The Coulomb Hole of the Ne Atom

We analyze the Coulomb hole of Ne from highly-accurate CISD wave functions obtained from optimized even-tempered basis sets. Using a two-fold extrapolation procedure we obtain highly accurate results that recover 97 % of the correlation energy. We confirm the existence of a shoulder in the short-range region of the Coulomb hole of the Ne atom, which is due to an internal reorganization of the K-shell caused by electron correlation of the core electrons. The feature is very sensitive to the quality of the basis set in the core region and it is not exclusive to Ne, being also present in most of second-row atoms, thus confirming that it is due to K-shell correlation effects.     

Comparative performance of extraction strategies for polycyclic aromatic hydrocarbons in peats

The assessment of historical trends in atmospheric deposition of organic contaminants by using peat samples has been reported on several occasions because these samples represent an almost ideal medium for recording temporal changes in organic contaminant deposition rates. The determination of polycyclic aromatic hydrocarbons (PAHs) in peat samples is complicated due to the high content of organic matter in peat, which affects both extraction efficiency and analytical quality. A rapid and simple method is proposed for the determination of 10 US Environmental Protection Agency indicator PAHs in complex matrices such as peat. This article reviews and addresses the most relevant analytical methods for determining PAHs in peat. We discuss and critically evaluate three different extraction procedures, such as ultrasound-assisted solvent extraction (UASE), shaking and pressurized liquid extraction (PLE). Clean-up of extracts was performed by solid-phase extraction using silica cartridges. Detection of the selected PAHs was carried out by high-performance liquid chromatography coupled with fluorescence detection for determination. Optimization of the variables affecting extraction by the selected extraction techniques was conducted, concluding that the UASE extraction method using hexane:dichloromethane (80:20) as extractant was robust enough to determine the selected PAHs in peat samples with estimated quantification limits between 0.050 and 3.5 μg/kg depending on the PAH. UASE did not demand sophisticated equipment and long extraction times. PLE involved sophisticated equipment and showed important variations in the results. The method proposed was applied to the determination of PAHs in peat samples from Xistral Mountains (Galicia, Spain).     

Resonance structures of the amide bond: the advantages of planarity

Delocalization indexes based on magnitudes derived from electron-pair densities are demonstrated to be useful indicators of electron resonance in amides. These indexes, based on the integration of the two-electron density matrix over the atomic basins defined through the zero-flux condition, have been calculated for a series of amides at the B3LYP/6-31+G* level of theory. These quantities, which can be viewed as a measure of the sharing of electrons between atoms, behave in concordance with the traditional resonance model, even though they are integrated in Bader atomic basins. Thus, the use of these quantities overcomes contradictory results from analyses of atomic charges, yet keeps the theoretical appeal of using nonarbitrary atomic partitions and unambiguously defined functions such as densities and pair densities. Moreover, for a large data set consisting of 24 amides plus their corresponding rotational transition states, a linear relation was found between the rotational barrier for the amide and the delocalization index between the nitrogen and oxygen atoms, indicating that this parameter can be used as an ideal physical-chemical indicator of the electron resonance in amides.     

The small anisotropy formulation of elastic deformation

The specific internal energy defines the constitutive relation (stress-strain function) in elastic deformations. We introduce a form for the specific internal energy that expresses the idea of small anisotropy. In this formulation, only one parameter is needed to specify the anisotropic part of the deformation.Supported in part by AFOSR-88-0025.     

Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus

 This paper reports a new AM1/d model for phosphorus that can be used to model nucleophilic attack of phosphates relevant for biological phosphate hydrolysis reactions. The parameters were derived from a quantum dataset calculated with hybrid density-functional theory [B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p)] of phosphates and phosphoranes in various charge states, and on transitions states for nucleophilic attacks. A suite of non-linear optimization methods is outlined for semiempirical parameter development based on integrated evolutionary (genetic), Monte Carlo simulated annealing and direction set minimization algorithms. The performance of the new AM1/d model and the standard AM1 and MNDO/d models are compared with the density-functional results. The results demonstrate that the strategy of developing semiempirical parameters specific for biological reactions offers considerable promise for application to large-scale biological problems. Received: 15 January 2002 / Accepted: 6 September 2002 / Published online: 28 March 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: D.M. York e-mail: york@chem.umn.edu Acknowledgements. D.M.Y. is grateful for financial support provided by the National Institutes of Health (grant 1R01-GM62248-01A1) and the Donors of The Petroleum Research Fund, administered by the American Chemical Society, and the Minnesota Supercomputing Institute through a 6-month research scholar award (X.L.). Computational resources were provided by the Minnesota Supercomputing Institute.     

A symmetry-breaking problem in the annulus

We study questions of degeneracy and bifurcation for radial solutions of the semilinear elliptic equation ?u(x) + f(u(x)) = 0, x isin; [math001], [math001]an annulus in Rⁿ, with homogeneous Dirichlet boundary conditions. For certain nonlinearities f(u), we prove existence of degenerate radial solutions u (for which the kernel of the linearized operator Lz = ?z + [math001](u)z, z isin; C²We study questions of degeneracy and bifurcation for radial solutions of the semilinear elliptic equation ?u(x) + f(u(x)) = 0, x isin; [math001], [math001]an annulus in Rⁿ, with homogeneous Dirichlet boundary conditions. For certain nonlinearities f(u), we prove existence of degenerate radial solutions u (for which the kernel of the linearized operator Lz = ?z + [math001](u)z, z isin; C²$⁰([math001]), is non-trivial) and existence of nonradial solutions for the semi-linear equation. These nonradial (asymmetric) solutions are obtained via a bifurcation procedure from the radial (symmetric) ones. This phenomena is called symmetry-breaking. The bifurcation results are proved by a Conley index argument     

On the affinity regulation of the metal-ion-dependent adhesion sites in integrins

Density functional theory and a polarizable continuum model are used to (i) understand the affinity modulating mechanisms of the interaction between the metal-ion-dependent adhesion site (MIDAS) of a selected integrin, lymphocyte function-associated antigen-1 (LFA-1) and a ligand mimetic acetate molecule and to (ii) propose a new, promising family of inhibitors to block the interaction of the integrin with intercellular adhesion molecule-1 (ICAM-1). We quantify the effect of isolated factors, such as the metal coordination, the nature of the ligand or the cation present on the MIDAS, and the effect of the permittivity of the media. We show that the affinity for ligand decreases when metal coordination changes from the open conformation to the closed conformation. In addition, Mn2+ and Zn2+ showed to be good competitors for the octahedrically coordinated Mg2+ and yielded excellent affinity values, whereas Ca2+ in an octahedric environment would decrease the affinity for the ligand. Our affinity studies of the open MIDAS showed that nitronate-derived or carboxylic acid-containing ligands may represent new promising scaffolds of future inhibitors. Finally, we show that affinities are always highly favored by low-dielectric environments, which explains the propensity of MIDAS motifs to be surrounded by hydrophobic residues in integrins and highlights the importance of including hydrophobic groups in the inhibitors.     

Quantitative evaluation of the catalytic activity of dendrimers with only one active center at the core: application to the nitroaldol (Henry) reaction

One reference tertiary amine and three families of structurally related trialkylamines and dendrimers have been synthesized, characterized, and studied by molecular dynamics simulations. The catalytic activity of these amines in the nitroaldol (Henry) reaction between 2-nitroethanol and benzaldehyde has been measured by FT-IR spectroscopy. It is found that, in this kind of molecule with only one catalytic center at the core, the efficiency of the catalytic process decreases with the size and/or the degree of ramification of the dendrimer. According to these results, there is a linear departure from the behavior predicted by the hard sphere collision theory (HSCT) as the size of the dendrimer increases. Therefore, the behavior of structurally related dendrimers can be quantified in terms of their molecular weight and reagent accessible surfaces.     

Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification

Density functional calculations of thio effects on the in-line mechanism of methanolysis of ethylene phosphate (a reverse reaction model for RNA phosphate transesterification) are presented. A total of 12 reaction mechanisms are examined using the B3LYP functional with large basis sets, and the effects of solvation were treated using the PCM, CPCM, and SM5 solvation models. Single thio substitutions at all of the distinct phosphoryl oxygen positions (2', 3', 5', pro-R) and a double thio substitution at the nonbridging (pro-R/pro-S) positions were considered. Profiles for each reaction were calculated in the dianionic and monoanionic/monoprotic states, corresponding to reaction models under alkaline and nonalkaline conditions, respectively. These models provide insight into the mechanisms of RNA transesterification thio effects and serve as a set of high-level quantum data that can be used in the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations and linear-scaling electronic structure calculations.