Comprehensive quantum chemical calculations and molecular docking analysis of uracil mustard by first principle

Uracil mustard belongs to the nitrogen mustard family and is primarily used in anticancer drugs. The research that follows, investigates many quantum chemical features such as the computation of global minimum energies with no negative wavenumber values using the Density Functional Theory (DFT) with Becke three functional and 6-311G (d, p)/6–311++G (d, p) basis sets. All the vibrational modes have been calibrated and justified in comparison to their experimental counterparts. Mustard's polarizability and hyperpolarizability components, Natural Bond Analysis (NBO), electronic properties, Fukui function analysis, various global parameters, Quantum Theory of Atoms In Molecule (QTAIM) analysis, ADMET analysis, and docking analysis have all been investigated using the same theory and basis sets, indicating its biochemical significance. The biological activity of the molecule is reported by using PASS software. The Full fitness score and binding affinity parameters are utilized to determine the binding strength with 6cq3 protein. The acidity of the title molecule is calculated in water solvent by polarizable continuum model (PCM) solvent effects (estimated in water). The HOMO, LUMO, and MESP plots are used to explore the nature of binding and surfaces. The Fukui functions are computed using Mulliken atomic charges for neutral atoms, cations, and anions. The Ultraviolet–visible (UV–vis) of the molecule is computed employing the TD-DFT method.     

Perturbed Markov Chains with Damping Component

The paper is devoted to studies of regularly and singularly perturbed Markov chains with damping component. In such models, a matrix of transition probabilities is regularised by adding a special damping matrix multiplied by a small damping (perturbation) parameter ε. We perform a detailed perturbation analysis for such Markov chains, particularly, give effective upper bounds for the rate of approximation for stationary distributions of unperturbed Markov chains by stationary distributions of perturbed Markov chains with regularised matrices of transition probabilities, asymptotic expansions for approximating stationary distributions with respect to damping parameter, explicit coupling type upper bounds for the rate of convergence in ergodic theorems for n-step transition probabilities, as well as ergodic theorems in triangular array mode.

     

Cartilage degradation by stimulated human neutrophils: reactive oxygen species decrease markedly the activity of proteolytic enzymes

BACKGROUND: Although neutrophilic granulocytes clearly contribute to cartilage degradation in rheumatic diseases, it is unclear if reactive oxygen species (ROS) or proteolytic enzymes are the most important components in cartilage degradation and how they interact. RESULTS: Neutrophils were stimulated by chemicals conferring a different degree of ROS formation and enzyme release. Supernatants of neutrophils were incubated with thin slices of pig articular cartilage. Supernatants of cartilage were assayed by NMR spectroscopy, MALDI-TOF mass spectrometry and relevant biochemical methods. Stimulation conditions of neutrophils correlated well with the extent of cartilage degradation. Due to the release of different enzymes, cartilage degradation could be best monitored by NMR since mainly low-mass degradation products were formed. Astonishingly, the suppression of the formation of ROS resulted in decreased cartilage degradation. CONCLUSION: ROS formed by neutrophils are not directly involved in cartilage degradation but influence the activity of proteolytic enzymes, which are the main effectors of cartilage degradation.     

Ab initio SCF calculations on [V10O28]6−: A benchmark for the classical calculation and processing of molecular integrals on large Gaussian basis sets

A vector efficient implementation of the McMurchie and Davidson algorithm for the calculation of one- and two-electron molecular integrals is presented, as available in the Cray version of the ASTERIX program system. The implementation and performance of a vector-oriented strategy for the generation and processing of the P supermatrix is also discussed. This program system has been applied to the ab initio SCF computation of the ground-state wave function for the [V₁₀O₂₈]^6? ion, with a basis set of triple-zeta quality for the valence shell of oxygen generating 1404 GTOS and 574 CGTOS for the complete system. The performance and the bottlenecks of the integral calculation are discussed as a function of the integral classes. Two-dimensional maps of the electrostatic potential are presented for this molecule and compared to experimental information about proton fixation.     

Electronic Structure of Rh(2)(&mgr;-CO)(CO)(2)(H(2)PCH(2)PH(2))(2). An Example of a Non-A-Frame Structure

Calculations based on density functional theory (DFT) and Hartree-Fock configuration interaction (HF-CI) methodology have been carried out to investigate the rhodium-rhodium coupling in Rh(2)(CO)(2)(dppm)(2), 1 (dppm = Ph(2)PCH(2)PPh(2)) and in Rh(2)(&mgr;-CO)(CO)(2)(dppm)(2), 2. DFT geometries, obtained with the Dgauss program, are in good agreement with those determined from X-ray, but HF geometries, calculated using the same basis sets, yield bond distances systematically too long. Calculations indicate that the rhodium atoms in 1 are linked by a single bond. The insertion of a semibridging carbonyl between the two metal atoms leads to a shortening of the rhodium-rhodium distance and also to a noticeable weakening of the metal-metal interaction. Both effects, and also the stabilization of the HOMO of 2, are related to an observed change from square planar to tetrahedral of the ligand environment of the Rh atom proximal to the inserted CO. Both MO analysis and bond characterization from the topology of the charge density confirm the existence of a bonding interaction between the semibridging carbonyl and the distal rhodium atom. The electronic structures of the dicationic complex [Rh(2)(CO)(3)(dppm)(2)](2+) and of the A-frame-like, isoelectronic system Rh(2)Br(2)(&mgr;-CO) (dppm)(2) are also discussed. The electron deformation density is derived from 2 by means of several methodological approaches, namely, HF, HF-CI, DFT, and DFT + gradient corrections. The HF deformation density obtained in the plane containing the metals and the three CO ligands is discussed, as well as the "correlation density" obtained from the difference maps DFT - HF and CI - HF.     

Birefringence of PrAlO3 in the vicinity of 118 K

We have measured the birefringence of PrAlO₃ from 300 to 77 K in several different crystalline orientations. The 205 K first order and 151 K second order structural phase transitions are clearly evident as are the effects of twinning below 151 K which take the form of regular oscillations. Near 118 K we have observed anomalies in the amplitude and frequency of the twinning effect which may relate to the Anderson-Blount phase transition reported by Fleury. Direct evidence of the 118 K transition was also obtained when birefringence measurements were taken in a geometry chosen to suppress the twinning effect.     

A systematic study of 3NF effects in p + d break-up with BINA at 190 MeV

A systematic study of three-nucleon force (3NF) effects in break-up reactions has been carried out at KVI at several energies. In this article, the p + d → p + p + n reaction with a polarized-proton beam of 190?MeV will be discussed. The experiment was performed by exploiting a new detector called BINA. Some results for high-precision vector analyzing powers and differential cross sections are presented and compared with state-of-the-art Faddeev calculations with or without 3NF.     

Reactions of metastable calcium 3P: quenching by Ca(1S), Mg1S) and inert gases

Rate constants have been measured (by laser induced fluorescence) for the quenching of metastable Ca(³P) by the ground states of Ca and Mg and by the inert gases. Rate constants for the metals were considerably larger than for the inert gases. The cross sections for the inert gases are well correlated by an orbiting model.     

Laser chemiluminescence of LiCa

Emission from diatomic LiCa molecules was obtained upon pumping a mixture of Li and Ca vapors with an Ar⁺ion laser. The excited LiCa molecules were formed via reactions of excited Li₂ dimers with Ca atoms. The LiCa emission was analyzed spectroscopically and found to be in good agreement with a synthetic spectrum derived from ab initio calculations of the LiCa potential-energy curves     

Influence of silica fillers during the electron irradiation of DGEBA/TETA epoxy resins, part II: Study of the thermomechanical properties

This work describes the influence of silica fillers on the thermomechanical properties of diglycidyl ether of bisphenol A/triethylenetetramine (DGEBA/TETA) epoxy resins during ageing under electron beam irradiation. Whatever be the silica filler (pure micrometric ground and spherical silicas, nanometric silicas and coupling agent treated silicas), the glass transition temperature of the epoxy resins decreases with increasing irradiation dose, meaning that the main effect of the irradiation is chain scission. No influence of the silica fillers has been detected from the changes in the glass transition temperature with the increase in the irradiation dose. The disappearance of the cooperativity of the γ relaxation, the decrease of the α relaxation and the decrease of the elastic modulus at the rubbery plateau observed by dynamic mechanical analyses involve a decrease in the crosslink density of the epoxy resins. The occurrence of chemical reactions between the epoxy resin and the silica surface at high irradiation doses has been shown. Moreover, we show evidence that chemical reactions between the epoxy resin and the silica surface occur at high irradiation dose.