Molecular mechanics parameters for the FapydG DNA lesion

FapydG is a common oxidative DNA lesion involving opening of the imidazole ring. It shares the same precursor as 8-oxodG and can be excised by the same enzymes as 8-oxodG. However, the loss of the aromatic imidazole in FapydG results in a reduction of the double bond character between C5 and N7, with an accompanying increase in conformational flexibility. Experimental characterization of FapydG is hampered by high reactivity, and thus it is desirable to investigate structural details through computer simulation. We show that the existing Amber force field parameters for FapydG do not reproduce X-ray structural data. We employed quantum mechanics energy profile calculations to derive new molecular mechanics parameters for the rotation of the dihedral angles in the eximidazole moiety. Using these parameters, all-atom simulations in explicit water reproduce the nonplanar conformation of cFapydG in the crystal structure of the complex with L. lactis glycosylase Fpg. We note that the nonplanar structure is stabilized by an acidic residue that is not present in most Fpg sequences. Simulations of the E-->S mutant, as present in E. coli, resulted in a more planar conformation, suggesting that the highly nonplanar form observed in the crystal structure may not have direct biological relevance for FapydG.     

Characterization of ovalbumin-containing polyurethane microcapsules with different structures

Ovalbumin (OVA)-containing polyurethane microcapsules were successfully prepared by a reaction between toluene diisocyanate (TDI) and different polyols such as glycerol, ethane diol, and propylene glycol. The structural and thermal properties of the resultant microcapsules and the release profile of the OVA from the wall membranes were studied. In conclusion, the microcapsules from the glycerol showed the highest thermal stability, with the formation of many hydrogen bonds. From the data of release profiles, it was confirmed that the particle size distribution and morphologies of microcapsules determined the release profiles of the OVA from the wall membranes.     

Molecular structures of adsorbed water

A method previously developed for calculating molecular nanostructures in liquid and adsorbed fluids based on the combination of molecular dynamics with graph theory is modified. In terms of the modified method, the concentrations of associates in water adsorbed in model pores of active carbon are calculated as functions of the degree of pore filling and temperature.     

Molecular structure,hydrostability and stabilization of polyurethane acetals

The effect of the nature and ratio of initial comonomers, the method of synthesis, hydrolysis level and the stabilizer type on the molecular-mass parameters of nonisocyanate polyurethane acetals (PUA) has been studied. The nature of active centres of polymerization has been suggested. The course of hydrolytic degradation of various PUAs has been investigated. It has been shown that the hydrostability of PUA can be increased by salt additives.     

Molecular structures of trinitromethane derivatives

The molecular structures of trinitromethane derivatives XC(NO₂)₃ (X = F, Cl, Br, NC, NF₂, N₃) were studied using the density functional approach. The rules for changing the configurations of substituents in these compounds were revealed. Acceptability of the method employed for the calculations of trinitromethane derivatives is discussed.     

Evaluation of near-infrared chemical imaging for the prediction of surface water quality parameters

Near-infrared (NIR) chemical imaging is an emerging technique with the potential for the detection of contaminants in the environmental field. In this study the potential of NIR chemical imaging (NIR-CI) to predict concentrations of nutrients (total nitrogen, total phosphorus) and indicator microorganisms (Escherichia coli) in surface water was investigated. Chemical images of multiple samples were obtained simultaneously using a pushbroom imaging system operating in the 950–1650 nm wavelength range with spectral resolution of 7 nm. Using partial least squares regression models, the relationship between these pollutants and NIR spectral data extracted from the chemical images in samples of aqueous surface water and filtered residue from surface water was assessed. When calibration models were tested on an independent data set, it was found that models developed on filtered residue spectra outperformed those developed on aqueous samples. For samples of filtered residue, the performance of the calibrations achieved for total nitrogen was reasonable (R² > 0.75); however, performance for total phosphorus and E. coli was poor (R² < 0.5). Lower concentrations of these parameters were detected in the surface water samples included in the study (<1 mg L^?1 and <20 colony-forming units per 100 mL, respectively), a likely reason for the poor performance. The results indicate that NIR-CI has the potential for screening samples in which the contaminant concentration exceeds 1 mg L^?1.     

Predicting discotic mesomorphism from molecular parameters for discogenic structures

Molecular parameters (M_m, M_r, K_p, K, K_c, and K_s) are calculated for polysubstituted cycloveratrilenes and cyclophanes as a continuation of our series of papers on prediction of discotic mesomorphism (DM). Histograms showing the distribution of 57 mesogenic and 28 nonmesogenic structures according to the first three parameters are constructed. Prediction probabilities are estimated at more than 50% for M_m and M_r. This approach is used to analyze 150 hypothetical structures of polysubstituted cycloveratrilenes and cyclophanes to examine the occurrence of a discophase. Several structures with predictable DM are selected for further research. Ivanovo State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 3, pp. 473–477, May–June, 1998.     

Contact model for the prediction of NMR N-H order parameters in globular proteins

An analytical relationship is presented for the estimation of NMR S2 order parameters of N-HN vectors of the protein backbone from high-resolution protein structures. The relationship solely depends on close contacts of the peptide plane to the rest of the protein. Application of the relationship to a number of proteins with high-resolution X-ray and NMR structures yields S2 values that are in good agreement with the ones determined from experimental relaxation data.     

Ab Initio prediction of possible crystal structures for general organic molecules

The performance of a new crystal packing procedure for the ab initio prediction of possible molecular crystal structures is presented. The method is based upon only molecular information, i.e., no unit cell parameters are assumed to be known. The search for the global crystal energy minimum and all local minima inside an energy window is derived from Monte Carlo simulated annealing methods and has been applied to various organic molecules containing heteroatoms and polar groups. A systematic evaluation of the search method and of the quality of the potential energy function has been established. It is demonstrated that the packing of general organic molecules is possible even with standard force fields like CHARMM provided that the charges defining the electrostatic interactions are based upon physical models rather than transferable empirical parameters. Concepts of crystal packing that were based till now upon assumptions and speculations could be proved or disproved by solving directly the extended global optimization problem related to crystal packing. Crystal structures of molecules as complex as those treated in this article have not been, till now, predicted by a computational approach. In one case, a disagreement between the predicted and experimental structure was evident and, based upon the computations, we suspect that the published structure is the wrong one. © 1992 by John Wiley & Sons, Inc.     

Molecular geometry and chain entanglement: parameters for the tube model

The tube diameter in the reptation model is the distance between a given chain segment and its nearest segment in adjacent chains. This dimention is thus related to the cross-sectional area of polymer chains and the nearest approach among chains, without effects of thermal fluctuation and steric repulsion. Prior calculated tube diameters are much larger, about 5 times, than the actual chain cross-sectional areas. This is ascribed to the local freedom required for mutual rearrangement among neighboring chain segments. This tube diameter concept seems to us to infer a relationship to the corresponding entanglement spacing. Indeed, we report here that the critical molecular weight, M_c, for the onset of entanglements is found to be M_c = 28 A/(〈R²〉₀/M), where A is the chain cross-sectional area and 〈R²〉₀ the mean-square end-to-end distance of a freely jointed chain of molecular weight M. The new, computed relationship between the critical number of backbone atoms for entanglement and the chain cross-sectional area of polymers, N_c = A^0,44, is concordant with the cross-sectional area of polymer chains being the parameter controlling the critical entanglement number of backbone atoms of flexible polymers.     

Performance evaluation of the GastroPlusTM software tool for prediction of the toxicokinetic parameters of chemicals

ABSTRACT

The accurate prediction of toxicokinetic parameters arising from oral, dermal and inhalation routes of chemical exposure is a key element in chemical safety assessments. In this research, the physiologically based pharmacokinetic (PBPK) GastroPlus^TM software was evaluated against a series of chemicals for the prediction of toxicokinetic parameters. Overall, 67% of predicted intrinsic clearance (Clint) values were within 1- to 10-fold of empirical data for 463 compounds, and 87% of the predicted fraction unbounded in plasma (Fup) values were 1- to 3-fold of empirical data for 441 compounds. The r² (coefficient of determination) of predicted C_max (maximum plasma concentration) and AUC (Area Under Curve) values versus the corresponding empirical values from oral, inhalation and dermal exposures ranged from 0.04 to 0.92. Among the three exposures, the highest r² values, ranging from 0.80 to 0.92, were observed for oral exposure predictions, where 88% of the compounds had 1- to 10-fold differences between predicted and empirical values for C_max and AUC. The predicted plasma C_ss (steady-state plasma concentration) values were consistent with those C_ss values calculated by in vitro-to-in vivo extrapolation (IVIVE) approaches using experimental parameters. Based on the evaluation results, GastroPlus? can be used as a QSAR/PBPK tool for toxicokinetic parameter predictions.     

Molecular shapes and molecular structures

The first part is a response to E.B. Wilson's remarks about molecular structure at the 1979 Sanibel Symposium; his proposed extension of the notion of “potential energy surface” is a convention, not a part of fundamental molecular quantum theory. An energy surface has no essential role in a non-adiabatic theory which, both in principle and practice, can account for the spectroscopic term formulae with greater accuracy than models based on PE surfaces. Results obtained from the generator coordinate method are cited as confirmation of this conclusion. Claverie and Diner's distinction between “quantum structure” and “classical molecular structure” is discussed; it is the latter that is problematic in molecular quantum theory. The use of molecular structure is optional, and determined by utility, rather than essential in chemical physics; photoelectron spectroscopy is an example where this appreciation has proved fruitful.     

The effect of electrospinning parameters on the compliance behavior of electrospun polyurethane tube for artificial common bile duct

The present research introduced a method to produce an artificial common bile duct using electrospinning technique. Also, the effect of electrospinning variables on the mechanical properties of produced prostheses is investigated. Using electrospinning of polyurethane nanofibres, cylindrical prostheses were produced on a rotating mandrel considering the different controllable factors such as the mandrel rotational speed, the applied voltage, and the flow rate of polymer solution. Taguchi method was used to investigate the effect of mentioned factors on the compliance of circular prostheses. MTT assay was performed to study the cytotoxicity of prostheses. The results of the signal-to-noise analysis showed that the mandrel rotational speed factor has the strongest effect on the compliance values. The flow rate was the second factor and it was followed by electrospinning voltage. In addition, the optimum conditions to reach the highest compliance value were determined. The results of MTT assay indicated no cytotoxic effects of prostheses on the cells. The compliance of optimum prosthesis was found close to the compliance value of a native common bile duct.     

Convenient synthesis of novel fluorinated polyurethane hybrid latexes and core-shell structures via emulsion polymerization process with self-emulsification of polyurethane

Novel fluorinated polyurethane hybrid latexes in the size range of 40–50 nm, fluoroalkyl acrylate as fluorinated monomers, with various fluorine content (F% = 9∼26 wt%) were successfully prepared via emulsion polymerization process without traditional emulsifier. The waterborne polyurethane, which was synthesized by using isophronediisocyanate, dimethylol propionic acid, polyethylene glycols, etc., served not only as copolymerizable macromonomer but also as polymeric high molecular weight emulsifier. The structures of polyurethane macromonomer and fluorinated polyurethane were characterized by Fourier transform infrared and H¹-NMR. Particle size, zeta potential, micromorphology of the latex par.ticles, and surface properties were investigated by dynamic light scattering, potential particle size analyzer, transmission electron microscopy, and contact angle measurement, respectively. Results illustrated that the advantage of this process is that the size of fluorinated polyurethane hybrid particle is less sensitive to the composition. Furthermore, it was showed that fluorinated polyurethane latex particles had core-shell structures, especially when the content of fluorine was 26.08 wt%. Moreover, there was an obvious migration of fluorinated groups to the surface during the formation of fluorinated polymer films, although fluorinated groups were covered by polyurethane in latex particles.     

Molecular associations: Values of the expansion parameters for new classes of atoms

Expansion parameters, for use in a 1/R expansion developed at this laboratory for the study of molecular interactions, have been determined for new classes of atoms. Test calculations with these new parameters have yielded very satisfactory results for the glycine zwitterion, in dimer form and solvated, confirming the goodness of the parameters and the appropriateness of the formulation.     

Molecular modeling approaches for the prediction of the nonspecific binding of drugs to hepatic microsomes

Molecular modeling approaches for the prediction of the nonspecific binding of drugs to hepatic microsomes were examined using a published database of 56 compounds. Models generated were evaluated using an independent test set of 13 compounds. A pharmacophore approach identified structural features of drugs associated with nonspecific binding. A side-chain amino group and complementary hydrophobic domain were the principal features noted. The use of shape overlays, based on the pharmacophore, in conjunction with a chemical force field in the program ROCS, yielded discrimination between molecules classified as strong binders (experimental fraction unbound in microsomes<0.50) and those with a lower degree of binding (experimental fraction unbound in microsomes>0.50). In the initial data set of 56 molecules, 18 were classified as strong binders (on the basis of the above criteria), and all of those were recovered in the top 22 molecular hits from ROCS. Additionally, computationally generated values of log P were shown to provide a reasonable estimate of the fraction unbound in microsomes, providing the compounds were in their basic form at physiological pH.