Nuclear motion effects on the density matrix of crystals: An ab initio Monte Carlo harmonic approach

In the frame of the Born-Oppenheimer approximation, nuclear motions in crystals can be simulated rather accurately using a harmonic model. In turn, the electronic first-order density matrix (DM) can be expressed as the statistically weighted average over all its determinations each resulting from an instantaneous nuclear configuration. This model has been implemented in a computational scheme which adopts an ab initio one-electron (Hartree-Fock or Kohn-Sham) Hamiltonian in the CRYSTAL program. After selecting a supercell of reasonable size and solving the corresponding vibrational problem in the harmonic approximation, a Metropolis algorithm is adopted for generating a sample of nuclear configurations which reflects their probability distribution at a given temperature. For each configuration in the sample the "instantaneous" DM is calculated, and its contribution to the observables of interest is extracted. Translational and point symmetry of the crystal as reflected in its average DM are fully exploited. The influence of zero-point and thermal motion of nuclei on such important first-order observables as x-ray structure factors and Compton profiles can thus be estimated.     

Analysis of Bile Acids Profile in Human Serum by Ultrafiltration Clean-up and LC-MS/MS

Bile acids (BAs) are useful biomarkers for the diagnosis of many diseases. The pathologies related to bile acid synthesis are often expressed in the first years of life and may lead to serious liver injury. Here we present a sensitive and rapid method for the analysis of the main 14 bile acids in human serum by liquid chromatography-tandem mass spectrometry. The chromatographic separation is performed using a core–shell column which provides improved separation, highly desirable considering the small structural differences among the analytes. All isomeric BAs of interest were resolved in less than 9 min. Sample pretreatment consisted in ultrafiltration of serum after addition of methanol by means of centrifugal filter devices. The calculated LOQs ranged between 2 and 5 ng mL⁻¹ with linearity of the calibration curves in the 5–5,000 ng mL⁻¹ range for all the BAs. The extraction recoveries for all the analytes were higher than 80 %. Intra-day and inter-day coefficients of variation were all below 15 %. The method proposed has been validated and has been applied for the analysis of serum of pediatric patients. This simple procedure allowed minimal consumption of serum sample (about 100 μL) and a rapid assay, easily implementable in routine analysis.

     

Mixed-Ligand Complex Formation Equilibria of Vanadium(III) with 2,2′-Bipyridine and the Amino Acids Glycine, Proline, α-Alanine and β-Alanine Studied in 3.0 mol?dm?3 KCl at 25 °C

We studied speciation of the mixed-ligand complex formation equilibria of vanadium(III) with both 2,2??-bipyridine (Bipy) and the amino acids glycine (HGly), proline (HPro), ??-alanine (H??Ala), and ??-alanine (H??Ala) by means of electromotive forces measurements emf(H) using 3.0?mol?dm^?3 KCl as the ionic medium at 25 °C. The experimental data were analyzed by means of the computational least-squares program LETAGROP, taking into account the hydrolysis of the vanadium(III) cation, the respective stability constants of the binary complexes, and the acid/base reactions of the ligands which were kept fixed during the analysis. In all four amino acid systems studied we observed the complexes [V₂O(Bipy)(B)]³⁺, [V₂O(Bipy)₂(B)₂]²⁺, [V(OH)(Bipy)(B)₂] and [V(OH)₂(Bipy)(B)], where B represents the deprotonated form of the amino acids studied in this work. The respective stability constants were determined and the species distribution diagrams as a function of pH are briefly discussed.     

Elasticity of flexible and semiflexible polymers with extensible bonds in the Gibbs and Helmholtz ensembles

Stretching experiments on single molecules of arbitrary length opened the way for studying the statistical mechanics of small systems. In many cases in which the thermodynamic limit is not satisfied, different macroscopic boundary conditions, corresponding to different statistical mechanics ensembles, yield different force-displacement curves. We formulate analytical expressions and develop Monte Carlo simulations to quantitatively evaluate the difference between the Helmholtz and the Gibbs ensembles for a wide range of polymer models of biological relevance. We consider generalizations of the freely jointed chain and of the worm-like chain models with extensible bonds. In all cases we show that the convergence to the thermodynamic limit upon increasing contour length is described by a suitable power law and a specific scaling exponent, characteristic of each model.     

A numerical analysis of flat internal cracks under mixed mode loading

A numerical/analytical approach is proposed to determine the stress intensity factors K_I, K_II, and K_III of a 3D internal crack. The main point of this approach is the meshing technique that can model very sharp crack fronts. The meshing technique is based on an elliptical coordinate transformation that starts from a circular crack. It allows the obtainment of a curved crack front with elements normal to the crack front. Remarkable accuracy can be obtained for elliptical crack fronts with axes ratio smaller that 0.01. Accuracy demonstration is provided for cylindrical element with an inclined internal crack subjected to uni-axial tension. This case corresponds to crack propagation for all three modes of loading, the solution of which can checked with references’ results.     

Direct and Inverse Problems for a Phase-Field Model with Memory

We consider a semilinear integrodifferential system in non-normal form. Such a system is a generalization of the one that arises in the phase-field theory with memory. We prove an abstract existence and uniqueness theorem and a continuous dependence result for the direct problem. Reformulating the direct problem in a suitable way we prove that the identification problem admits a unique solution.     

Modelling of Enzyme Properties in Organic Solvents

Summary.  In this article we review how molecular modeling techniques can be used to shed some light on the influence of organic solvents on the molecular characteristics of proteins and enzymes. Molecular dynamic simulations on bovine pancreas trypsin inhibitor, chymotrypsin, and subtilisin make it possible to get a deeper understanding into how increased intramolecular interactions improve conformational rigidity, thus explaining the lower reactivity and the higher thermostability of enzymes in non-aqueous media. The application of thermodynamics-based models allows first qualitative predictions on the selectivity of many reaction types; however, the application of quantum mechanical/molecular mechanical methods is required for the development of quantitative models of actual reactivity patterns. Received November 18, 1999. Accepted (revised) February 8, 2000     

Aging Process Effects on the Characteristics of Vacuum Residue Oxidation Products with the Addition of Crumb Rubber

This paper considers the effect of aging processes on viscoelastic characteristics of vacuum residue oxidation products modified with crumb rubber. Viscoelastic properties were compared to original bitumen raw material-vacuum residue and vacuum residue oxidation products during short-term and long-term aging. The complex shear modulus of the vacuum residue and its oxidation products decreased with an increase in temperature. Short-term aging resulted in increased shear modulus for all samples.The vacuum residue oxidation product modified with crumb rubber had the maximum values of the rutting parameter and fatigue parameter. There was an expansion of the temperature range of plasticity: for the vacuum residue oxidation product with crumb rubber, its value was 67.2 °C. The curves of the black diagram of the modified vacuum residue oxidation product are shifted towards smaller phase angles with the increase in the shear modulus, which indicates the increase in the stiffness and elasticity of the rubber bitumen binders. The vacuum residue oxidation product modified with crumb rubber corresponded to the rubber bitumen binder of the grade RBB 60/90, according to its physical and mechanical indicators.     

Novel Ferrocene-Appended β-Ketoimines and Related BF2 Derivatives with Significant Aggregation-Induced Emission and Second-Order Nonlinear Optical Properties

A series of new β-ketoimines containing a ferrocene moiety and their BF₂ complexes have been synthesized and structurally characterized. The solvatochromism of the β-ketoimines was studied, putting in evidence a redshift with increasing solvent polarity. This positive solvatochromism can be attributed to a more polarized excited state compared with the ground state, due to intramolecular charge transfer (ICT) transitions. The β-ketoimines exhibited weak emission, attributable to the excited-state intramolecular proton transfer (ESIPT) phenomenon. This ESIPT effect is suppressed upon restriction of the keto-enamine tautomerism, induced upon addition of BF₃ ⋅ OEt₂, which afforded the related BF₂ complexes, characterized by an enhancement of the fluorescence through the ICT effect. Both the β-ketoimines and BF₂ complexes exhibited significant aggregation-induced emission behavior in mixtures of CH₃CN/H₂O, due to restriction of intramolecular rotation in the aggregated state. The frontier molecular orbital levels, ground- and excited-state dipole moments (μ_g and μ_e), and the origin of electronic absorption spectra were studied by time-dependent DFT calculations. The second-order nonlinear optical (NLO) properties were determined by the electric-field-induced second-harmonic generation technique. The μβ₁₉₀₇ values of the β-ketoimines increased upon the formation of the related BF₂ complexes, mainly due to an enhancement of the ground-state dipole moment. The results presented here reveal that some of these novel compounds are excellent multifunctional candidates for NLO and luminescence applications.     

High-Energy Proton-Beam-Induced Polymerization/Oxygenation of Hydroxynaphthalenes on Meteorites and Nitrogen Transfer from Urea: Modeling Insoluble Organic Matter?

Formation and structural modification of oxygenated polycyclic aromatic hydrocarbons (oxyPAHs) by UV irradiation on minerals have recently been proposed as a possible channel of PAH transformation in astrochemical and prebiotic scenarios of possible relevance for the origin of life. Herein, it is demonstrated that high-energy proton-beam irradiation in the presence of various meteorites, including stony iron, achondrite, and chondrite types, promotes the conversion of two representative oxyPAH compounds, 1-naphthol and 1,8-dihydroxynaphthalene, to complex mixtures of oxygenated and oligomeric derivatives. The main identified products include polyhydroxy derivatives, isomeric dimers encompassing benzofuran and benzopyran scaffolds, and, notably, a range of quinones and perylene derivatives. Addition of urea, a prebiotically relevant chemical precursor, expanded the range of identified species to include, among others, quinone diimines. Proton-beam irradiation of oxyPAH modulated by nitrogen-containing compounds such as urea is proposed as a possible contributory mechanism for the formation and processing of insoluble organic matter in meteorites and in prebiotic processes.