Solvent effects on 17O nuclear magnetic shielding: N-methylformamide in polar and apolar solutions

The solvent effect on ¹⁷O isotropic shielding was computed by different methods: the polarizable continuum model and a mixed approach, including a few real solvent molecules treated as the solute. The experimental data show that the behavior of protic and aprotic solvents is markedly different: we found that the continuum approach describes well the observed shielding at various dielectric constants for aprotic solvents, while the mixed procedure is needed when hydrogen bonds to the magnetic centre are present.Contribution to the Jacopo Tomasi Honorary Issue     

Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes

An essential element of implicit solvent models, such as the generalized Born method, is a knowledge of the volume associated with the individual atoms of the solute. Two approaches for determining atomic volumes for the generalized Born model are described; one is based on Voronoi polyhedra and the other, on minimizing the fluctuations in the overall volume of the solute. Volumes to be used with various parameter sets for protein and nucleic acids in the CHARMM force field are determined from a large set of known structures. The volumes resulting from the two different approaches are compared with respect to various parameters, including the size and solvent accessibility of the structures from which they are determined. The question of whether to include hydrogens in the atomic representation of the solute volume is examined. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1857-1879, 2001     

Ab initio quasirelativistic calculations on electronic transitions in ICl by the multireference many‐body perturbation theory

A quasirelativistic perturbative method of ab initio calculations on ground and excited molecular electronic states and transition properties within the relativistic effective core potential approximation is presented and discussed. The method is based on the construction of a state‐selective many‐electron effective Hamiltonian in the model space spanned by an appropriate set of Slater determinants by means of the second‐order many‐body multireference perturbation theory. The neglect of effective spin–orbit interactions outside of the model space allows the exploitation of relatively high nonrelativistic symmetry during the evaluation of perturbative corrections and therefore dramatic reduction of the cost of computations without any contraction of the model‐space functions. One‐electron transition properties are evaluated via the perturbative construction of spin‐free transition density matrices. Illustrative calculations on the X0⁺ ? A1, B0⁺, and (ii)1 transitions in the ICl molecule are reported. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: new energy gradients and molecular surface tessellation

New equations are derived and implemented for efficient and accurate computation of solvation energy derivatives for the conductor-like polarizable continuum model (C-PCM) and the isotropic integral equation formalism polarizable continuum model (IEF-PCM). Two new molecular surface tessellation procedures GEPOL-RT and GEPOL-AS that generate near continuous potential energy surfaces are proposed for PCM geometry optimization. The combined use of these new techniques leads to efficient and convergent geometry optimizations with the PCMs.     

Molecular mechanics and dynamics of biomolecules using a solvent continuum model

An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson-Boltzmann equation (polar contribution) and the solvent-accessible surface area approach (nonpolar contribution). The feasibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simulations. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1830-1842, 2001     

Determination of aluminum in highly concentrated iron samples: Study of interferences using high-resolution continuum source atomic absorption spectrometry

High-resolution continuum source atomic absorption spectrometry (HR-CS AAS) has been used to investigate spectral and non-spectral interferences found with a conventional line source atomic absorption spectrometer in the determination of aluminum in pharmaceutical products containing elevated iron and sugar concentrations. A transversely heated graphite furnace was used as the atomizer in both spectrometers. The two most sensitive aluminum lines at 309.3 nm and 396.2 nm were investigated and it was found that an iron absorption line at 309.278 nm, in the vicinity of the aluminum line at 309.271 nm, could be responsible for some spectral interference. The simultaneous presence of iron and the organic components of the matrix were responsible for radiation scattering, causing high continuous and also structured background absorption at both wavelengths. The aluminum and iron absorption could not be separated in time, i.e., the iron interference could not be eliminated by optimizing the graphite furnace temperature program. However, an interference-free determination of aluminum was possible carrying out the measurements with HR-CS AAS at 396.152 nm after applying least squares background correction for the elimination of the structured background. Analytical working range and other figures of merit were determined and are presented for both wavelengths using peak volume registration (center pixel ± 1) and the center pixel only. Limits of detection and characteristic masses ranged from 1.1 to 2.5 pg and 13 to 43 pg, respectively. The method was used for the determination of the aluminum contamination in pharmaceutical formulations for iron deficiency treatment, which present iron concentrations from 10 to 50 g l^− 1. Spike recoveries from 89% to 105% show that the proposed method can be satisfactorily used for the quality control of these formulations.     

Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient

Summary The use of a recently proposed hydrophobic similarity index for the alignment of molecules and the prediction of their differences in biological activity is described. The hydrophobic similarity index exploits atomic contributions to the octanol/water transfer free energy, which are evaluated by means of the fractional partitioning scheme developed within the framework of the Miertus-Scrocco-Tomasi continuum model. Those contributions are used to define global and local measures of hydrophobic similarity. The suitability of this computational strategy is examined for two series of compounds (ACAT inhibitors and 5-HT₃ receptor agonists), which are aligned to maximize the global hydrophobic similarity using a Monte Carlo-simulated protocol. Indeed, the concept of local hydrophobic similarity is used to explore structure–activity relationships in a series of COX-2 inhibitors. Inspection of the 3D distribution of hydrophobic/hydrophilic contributions in the aligned molecules is valuable to identify regions of very similar hydrophobicity, which can define pharmacophoric recognition patterns. Moreover, low similar regions permit to identify structural elements that modulate the differences in activity between molecules. Finally, the quantitative relationships found between the pharmacological activity and the hydrophobic similarity index points out that not only the global hydrophobicity, but its 3D distribution, is important to gain insight into the activity of molecules. J.M.M. and S.P. have contributed equally to this study.     

Cation-crown ether complex formation in water. II. Alkali and alkaline earth cations and 12-crown-4, 15-crown-5, and 18-crown-6

The stability constants and the partial molal volume and isentropic partial molal compressibility changes of complex formation between cations and crown ethers in water at 25°C are presented. The cations involved are Na⁺, K⁺, Rb⁺, Cs⁺, Ca²⁺, and Ba²⁺, and the crown ethers are 12-crown-4, 15-crown-5, and 18-crown-6. Values of V of complex formation have been discussed in terms of two simple models, one based on the scaled particle theory, and the others on the Drude-Nernst continuum model. The results indicate that the charge of the potassium cation in 18-crown-6 is especially well screened from the water. On this basis hydration numbers of complexed cations have been calculated. This shows that the size of the cation compared to the crown ether hole is important for the contacts between complexed cations and water.     

Ab initio study of Rg2I− (Rg = Ar,Kr, Xe)

The equilibrium geometries, vibrational frequencies, and dissociation energies of rare gas iodine clusters Rg₂I^?(Rg = Ar, Kr, Xe) were calculated at the Hartree–Fock (HF), second‐order Møller–Plesset (MP2), the coupled cluster method with single and double excitation and a noniterative correction for triple excitations method [CCSD(T)] levels. The title species have bent C_2v structure of about 60° angle. The electron correlation effects and relativistic effects on the geometry and stability were investigated at CCSD(T) level. Both effects stabilize title species. The calculated electron affinities are in good agreement with the experimental results available. The effect of high angular momentum functions (g and h) was studied. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006