A fast pairwise evaluation of molecular surface area

A fast and general analytical approach was developed for the calculation of the approximate van der Waals and solvent-accessible surface areas. The method is based on three basic ideas: the use of the Lorentz transformation formula, a rigid-geometry approximation, and a single fitting parameter that can be refitted on the fly during a simulation. The Lorentz transformation equation is used for the summation of the areas of an atom buried by its neighboring contacting atoms, and implies that a sum of the buried pairwise areas cannot be larger than the surface area of the isolated spherical atom itself. In a rigid-geometry approximation we numerically calculate and keep constant the surface of each atom buried by the atoms involved in 1-2 and 1-3 interactions. Only the contributions from the nonbonded atoms (1-4 and higher interactions) are considered in terms of the pairwise approximation. The accuracy and speed of the method is competitive with other pairwise algorithms. A major strength of the method is the ease of parametrization.     

Apparent molar heat capacities and volumes,van der Waals volumes and accessible surface areas of alkylated derivatives of cytosine and uracil in aqueous solutions at 25°C.

Densities and specific heat capacities of aqueous solutions: 1,3,5,6-tetramethyluracil, 1,6-dimethyl-3-ethyluracil, 1,6-dimethyl-3-propyluracil, 1,6-dimethyl-3-butyluracil, 1,N⁴-trimethylcytosine, 1,N⁴-dimethyl-5-ethylcytosine, 1,N⁴ dimethyl-5-propylcytosine, 1,N⁴-dimethyl-5-butylcytosine were determined using flow calorimetry and flow densimetry at 25°C. Apparent molar volumes and heat capacities, van der Waals volumes and accessible surface areas were determined. It was stated that for alkylcytosines and alkyluracils partial molar volumes and heat capacities correlate linearly with the number of substituted methylene groups-CH₂-as well as with the van der Waals volumes and accessible surface areas of the compounds studied; for cyclooligouracils the cyclization effect was discussed.     

Beta‐decomposition for the volume and area of the union of three‐dimensional balls and their offsets

Given a set of spherical balls, called atoms, in three‐dimensional space, its mass properties such as the volume and the boundary area of the union of the atoms are important for many disciplines, particularly for computational chemistry/biology and structural molecular biology. Despite many previous studies, this seemingly easy problem of computing mass properties has not been well‐solved. If the mass properties of the union of the offset of the atoms are to be computed as well, the problem gets even harder. In this article, we propose algorithms that compute the mass properties of both the union of atoms and their offsets both correctly and efficiently. The proposed algorithms employ an approach, called the Beta‐decomposition, based on the recent theory of the beta‐complex. Given the beta‐complex of an atom set, these algorithms decompose the target mass property into a set of primitives using the simplexes of the beta‐complex. Then, the molecular mass property is computed by appropriately summing up the mass property corresponding to each simplex. The time complexity of the proposed algorithm is O(m) in the worst case where m is the number of simplexes in the beta‐complex that can be efficiently computed from the Voronoi diagram of the atoms. It is known in ?³ that m = O(n) on average for biomolecules and m = O(n²) in the worst case for general spheres where n is the number of atoms. The theory is first introduced in ?² and extended to ?³. The proposed algorithms were implemented into the software BetaMass and thoroughly tested using molecular structures available in the Protein Data Bank. BetaMass is freely available at the Voronoi Diagram Research Center web site. © 2012 Wiley Periodicals, Inc.     

Correlation of retention indices with van der Waals’ volumes and surface areas: Alkanes and azo compounds

Summary Van der Waals’ volumes (V _W) and surface areas (S _W) of alkanes, (E)-azoalkanes and structurally similar alkenes (R₁-X=X-R₂, X=N, CH) were calculated by a semiempirical quantum-chemical method (AM1). The calculated data are in reasonable agreement with the experimental values of Bondi and good correlations were found between the calculated data and Kovats’ retention indices (I _R). While theV _Ws of alkanes with the same carbon number are very close to one another, theS _Ws follow the scatter of theI _R values for branched alkanes. The difference in theI _R of (E)-azo compounds and the structurally similar alkenes can be explained by the difference inV _Ws.     

Total surface areas of Group IVA organometallic compounds: Predictors of toxicity to algae and bacteria

There is a high correlation between molecular surface area (TSA) of triorganotin and triorganolead compounds and their toxicity towards a bacterium (Escherichia coli) and an alga (Selenastrum capricornutum). Parallel attempts to correlate other Group IVA organometals incorporating silicon or germanium were unsuccessful. It was further demonstrated, however, that a high correlation was obtainable between certain series of compounds with the same organic substituent but different metal centers involving all Group IVA elements. In both instances, the inability to obtain a quantitative structure-activity relationship (QSAR) for all systems studied appears to be a function of the solubility of the compounds. While organotin TSA values have been found to correlate well with their toxicities toward various organisms, this study clearly suggests that this type of QSAR can be readily extended to include other organometal systems, provided that there is no solubility problem and the toxicity is a function of the hydrophobicity of the organometal compounds.     

Investigation of radionuclide 60Co(II) binding to TiO2 by batch technique, surface complexation model and DFT calculations

The interaction between radionuclides and solid/water interfaces is important to understand the physicochemical processes of radionuclides in the natural environment.Herein,the interaction of 60Co(Ⅱ) with TiO 2 in aqueous solution as a function of pH and ionic strength was studied by using batch technique combined with surface complexation model and density functional theory(DFT) calculations.The batch experimental results showed that the adsorption of 60Co(Ⅱ) was dependent on pH and independent of ionic strength,indicating the formation of inner-sphere surface complexes on TiO 2 surfaces.The results of surface complexation models and DFT calculations indicated that the surface species of 60Co(Ⅱ) adsorbed on TiO 2 followed the trend:B structure(i.e.,60Co(Ⅱ) was linked to one bridge oxygen site) was the dominant surface species at low pH,and TT structure(i.e.,60Co(Ⅱ) was linked to two terminal oxygen sites) became the important surface complex at neutral and alkaline pH values.These results demonstrated that a multi-technique approach could lead to definitive information on the structures of adsorbed 60Co(Ⅱ) at the molecular level at the TiO 2 /water interfaces,as well as realistic models to rationalize and accurately evaluate the macroscopic manifestations of radionuclide adsorption phenomena.