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PubMed1985

Conformationally defined adrenergic agents. 1. Design and synthesis of novel alpha 2 selective adrenergic agents: electrostatic repulsion based conformational prototypes.

A previous report of the adrenergic selectivity of 2- and 6-fluoronorepinephrine prompted us to formulate a hypothesis that accounted for this selectivity on the basis of a conformational preference induced by electrostatic repulsion between the aromatic fluorine atom and the side-chain hydroxyl group. A series of nitrogen-substituted catechol (aminomethyl)benzocyclobutenes, indanes, tetralins, and benzocycloheptenes were prepared, and when their radioligand binding affinities were determined, it was found that the overall pattern of binding affinity results supported the electrostatic repulsion hypothesis. The radioligand binding assay also revealed several highly alpha 2 selective adrenergic agents among these compounds, with the binding selectivity maximizing for compounds having nitrogen substituted with a group no larger than methyl and having a five-membered carbocyclic ring (i.e., 16, 17, and 19).

Adrenergic alpha-Agonists↗
PubMed1986

Conformational energy calculations and electrostatic potentials of dihydrofolate reductase ligands: relevance to mode of binding and species specificity.

Classical potential energy calculations are reported for a series of 11 structurally diverse substrates, products, and inhibitors of dihydrofolate reductase. In almost every case, the calculations reveal a range of potential biologically active conformations accessible to the molecule, and geometry optimization with molecular mechanics and molecular orbital calculations further expands the range of accessible conformations. The energy calculations are supplemented with electrostatic potential energy surfaces for the heterocyclic components of each molecule. These data are used in conjunction with the energy calculations and the crystallographically determined enzyme structures to compare two alternative proposed binding modes of folates known to bind with their pteridine rings inverted relative to that of methotrexate. It is shown that the conformational flexibility of the connecting chain between the benzoyl glutamate and pteridine moieties in the folates actually allows the pteridine ring to shift between these alternative binding modes, a combination of which may offer the best explanation for the observed activity. The electrostatic potentials and conformational energy data are also used in an attempt to account for the species specificity of inhibitors of mammalian, bacterial, and protozoal dihydrofolate reductases. The results show that while these techniques can be used to explain many of the observed results, others require recourse to the observed crystal structures to provide a satisfactory explanation.

Aminopterin↗
PubMed1979

Electrostatic potentials of deoxydinucleoside monophosphates. 1. Deoxydinucleoside monophosphates and actinomycin chromophore interactions.

We present electrostatic potential maps for the ten Watson-Crick base-pair combinations of dinucleoside monophosphates in a conformation appropriate for intercalation of drugs to occur. These maps reveal interesting differences among the base-pair combinations and suggest reasons for the base-pair specificities often observed upon intercalation. Simple electrostatic calculations on the intercalation energy of substituted actinomycin chromophores correlate qualitatively with the relative biological activity of these compounds, although the correlation with binding affinity is not as satisfactory.

Dactinomycin↗
PubMed2003

Effects of heterocyclic aromatic substituents on binding affinities at two distinct sites of somatostatin receptors. Correlation with the electrostatic potential of the substituents.

In our continuing program exploring glucose-based peptidomimetics of somatostatin (SRIF-14), we sought to improve the water solubility of our glycosides. This led to insights into the nature of the ligand binding sites at the SRIF receptor. Replacement of the C4 benzyl substituent in glucoside (+)-2 with pyridinylmethyl or pyrazin-2-ylmethyl congeners increased water solubility and enhanced affinity for the human SRIF subtype receptor 4 (sst4). We attribute this effect to hydrogen bond formation. The pyridin-3-ylmethyl substituent at C4, when combined with the imidazol-4-ylmethyl group at C2, generated (-)-19, which has the highest affinity of a glucose-based peptidomimetic at a human SRIF receptor to date (K(i) 53 +/- 23 nM, n = 6 at sst4). The C4 heterocyclic congeners of glucosides bearing a 1-methoxy substituent rather than an indole side chain at the anomeric carbon, such as (+)-16, also provided information about the Trp(8) binding pocket. We correlated the SARs at both the C4 and the Trp(8) binding pockets with calculations of the electrostatic potentials of the diverse C4 aromatic substituents using Spartan 3-21G(*) MO analysis. These calculations provide an approximate analysis of a molecule's ability to interact within a receptor binding site. Our binding studies show that benzene and indole rings, but not pyridinylmethyl nor pyrazin-2-ylmethyl rings, can bind the hydrophobic Trp(8) binding pocket of sst4. The Spartan 3-21G(*) MO analysis reveals significant negative electrostatic potential in the region of the pi-clouds for the benzene and indole rings but not for the pyridinylmethyl or pyrazin-2-ylmethyl congeners. Our data further demonstrate that the replacement of benzene or indole side chains by heterocyclic aromatic rings typified by pyridine and pyrazine not only enhances water solubility and hydrogen bonding capacity as expected, but can also profoundly diminish the ability of the pi-cloud of the aromatic substituent to interact with side chains of an aromatic binding pocket such as that for Trp(8) of SRIF-14. Conversely, these calculations accommodate the experimental findings that pyrazin-2-ylmethyl and pyridinylmethyl substituents at C4- of C1-indole-substituted glycosides afford higher affinities at sst4 than the C4-benzyl group of (+)-2. This result is consistent with the high electron density in the plane of the heterocycle depicted in Figure 6 which can accept hydrogen bonds from the C4 binding pocket of the receptor. Unexpectedly, we found that the 2-fluoropyridin-5-ylmethyl analogue (+)-14 more closely resembles the binding affinity of (+)-8 than that of (+)-2, thus suggesting that (+)-14 represents a rare example of a carbon linked fluorine atom acting as a hydrogen bond acceptor. We attribute this result to the ability of the proton to bind the nitrogen and fluorine atoms simultaneously in a bifurcated arrangement. At the NK1 receptor of substance P (SP), the free hydroxyl at C4 optimizes affinity.

Binding Sites↗
PubMed2004

Efficient evaluation of binding free energy using continuum electrostatics solvation.

The linear interaction energy (LIE) method is combined with energy minimization and finite-difference Poisson calculation of electrostatic solvation for the estimation of the absolute free energy of binding. A predictive accuracy of about 1.0 kcal/mol is obtained for 13 and 29 inhibitors of beta-secretase (BACE) and HIV-1 protease (HIV-1 PR), respectively. The multiplicative coefficients for the van der Waals and electrostatic terms are not transferable between BACE and HIV-1 PR although they are both aspartic proteases. The present approach is about 2 orders of magnitude faster than previous LIE methods and can be used for ranking large libraries of structurally diverse compounds docked by automatic computational tools.

Amyloid Precursor Protein Secretases↗
PubMed1996

Synthesis, ligand binding, and quantitative structure-activity relationship study of 3 beta-(4'-substituted phenyl)-2 beta-heterocyclic tropanes: evidence for an electrostatic interaction at the 2 beta-position.

A set of 3 beta-(4'-substituted phenyl)-2 beta-heterocyclic tropanes was designed, synthesized, and characterized. We discovered that these compounds can function as bioisosteric replacements for the corresponding WIN 35,065-2 analogs which possess a 2 beta-carbomethoxy group. Several of the compounds showed high affinity and selectivity for the dopamine transporter (DAT) relative to the serotonin and norepinephrine transporters. From the structure-activity relationship study, the 3 beta-(4'-chlorophenyl)-2 beta-(3'-phenylisoxazol-5-yl)tropane (5d) emerged as the most potent and selective compound. The binding data for 2 beta-heterocyclic tropanes were found to show a high correlation with molecular electrostatic potential (MEP) minima near one of the heteroatoms in the 2 beta-substituents. In contrast, low correlations were found for other MEP minima near the 2 beta-substituent as well as for calculated log P or substituent volume. These quantitative structure-activity relationship studies are consistent with an electrostatic contribution to the binding potency of these WIN 35,065-2 analogs at the DAT.

Animals↗
PubMed2001

An examination of hyperconjugative and electrostatic effects in the hydride reductions of 2-substituted-4-tert-butylcyclohexanones.

To better understand electronic effects on the diastereoselectivity of nucleophilic additions to the carbonyl group, a series of 2-X-4-tert-butylcyclohexanones (X = H, CH(3), OCH(3), F, Cl, Br) were reacted with LiAlH(4). Reduction of ketones with equatorial substituents yields increasing amounts of axial alcohol in the series for X [H < CH(3) < Br < Cl < F << OCH(3)]. These data cannot be explained by steric or chelation effects or by the theories of Felkin-Anh or Cieplak. Instead, an electrostatic argument is introduced: due to repulsion between the nucleophile and the X group, axial approach becomes energetically less favorable with an increase in the component of the dipole moment anti to the hydride approach trajectory. The ab initio calculated diastereoselectivities were close to the experimental values but did not reproduce the relative selectivity ordering among substituents. For reduction of ketones with axial substituents, increasing amounts of axial alcohol are seen in the series for X [Cl < Br < CH(3) < OCH(3) < H < F]. After some minor adjustments are made, this ordering is consistent with both the electrostatic model and Felkin-Anh theory. Cieplak theory cannot account for these data regardless of adjustments. Ab initio calculated diastereoselectivities were reasonably accurate for the nonpolar substituents but were poor for the polar substituents.

Journal Article↗
PubMed2001

Ion-dipole S(N)2 reaction in acetone-water mixtures. Electrostatic and specific solute-solvent interactions.

The rate constants of the S(N)2 reaction of sodium 4-nitrophenoxide (1) and iodomethane were determined by UV-visible spectrophotometry in acetone-water mixtures at 25, 30, and 35 degrees C. The rate-Xwater (mole fraction of water) profile shows that the reaction depends strongly on the medium. The fastest rate constant was obtained in pure acetone, and a minimum occurred at Xwater= 0.4, whereas the observed second-order rate constants increases again in the water-rich region. In pure acetone, in the presence of dicyclohexano-[18]-crown-6, increases linearly with the concentration of the crown ether as a result of the complexation of the sodium ion (KS = 104.8 M) of the ion-pair and the increase in the effective concentration of free 4-nitrophenoxide ion, which was assumed to be the only reactive species. Ion-pairing was also detected at Xwater= 0.65 with a dissociation constant Kd = 7.82 x 10(-4) M(-1). The solvatochromic behaviors of 2,6-diphenyl-4-(2,4,6-triphenyl-1-pyridinio)-1-phenoxide (2), 4-[(1-methyl-4(1H)-pyridinylidene)ethylidene]-2,5-cyclohexadien-1-one (3), and 1-methyl-8-oxy-quinolinium betaine (4) were investigated in the entire range of acetone-water mixtures. The dyes presented an increasing order of hydrophilicity compatible with their chemical structure, i.e., 2 < 3 < 4. Kinetic parameters for the methylation of 1 and the ET values of the dyes show a linear correlation of the polarity in the region of Xwater = 1.0-0.40 for 3 and 4, and it was observed that the more hydrophilic the dye the better the correlation coefficient, because of the structural similarity with 1. The activation parameter-Xwater profile shows extrema at Xwater < 0.4, reflecting an important change in the structure of the solvent that is responsible for the changes in the solvation of the reactive species including ion-pairs. These results suggest that the addition of water to acetone reduces abruptly the rate of substitution due to the preferential solvation (PS) of the phenoxide ion by the hydrogen-bonding donor (HBD) solvent. Nevertheless, the real second-order rate constant is "masked" by the association involving Na+ and 4-nitrophenoxide that extends even to water-rich mixtures. A model, based on the assumption that the free-energy terms involved in the second-order rate constant and the dissociation constant of the ion-pair have two components, is invoked to explain the kinetic data. One of the components depends on electrostatic interactions for which the main variable is the dielectric constant of the solvent mixture, and the other depends on the specific solute-solvent interactions, expressed by the activity coefficients of transfer of the species involved. The model indicates that in the range of Xwater = 1.0-0.40 the interactions are exclusively electrostatic, while for the rest of the acetone-rich region they are specific with a large contribution of the 4-nitrophenoxide ion.

Journal Article↗
PubMed2005

Electrostatic surface charge at aqueous/alpha-Al2O3 single-crystal interfaces as probed by optical second-harmonic generation.

Second harmonic generation (SHG) spectroscopy was used to characterize the pH-dependent electrostatic charging behavior of (0001) and (102) crystallographic surfaces of corundum (alpha-Al2O3) single-crystal substrates. The pH value of the point of zero charge (pH(pzc)) for each surface was determined by monitoring the SH response during three consecutive pH titrations conducted with 1, 10, and 100 mM NaNO3 carbonate-free aqueous solutions. The crossing point of the three titration curves, which corresponds to the pH(pzc), occurs at pH 4.1 +/- 0.4 for the (0001) surface and pH 5.2 +/- 0.4 for the (102) surface. SHG measurements that were recorded as a function of NaNO3 concentration at fixed pH values were found to corroborate the pH(pzc) values identified in the pH titrations. A comparison of the SHG results with surface protonation constants calculated using a simple electrostatic model suggests that surface relaxation and bonding changes resulting from surface hydration do not account for differences between experimental observations and model predictions. The measured pH(pzc) values for the alpha-Al2O3 single-crystal surfaces are significantly more acidic than published values for Al-(hydr)oxide particles which typically range from pH 8 to 10. This discrepancy suggests that the charging behavior of Al-(hydr)oxide particles is determined by surface sites associated with defects assuming that differences in surface acidity reflect differences in the coordination environment and local structure of the potential-determining surface groups.

Journal Article↗
PubMed2005

Limitations of the molecular multipole expansion treatment of electrostatic interactions for C-H...O and O-H...O hydrogen bonds and application of a general charge density approach.

A molecular multipole expansion treatment (up to hexadecapole) is examined for its accuracy in describing hydrogen-bond electrostatic interactions, with particular reference to explaining the differences between blue-shifted C-H...O and red-shifted O-H...O bonds. In interactions of H2O and CH4 with point charges at hydrogen-bonding distances, we find that the molecular multipole treatment not only fails to reproduce ab initio energies but also forces on OH or CH bonds, and therefore cannot properly account for the electrostatic component of the interaction. A treatment based on a molecule's permanent charge density and its derivatives and the charge density and its derivatives induced by an external multipole distribution is in full accord with ab initio results, as shown by application to models of the H2O-H2O and CH4-FH systems. Such a charge density approach provides a fundamental basis for understanding the importance of interaction forces in initiating structural change and thereby altering molecular properties.

Journal Article↗
PubMed2005

Electrostatic patterning of a silica surface: a new model for charge build-up on a dielectric solid.

The polarization of interdigitated gold electrodes mounted over a silica thin film formed by oxidation of a Si wafer produces reproducible electrostatic patterns with overall excess negative charge, as observed by scanning electric potential microscopy. Domain charge concentrations as high as 76 charge units per square micrometer are obtained when a 5 V difference is applied to the electrodes thus producing fields in the 10(6) V m(-1) range. These patterns vanish when the electrodes are short-circuited and grounded. Characteristic times for pattern formation and relaxation are in the order of 10 min. The results are consistent with a model based on the discharge of H(+) ions at the negative electrodes, leaving behind immobile surface-bound SiO(-) groups and thus showing that chemisorption phenomena are decisive for electrostatic charging of insulators.

Journal Article↗
PubMed2005

Collective solvent coordinates for the infrared spectrum of HOD in D2O based on an ab initio electrostatic map.

An ab initio MP2 vibrational Hamiltonian of HOD in an external electrostatic potential parametrized by the electric field and its gradient-tensor is constructed. By combining it with the fluctuating electric field induced by the D(2)O solvent obtained from molecular dynamics simulations, we calculate the infrared absorption of the O-H stretch. The resulting solvent shift and infrared line shape for three force fields (TIP4P, SPC/E, and SW) are in good agreement with the experiment. A collective coordinate response for the solvent effect is constructed by identifying the main electrostatic field and gradient components contributing to the line shape. This allows a realistic stochastic Liouville equation simulation of the line shapes which is not restricted to Gaussian frequency fluctuations.

Computer Simulation↗
PubMed2005

Amide I vibrational dynamics of N-methylacetamide in polar solvents: the role of electrostatic interactions.

The vibrational frequency of the amide I transition of peptides is known to be sensitive to the strength of its hydrogen bonding interactions. In an effort to account for interactions with hydrogen bonding solvents in terms of electrostatics, we study the vibrational dynamics of the amide I coordinate of N-methylacetamide in prototypical polar solvents: D2O, CDCl3, and DMSO-d6. These three solvents have varying hydrogen bonding strengths, and provide three distinct solvent environments for the amide group. The frequency-frequency correlation function, the orientational correlation function, and the vibrational relaxation rate of the amide I vibration in each solvent are retrieved by using three-pulse vibrational photon echoes, two-dimensional infrared spectroscopy, and pump-probe spectroscopy. Direct comparisons are made to molecular dynamics simulations. We find good quantitative agreement between the experimentally retrieved and simulated correlation functions over all time scales when the solute-solvent interactions are determined from the electrostatic potential between the solvent and the atomic sites of the amide group.

Amides↗
PubMed2005

Structure of mixed anionic/nonionic surfactant micelles: experimental observations relating to the role of headgroup electrostatic and steric effects and the effects of added electrolyte.

The structures of the mixed anionic/nonionic surfactant micelles of SDS/C12E6 and SDS/C12E8 have been measured by small angle neutron scattering (SANS). The variations in the micelle aggregation number and surface charge with composition, measured in D2O and in dilute electrolyte, 0.01 and 0.05 M NaCl, provide data on the relative roles of the surfactant headgroup steric and electrostatic interactions and their contributions to the free energy of micellization. For the SDS/C12E8 mixture, solutions increasingly rich in C12E8 show a modest micellar growth and an increase in the surface charge. The changes with increasing electrolyte concentration are similarly modest. In contrast, for the SDS/C12E6 mixture, solutions rich in C12E6 show a more significant increase in aggregation number. Furthermore, electrolyte has a more substantial effect on the aggregation for the nonionic (C12E6) rich mixtures. The experimental results are discussed in the context of estimates of the steric and electrostatic contributions to the free energy of micellization, calculated from the molecular thermodynamic approach. The variation in micelle surface charge is discussed in the context of the "dressed micelle" theory for micelle ionization, and other related data.

Journal Article↗
PubMed2005

Role of electrostatic interactions for the domain shapes of Langmuir monolayers of monoglycerol amphiphiles.

The role of electrostatic interaction in the domain morphology of amide, ether, ester, and amine monoglycerol monolayers (abbreviated as ADD, ETD, ESD, and AMD, respectively) with systematic variation in the molecular structure of the headgroup region is investigated. Experimental studies using Brewster angle microscopy (BAM) and grazing incidence X-ray diffraction (GIXD) show that the characteristic features of the condensed monolayer phase, such as domain morphology, crystallinity, and lattice parameters, are very different for these monoglycerols. Therefore, the intermolecular interactions of the four amphiphilic monoglycerols are investigated in detail. First, the dipole moments of four monoglycerols of similar structure but with different functional groups are calculated by a semiempirical quantum mechanical technique. The dipole moments for monoglycerols follow the sequence AMD < ETD < ESD < ADD for the population of conformers of compounds investigated. The dipolar repulsion energies for the amphiphilic monoglycerols are also calculated for different possible mutual orientations between the dipoles. The calculated dipolar energies also follow the same trend for different possible headgroup orientations. These results can explain the domain shape of the monoglycerols observed experimentally. Second, ab initio calculations on the basis of the HF/6-31G** method are performed for representative monoglycerol headgroup segments. The results show that the intermolecular interaction energy related to dimer formation follows the order ETD < ESD < AMD < ADD segments, similar to that observed in experiment except in the case of the AMD segment. The relative importance of intra- and intermolecular hydrogen bonding in dimers is analyzed. The enhanced role of the intermolecular interaction relative to intramolecular interaction in the case of AMD contributes to the relatively high intermolecular interaction energy for the particular conformation of the dimer of AMD segment as observed from ab initio calculation. The present work shows that the variations in headgroup molecular structure alter drastically the domain shape, and the theoretical calculations conclusively reveal the important role of the electrostatic interactions for the mesoscopic domain architecture.

Journal Article↗
PubMed2005

Electrostatic DFT map for the complete vibrational amide band of NMA.

An anharmonic vibrational Hamiltonian for the amide I, II, III, and A modes of N-methyl acetamide (NMA), recast in terms of the 19 components of an external electric field and its first and second derivative tensors (electrostatic DFT map), is calculated at the DFT(BPW91/6-31G(d,p)) level. Strong correlations are found between NMA geometry and the amide frequency fluctuations calculated using this Hamiltonian together with the fluctuating solvent electric field obtained from the MD simulations in TIP3 water. The amide I and A frequencies are strongly positively correlated with the C=O and N-H bond lengths. The C=O and C-N amide bond lengths are negatively correlated, suggesting the solvent-induced fluctuations of the contribution of zwitterionic resonance form. Sampling the global electric field in the entire region of the transition charge densities (TCDs) is required for accurate infrared line shape simulations. Collective electrostatic solvent coordinates which represent the fluctuations of the 10 lowest amide fundamental and overtone states are reported. Normal-mode analysis of an NMA-3H(2)O cluster shows that the 660 cm(-1) to 1100 cm(-1) oscillation found in the frequency autocorrelation functions of the amide modes may be ascribed to the two bending vibrations of intermolecular hydrogen bonds with the amide oxygen of NMA.

Amides↗
PubMed2005

The interplay of hydrophobic and electrostatic effects in the surfactant-induced aggregation/deaggregation of chlorin p6.

The aggregation/deaggregation of chlorin p6 with the surfactants CTAB, SDS, and TX 100 have been studied by using absorption, fluorescence, and light scattering techniques. The ionic surfactants are found to cause aggregation of fluorophore at submicellar concentrations. The aggregates dissolve at higher surfactant concentrations to yield micellized monomers. This is rationalized by the interplay of electrostatic and hydrophobic effects. A prominent pH effect is observed in the ionic surfactant induced aggregation process as the charge on the fluorophore is controlled by the pH of the medium. Interestingly, the neutral TX-100 also induces aggregation of chlorin p6 at low concentrations, indicating that hydrophobic effects by themselves can cause aggregation unless there is a hindrance by repulsive electrostatic effects.

Journal Article↗
PubMed2005

Nature of the Lewis acid sites on molybdenum and ruthenium sulfides: an electrostatic potential study.

The energy of formation and the Lewis acid strength of sulfur vacancies or coordinative unsaturated sites on the MoS2 edges were studied using density functional theory for periodic systems and an electrostatic potential-based methodology. The results suggest that the more energetically favorable sites are located on the sulfur edges; however, their Lewis acid strength is considerably smaller than the site acidity at the molybdenum edges. The acid strength for the reported most hydrodesulfurization active site of RuS2 was also determined. In general, the Lewis acid for the site on RuS2 is 100% smaller than the sites on the Mo edges and around 20% larger than the most favorable site on the S edges of MoS2. Binding of the pyridine molecule in the eta1 adsorption configuration on the considered sites has corroborated the trend of Lewis acidity suggested by the electrostatic potential methodology.

Journal Article↗