin or intermediate spin iron centers gives rise to two structurally distinct spin-coupled states of the cluster for which calculated geometries, net spin populations, Heisenberg J values, Mössbauer isomer shifts, and quadrupole splittings are compared and contrasted with the available spectroscopic data.

Binding Sites↗
PubMed2002

Thermodynamics of cationic lipid binding to DNA and DNA condensation: roles of electrostatics and hydrophobicity.

Alkylammonium binding to DNA was studied by isothermal titration calorimetry. Experimental data, obtained as functions of alkyl chain length, salt concentration, DNA concentration, and temperature, provided a detailed thermodynamic description of lipid-DNA binding reactions leading to DNA condensation. Lipid binding, counterion displacement, and DNA condensation were highly cooperative processes, driven by a large increase in entropy and opposed by a relatively small endothermic enthalpy at room temperature. Large negative heat capacity change indicated a contribution from hydrophobic interactions between aliphatic tails. An approximation of lipid-DNA binding as dominated by two factors-ionic and hydrophobic interactions-yielded a model that was consistent with experimental data. Chemical group contributions to the energetics of binding were determined and could be used to predict energetics of other lipid binding to DNA. Electrostatic and hydrophobic contributions to Gibbs free energy, enthalpy, entropy, and heat capacity could be distinguished by applying additivity principles. Binding of lipids with two, three, and four aliphatic tails was investigated and compared to single-tailed lipid binding. Structurally, the model suggests that lipid cationic headgroups and aliphatic tails distribute evenly and lay down on DNA surface without the formation of micelles.

Calorimetry↗
PubMed2002

A molecular electrostatic potential bond critical point model for atomic and group electronegativities.

A consistent set of atomic electronegativities of main block and d-block transition elements has been obtained from the position and value of the molecular electrostatic potential bond critical point of the C-E bond of a methyl-element-hydride system, H(3)C-EH(n) (E is an element and n = 0, 1, 2, 3, 4, and 5 depending on the position of E in the periodic table). The new scale shows very good agreement with the popular electronegativity scales such as Pauling, Allen, Allred-Rochow, Mulliken, and Sanderson scales of electronegativity, especially for the main block elements. The present scale of electronegativity for transition elements is expected to be more accurate than the previously derived values because of a more consistent approach. Further, the same approach has led to the evaluation of group electronegativities when the hydrogens of E are replaced by other substituent groups. These group electronegativity values are found to correlate well with Inamoto and Mullay scales.

Journal Article↗
PubMed2002

An electrostatic model for the frequency shifts in the carbonmonoxy stretching band of myoglobin: correlation of hydrogen bonding and the stark tuning rate.

The effect of internal and applied external electric fields on the vibrational stretching frequency for bound CO (nu(CO)) in myoglobin mutants was studied using density functional theory. Geometry optimization and frequency calculations were carried out for an imidazole-iron-porphine-carbonmonoxy adduct with various small molecule hydrogen-bonding groups. Over 70 vibrational frequency calculations of different model geometries and hydrogen-bonding groups were compared to derive overall trends in the C-O stretching frequency (nu(CO)) in terms of the C-O bond length and Mulliken charge. Simple linear functions were derived to predict the Stark tuning rate using an approach analogous to the vibronic theory of activation.(1) Potential energy calculations show that the strongest interaction occurs for C-H or N-H hydrogen bonding nearly perpendicular to the Fe-C-O bond axis. The calculated frequencies are compared to the structural data available from 18 myoglobin crystal structures, supporting the hypothesis that the vast majority of hydrogen-bonding interactions with CO occur from the side, rather than the end, of the bound CO ligand. The nu(CO) frequency shifts agree well with experimental frequency shifts for multiple bands, known as A states, and site-directed mutations in the distal pocket of myoglobin. The model calculations quantitatively explain electrostatic effects in terms of specific hydrogen-bonding interactions with bound CO in heme proteins.

Carbon Monoxide↗
PubMed2002

Electrostatic properties of membrane lipids coupled to metarhodopsin II formation in visual transduction.

Changes in lipid composition have recently been shown to exert appreciable influences on the activities of membrane-bound proteins and peptides. We tested the hypothesis that the conformational states of rhodopsin linked to visual signal transduction are related to biophysical properties of the membrane lipid bilayer. For bovine rhodopsin, the meta I-meta II conformational transition was studied in egg phosphatidylcholine (PC) recombinants versus the native rod outer segment (ROS) membranes by means of flash photolysis. Formation of metarhodopsin II was observed by the change in absorbance at 478 nm after a single actinic flash was delivered to the sample. The meta I/meta II ratio was investigated as a function of both temperature and pH. The data clearly demonstrated thermodynamic reversibility of the transition for both the egg PC recombinants and the native ROS membranes. A significant shift of the apparent pK(a) for the acid-base equilibrium to lower values was evident in the egg PC recombinant, with little meta II produced under physiological conditions. Calculations of the membrane surface pH using a Poisson-Boltzmann model suggested the free energies of the meta I and meta II states were significantly affected by electrostatic properties of the bilayer lipids. In the ROS membranes, phosphatidylserine (PS) is needed for full formation of meta II, in combination with phosphatidylethanolamine (PE) and polyunsaturated docosahexaenoic acid (DHA; 22:6omega3) chains. We propose that the PS surface potential leads to an accumulation of hydronium ions, H(3)O(+), in the electrical double layer, which drive the reaction together with the large negative spontaneous curvature (H(0)) conferred by PE plus DHA chains. The elastic stress/strain of the bilayer arises from an interplay of the approximately zero H(0) from PS and the negative H(0) due to the PE headgroups and polyunsaturated chains. The lipid influences are further explained in terms of matching of the bilayer spontaneous curvature to the curvature at the lipid/rhodopsin interface, as formulated by the Helfrich bending energy. These new findings guide current ideas as to how bilayer properties govern the conformational energetics of integral membrane proteins. Moreover, they yield knowledge of how membrane lipid-protein interactions involving acidic phospholipids such as PS and neutral polyunsaturated DHA chains are implicated in key biological functions such as vision.

Animals↗
PubMed2002

Polyferrocenylsilane microspheres: synthesis, mechanism of formation, size and charge tunability, electrostatic self-assembly, and pyrolysis to spherical magnetic ceramic particles.

Pt(0)-catalyzed ring-opening precipitation copolymerization of [1]silaferrocenophanes fcSiMe(2) (3) and the spirocyclic cross-linker fcSi(CH(2))(3) (4) (fc = Fe(eta(5)-C(5)H(4))(2)) was used to prepare polyferrocenylsilane microspheres (PFSMSs) under mild conditions. By varying the reaction conditions, a wide variety of other morphologies was obtained. The effects of temperature, monomer ratio, solvent composition, catalyst concentration, and time on the observed morphology were investigated and interpreted in terms of a mechanism for microsphere formation. The most well-defined particles were formed using equimolar amounts of 3 and 4, in a 50:50 mixture of xylenes and decane at 60 degrees C with gentle agitation. Chemical oxidation of the polymeric microspheres led to positively charged particles (OPFSMSs) which underwent electrostatically driven self-assembly with negatively charged silica microspheres to form core-corona composite particles. Redox titration with controlled amounts of the one-electron oxidant [N(C(6)H(4)Br-p)(3)][PF(6)] in acetonitrile led to the oxidation of the outer 0.15 microm (ca. 32%) of the PFSMSs. The resulting OPFSMSs were reduced back to their neutral form by reaction with hydrazine in methanol. Pyrolysis of the PFSMSs led to spherical magnetic ceramic replicas with tunable magnetic properties that organize into ordered 2-D arrays at the air-water interface under the influence of a magnetic field.

Journal Article↗
PubMed2003

A sphere-based model for the electrostatics of globular proteins.

We propose a model for the electrostatics of globular proteins in which the low dielectric region is replaced by concentric spheres of the appropriate size. The method uses analytical formulas for the dielectric sphere and allows an efficient and accurate treatment of bulk charges. For surface charges, we propose a numerical determination of the sphere radius based on the solvent exposure of the individual atoms. The present implementation of the sphere model yields a good approximation of finite-difference Poisson solvation and interaction energies for a test set of 12 proteins.

Models, Chemical↗
PubMed2003

Self-assembly combining two bioactive peptide-amphiphile molecules into nanofibers by electrostatic attraction.

We describe a new approach to peptide-amphiphile (PA) nanofiber preparation that allows PAs with different bioactive amino acid sequences to be combined into a single fiber. Oppositely charged PAs are synthesized separately and then mixed to produce gels of nanofiber networks at physiological pH. Transmission electron microscopy reveals the formation of fibers approximately 7 nm in diameter and several micrometers long in these dimeric systems. On the basis of NMR and microscopy, we suggest that these nanofibers are cylindrical micelles of mixed composition, formed due to electrostatic attraction between the oppositely charged PAs. This strategy for self-assembly may be useful in cell therapies that can be implemented without invasive surgery or in in vitro tissue engineering.

Amino Acid Sequence↗
PubMed2003

Stereochemistry of nucleophilic substitution reactions depending upon substituent: evidence for electrostatic stabilization of pseudoaxial conformers of oxocarbenium ions by heteroatom substituents.

Lewis acid-mediated nucleophilic substitution reactions of substituted tetrahydropyran acetates reveal that the conformational preferences of six-membered-ring cations depend significantly upon the electronic nature of the substituent. Nucleophilic substitutions of C-3 and C-4 alkyl-substituted tetrahydropyran acetates proceeded via pseudoequatorially substituted oxocarbenium ions, as would be expected by consideration of steric effects. Substitutions of C-3 and C-4 alkoxy-substituted tetrahydropyran acetates, however, proceeded via pseudoaxially oriented oxocarbenium ions. The unusual selectivities controlled by the alkoxy groups were demonstrated for a range of other heteroatom substituents, including nitrogen, fluorine, chlorine, and bromine. It is believed that the pseudoaxial conformation is preferred in the ground state of the cation because of an electrostatic attraction between the cationic carbon center of the oxocarbenium ion and the heteroatom substituent. This analysis is supported by the observation that selectivity diminishes down the halogen series, which is inconsistent with electron donation as might be expected during anchimeric assistance. The C-2 heteroatom-substituted systems gave moderately high 1,2-cis selectivity, while small alkyl substituents showed no selectivity. Only in the case of the tert-butyl group at C-2 was high 1,2-trans selectivity observed. These studies reinforce the idea that ground-state conformational effects need to be considered along with steric approach considerations.

Cations↗
PubMed2004

OMP decarboxylase: an experimental test of electrostatic destabilization of the enzyme-substrate complex.

6-Methylaminouridine 5'-phosphate (MAUMP) inhibits OMP decarboxylase (Ki = 3 x 10-6 M) maximally at pH values where its amino group is uncharged. Comparison of the chemical shift of free [7-13C]-MAUMP in solutions of varying pH, with that of the enzyme-bound species confirms that this inhibitor is bound with its amino group uncharged. This enzyme's apparent lack of affinity for a cationic substituent, located near the position that would ordinarily be occupied by the scissile carboxylate group of the substrate, does not appear to support the view that the E-S complex is destabilized by electrostatic repulsion in the ground state.

Enzyme Stability↗
PubMed2004

Electrostatic interactions dominate the catalytic contribution of arg39 in 4-oxalocrotonate tautomerase.

The synthesis and kinetic parameters of a comprehensive set of 4-OT analogues with arginine (X = NH2+) to citrulline (X = O) substitutions at positions 11, 39, and 61 are reported. These data suggest that the main contribution of Arg39' ' to catalysis is by electrostatic stabilization of the anionic transition state leading to intermediate 2, and not by hydrogen bonding.

Amino Acid Substitution↗
PubMed2005

Dynamic and electrostatic effects in enzymatic processes. An analysis of the nucleophilic substitution reaction in haloalkane dehalogenase.

We present an analysis of rare event trajectories for the nucleophilic displacement of a chloride anion of 1,2-dichloroethane by a carboxylate group in haloalkane dehalogenase from Xanthobacterautotrophicus (DhlA) and in aqueous solution. Differences in the transmission coefficient are rationalized on the basis of the electrostatic coupling between the chemical system and the environment. Detailed analysis of the reactive trajectories reveals that the evolution of the hydrogen bond interactions established between the substrate and the environment present significant differences in aqueous solution and in the enzyme. The structure of the enzymatic active site provides a more adequate interaction pattern for the reaction progress.

Chlorides↗
PubMed2004

Key role of electrostatic interactions in bacteriorhodopsin proton transfer.

The first proton transport step following photon absorption in bacteriorhodopsin is from the 13-cis retinal Schiff base to Asp85. Configurational and energetic determinants of this step are investigated here by performing quantum mechanical/molecular mechanical minimum-energy reaction-path calculations. The results suggest that retinal can pump protons when in the 13-cis, 15-anti conformation but not when 13-cis, 15-syn. Decomposition of the proton transfer energy profiles for various possible pathways reveals a conflict between the effect of the intrinsic proton affinities of the Schiff base and Asp85, which favors the neutral, product state (i.e., with Asp85 protonated), with the mainly electrostatic interaction between the protein environment with the reacting partners, which favors the ion pair reactant state (i.e., with retinal protonated). The rate-limiting proton-transfer barrier depends both on the relative orientations of the proton donor and acceptor groups and on the pathway followed by the proton; depending on these factors, the barrier may arise from breaking and forming of hydrogen bonds involving the Schiff base, Asp85, Asp212, and water w402, and from nonbonded interactions involving protein groups that respond to the charge rearrangements in the Schiff base region.

Bacteriorhodopsins↗
PubMed2004

Hydrogen-bonding-induced shifts of the excitation energies in nucleic acid bases: an interplay between electrostatic and electron density overlap effects.

The theoretically calculated dimerization-induced shifts of the lowest excitation energies in two model systems, adenine-thymine and guanine-cytosine base pairs, are analyzed. The applied formalism is based on first principles and allows one to study the influence of the microscopic environment of a given molecule on its ground- [Wesolowski, T. A.; Warshel, A. J. Phys. Chem. 1993, 97, 8050] and excited-state [Casida, M. E.; Wesolowski, T. A. Int. J. Quantum Chem. 2004, 96, 577] properties. The assessment of the relative importance of such effects as (a) Coulomb interactions, (b) orbital interactions, (c) electronic polarization of the environment, and (d) electron density overlap effects is straightforward in this formalism. In the applied formalism, electron density overlap effects can be further decomposed into the exchange-correlation component which provides a small attractive contribution and the repulsive kinetic energy-dependent component. It is shown that the shifts can be attributed to the electrostatic interactions and the repulsive overlap-dependent term in the embedding potential. The electronic polarization of the environment plays a significant role (up to 30% of the total shift) only in transitions involving the orbitals localized on hydrogen bond donor groups. For all analyzed shifts, the contribution of the intermolecular orbital interactions is negligible. The analysis of this work provides strong evidence supporting the use of the widely applied embedding-molecule strategy in computational studies of chromophores in a condensed phase even in such cases where only one end of the hydrogen bond is included in the quantum mechanical part.

Adenine↗
PubMed2005

Electrostatic control of aromatic stacking interactions.

A supramolecular approach has been used to investigate the free energies of intermolecular aromatic stacking interactions. Chemical double mutant cycles have been used to measure the effect of a range of substituents on face-to-face stacking interactions with phenyl and pentafluorophenyl rings. Electrostatic effects dominate the trends in interaction energy.

DNA↗
PubMed2005

Electrostatic versus steric effects in peptidomimicry: synthesis and secondary structure analysis of gramicidin S analogues with (E)-alkene peptide isosteres.

A concise synthetic strategy was used for the first preparation of GS analogues with trisubstituted (E)-alkene peptide bond replacements. Solution and solid state conformational analysis demonstrated that the bistrifluoromethylated analogue was a superior mimic of the natural product, whereas the incorporation of methyl groups into the alkene peptide isostere led to a far greater perturbation of the secondary structure features of GS. The difference between CF3- and CH3-substitution can be explained by the superior electrostatic carbonyl group mimicry of the former function.

Alkenes↗