Determining a 'safe' high-mass limit in matrix-assisted laser desorption/ionisation time-of-flight mass spectra of coal derived materials with reference to instrument noise

Three methods for determining a 'safe' estimate for high-mass limits of MALDI spectra of coal derived liquids were explored, using a sample of coal-tar pitch and its pyridine-insoluble fraction. Co-addition of increasing numbers of single-shot spectra (10, 30, 50 and 100 pulses) showed visually observable reductions in noise levels, consistent with robust and statistically meaningful signals. Three separate types of post-acquisition calculation were used to identify high-mass limits of the spectra. (i) A literature method indicated high-mass limits similar to those observed visually-as a shift from baseline at the highest masses, nearly 350 000 u for the coal tar pitch and about 390 000 u for its pyridine insoluble fraction. (ii) Comparing instrument signal with pre-selected multiples of the standard deviation, upper mass estimates of between 40-60 000 u for the coal-tar pitch and about 95 000 u for its pyridine-insoluble fraction were found. (iii) Calculation of the slope was used to identify 'lift-off' of the spectrum from baseline. The angle between the smoothed spectrum and the baseline was matched to a pre-selected value (e.g. 0.5 degrees and 1 degrees ). However, the arbitrary specification of the key parameter did not establish this last method on a firm basis. The choice of a criterion for estimating high-mass limits of MALDI spectra remains a semi-quantitative procedure; a reasonably conservative high-mass limit may be estimated by comparison of signal with five times the standard deviation. However, evaluation of size exclusion chromatograms of the present samples using polystyrene standards suggests that molecular mass distributions of pitch samples arrived at by MALDI mass spectrometry are, at least partly, determined by the limitations of available instruments. Copyright 1999 John Wiley & Sons, Ltd.     

The virial theorem and the ground state problem in polaron theory

The virial theorem for the translation-invariant theory of a polaron [3] is discussed. It is shown that, in [3], Tulub made a nonoptimal choice of variational parameters in the strong-coupling limit, which led to the violation of the virial relations. The introduction of an additional variational parameter to the test function reduces the polaron energy and makes it possible to satisfy the relations of the virial theorem for a strong-coupling polaron (the Pekar 1: 2: 3: 4 theorem).     

Peroxynitrite in the hemoglobin composition

Electronic characteristics of trHbN hemoglobin whose composition contains the (ONOO) group with the structure close to the structure of 1) peroxynitrite and 2) a nitrate anion in the gas phase are calculated. Electron correlation is considered by the multiconfigurational self-consistent field (MCSCF) method during the optimization of the geometry of the whole structure. Localized molecular orbitals (MOs) are used as starting ones. In the wave function of the MCSCF method two complete active subspaces (CASs) are set. These are the subspace of iron atom 3d orbitals and the subspace describing chemical bonds in peroxynitrite (bonding and antibonding MOs plus the orbital of one lone pair on the O₂ moiety. The composition of the system involves two water molecules. The peroxynitrite structure is considered in two different spin states that correspond to the singlet and triplet states of this anion in the gas phase where the vibrational spectrum is characterized by frequencies of about (70-30) cm^?1. The protective reaction of the active center of the tubercule bacillus is discussed.     

The effect of the oxidative properties of [Mg(H2O)6] in the triplet and singlet states on the energetics of adenosine triphosphate cleavage

The interaction of the adenosine triphosphate (ATP) molecule (the ATP subsystem) with the magnesium complex [Mg(H₂O)₆]²⁺ (the Mg subsystem) in the singlet (S) and triplet (T) states in an aqueous medium mimicked by 78 water molecules was studied by the molecular dynamics (density functional theory) method MD DFT:B3LYP with the 6–31G** basis set at T = 310 K. Potential energy surfaces for the S (lowest-lying) and T (highest-lying) states are significantly separated in space. The Mg complex moves along these surfaces to approach either oxygen atoms of the γ-β phosphate groups (O1–O2) (S PES) or oxygen atoms of β-α phosphate groups (O2–O3) (T PES). Chelation of the γ-β β-α and phosphates yields, respectively, a stable low-energy complex ([Mg(H₂O)₄-(O1–O2)ATP]²⁻) and a metastable high-energy complex ([Mg(H₂O)₂-(O2–O3)ATP]²⁻), which differ in the number of water molecules surrounding the Mg atom. Crossing of two triplet PESs is accompanied by the formation of an unstable state characterized by redistribution of spins between the Mg and ATP subsystems. This state, sensitive to interaction with the ²⁵Mg nuclear spin, induces an unpaired electron spin, which initiates the ATP cleavage by the ion-radical mechanism, yielding a reactive radical ion of adenosine monophosphate (•AMP⁻), which was earlier found experimentally by the of chemically induced dynamic nuclear polarization (CIDNP) method. Biological aspects of the results obtained are discussed. Original Russian Text ? A.A. Tulub, V.E. Stefanov, 2009, published in Zhurnal Neorganicheskoi Khimii, 2009, Vol. 54, No. 7, pp. 1188–1195.     

Molecular dynamics DFT:B3LYP study of guanosinetriphosphate conversion into guanosinemonophosphate upon Mg2+ chelation of alpha and beta phosphate oxygens of the triphosphate tail

A molecular dynamics DFT:B3LYP (6-31G(**) basis set) study is used to elucidate the mechanism of guanosinetriphosphate (GTP) conversion into guanosinemonophosphate (GMP) upon the action of Mg(2+) (magnesium cofactor). The computations are carried out at 310 K in a volume of 178 water molecules, which surround the Mg(2+)-GTP complex and imitate the effect of solution. Over 5 ps, Mg(2+)-GTP appears to be fully decomposed, yielding five final products: two hydrated molecules of inorganic phosphate Pi, a hydrated Mg(2+), atomic oxygen (which in the course of a couple of subsequent reactions gains two hydrogens and converts into a water molecule) and a highly active *GMP radical. The radical production is linked to presence of Mg(2+), which initiates a radical mechanism of GTP cleavage. At the initial stage, Mg(2+) undergoes reduction to Mg(+), accompanied by the formation of an ion-radical pair with GTP, (+)Mg*-*GTP(3-). Without Mg(2+), an inert form of GMP (the ionic mechanism of GTP hydrolytic cleavage) rather than GMP is produced. *GMP production, which is similar to that of *AMP (adenosinemonophosphate), *CMP (cytidinemonophosphate), TMP (thymidinemonophosphate) and *UMP (uridinemonophosphate), plays a crucial role in DNA and RNA single chain synthesis.     

Nonempirical atomic potential method in the study of the surface states of ionic crystals

The electron density functional method was used to construct and compare the pairwise potentials in the bulk and (100) surface of the MgO crystal. Both pairwise and nonadditive ternary dispersion forces were considered in analyzing the compressibility. The pairwise forces tend to decrease, while the ternary forces tend to increase the lattice constant. The dispersion forces taken into account in the framework of the perturbation theory in the case of a Hartree-Fock nuclear configuration provide a corrective contribution to the crystal compressibility in rather precise agreement with the experimental data.Leningrad State University. Translated from Zhurnal Strukturnoi Khimii, Vol. 30, No. 6, pp. 7–12, November–December, 1989.     

Dimeric form of peroxynitrite

The (ONOO)^? anion, known as peroxynitrite, is characterized by a singlet spin state. A new stable dimer form of peroxynitrite [NO-O₂]^? in the triplet state at distances close to r(O-N) ≈ 2.885 Å between oxygen in the O₂ structure and nitrogen has been established within the quantum-chemical CASSCF approximation. The vibrational motion of the dimer is significantly anharmonic; for the ¹⁶O and ¹⁴N isotopes, the differences in the energies of two neighboring levels correspond to frequencies of about 70–30 cm^?1. The triplet dimer structure retains stability in the case of interaction with water molecules. The activation barriers caused by rearrangement of the peroxynitrite structure into the ground state of the NO ₃ ^? anion with the symmetry D _3h are found.