Normal mode analysis of molecular motions in curvilinear coordinates on a non-Eckart body-frame: an application to protein torsion dynamics

Normal mode analysis (NMA) was introduced in 1930s as a framework to understand the structure of the observed vibration-rotation spectrum of several small molecules. During the past three decades NMA has also become a popular alternative to figuring out the large-scale motion of proteins and other macromolecules. However, the “standard” NMA is based on approximations, which sometimes are unphysical. Especially problematic is the assumption that atoms move only “infinitesimally”, which, of course, is an oxymoron when large amplitude motions are concerned. The “infinitesimal” approximation has the further unfortunate side effect of masking the physical importance of the coupling between vibrational and rotational degrees of freedom. Here, we present a novel formulation of the NMA, which is applied for finite motions in non-Eckart body-frame. Contrary to standard normal mode theory, our approach starts by assuming a harmonic potential in generalized coordinates, and tries to avoid the linearization of the coordinates. It also takes explicitly into account the Coriolis terms, which couple vibrations and rotations, and the terms involving Christoffel symbols, which are ignored by default in the standard NMA. We also computationally explore the effect of various terms to the solutions of the NMA equation of motions.     

Reaction of Selenium with Bromine in the Presence of Methyltriphenylphosphonium Bromide: Syntheses and Crystal Structures of [PMePh3]2[Se2Br6] and [PMePh3]2[SeBr6(SeBr2)2]

The brown crystals of [PMePh₃]₂[Se₂Br₆] ( 1 ) and red crystals of [PMePh₃]₂[SeBr₆(SeBr₂)₂] ( 2 ) were obtained when selenium and bromine reacted in the solution of acetonitrile in the presence of methyltriphenylphosphonium bromide. The crystal structures of 1 and 2 has been determined by the X‐ray methods and refined to R = 0.0373 for 2397 reflections and 0.0397 for 3417 reflections, respectively. The salt 1 crystallizes in the monoclinic space group P2₁/n with the cell dimensions a = 13.202(5) Å, b = 11.954(4) Å, c = 13.418(6) Å, β = 93.08(4)° (193(2)). The crystals of 2 are triclinic, space group with the cell dimensions a = 10.266(3) Å, b = 11.311(3) Å, c = 11.619(2) Å, α = 108.87(2)°, β = 105.72(2)°, γ = 99.40(2)° (193(2) K). In the solid state structure of 1 the dinuclear hexabromo‐diselenate(II) anion is centrosymmetric and consists of two distorted almost square planar SeBr₄ units sharing a common edge through two μ‐bridging Br atoms. The terminal Se^II–Br bonds are 2.3984(11) and 2.4273(11) Å, whereas the bridging μBr–Se^II bonds are 2.7817(11) and 2.9081(12) Å. In the solid state the trinuclear [SeBr₆(SeBr₂)₂]^2? anion of 2 is centrosymmetric too and contains a nearly regular [SeBr₆] octahedron where the four equatorial bromo ligands each have developed bonds to the Se^II atoms of the SeBr₂ molecules. The contacts between the bridging bromo and the Se^II atoms of the SeBr₂ molecules are 3.0603(15) and 3.1043(12) Å, and can be interpreted as bonds of the donor‐acceptor type with the bridging bromo ligands as donors and the SeBr₂ molecules as acceptors. The Se^IV–Br distances are in the range 2.5570(9)–2.5773(11) Å and the Se^II–Br bond lengths in coordinated SeBr₂ molecules – 2.3411(12) and 2.3421(10) Å.     

Neutrino masses in supersymmetry: R-parity and leptogenesis

In the supersymmetric standard model of particle interactions, R-parity nonconservation is often invoked to obtain nonzero neutrino masses. We point out here that such interactions of the supersymmetric particles would erase any pre-existing lepton or baryon asymmetry of the universe before the electroweak phase transition through the B+L violating sphaleron processes. We also point out that all models of radiative generation of neutrino masses suffer from the same problem. We then show how neutrino masses may be obtained in supersymmetry (assuming R-parity conservation) together with successful leptogenesis and predict the possible existence of new observable particles.     

Analysis of nitromethane from samples exposed in vitro to chloropicrin by stable isotope dilution headspace gas chromatography with mass spectrometry

Chloropicrin (trichloronitromethane) is a widely used soil fumigant and an old chemical warfare agent. The metabolism of chloropicrin is not well known in mammals but nitromethane has been shown to be one of its main metabolites. Here, a fast and simple headspace gas chromatography with mass spectrometry method was applied for the measurement of nitromethane from aqueous samples. The analytical method was validated using stable isotope labeled internal standard and a small sample volume of 260 μL. No conventional sample preparation steps were needed. The method was accurate (relative standard deviations ≤1.5%) and linear (R² = 0.9996) within the concentration range of 0.1?6.0 μg/mL. This method was used to measure nitromethane in in vitro incubations with human and pig liver cell fractions containing enzymes for xenobiotic metabolism, exposed to chloropicrin. The results indicate that the presence of glutathione is necessary for the formation of nitromethane from chloropicrin. Also, nitromethane was formed mostly in liver cytosol fractions, but not in microsomal fractions after the incubation with chloropicrin. Our results suggest that although nitromethane is not the unequivocal biomarker of chloropicrin exposure, this method could be applied for screening the elevated levels in humans after chloropicrin exposure.     

Polarized infrared spectra: Part 1. Stretched polymer method. Fundamental vibrations of some mono- and di-substituted benzenes

Polarized IR spectra of five benzene derivatives (four of C_2v symmetry and one of D_2h symmetry) have been recorded using the stretched polymer method. It has been found that the values of the dichroic ratios depend systematically on the symmetry class of the vibration in question. The IR-active vibrations can thus be unambiguously divided into the correct symmetry classes. The general validity of the method, as well as its value for vibrational analysis, is discussed.     

Dispersion Theory of Liquids Containing Optically Linear and Nonlinear Maxwell Garnett Nanoparticles

Kramers-Kronig relations and sum rules for effective linear permittivity of the Maxwell Garnett liquid-nanosphere system were obtained using complex analysis and general expression of the effective permittivity. When reflectance from optically linear and nonlinear Maxwell Garnett nanoparticles was calculated it was observed that the reflectance, in the case of attenuated total reflection, depends on the fill fraction of the nanospheres and their nonlinear susceptibility. According to simulations a good sensitivity of the nonlinear contribution on the reflectance can be obtained by using a probe wavelength corresponding to the resonance frequency of the nanosphere system. In Kretchmann#x0027;s configuration it was observed that the surface-plasmon-resonance angle depends on the fill fraction and on the intensity of the incident light. By using reflectance, it is possible to detect optically nonlinear nanospheres in liquids.     

Practical Method for 2‐Hydroxyphenylketimine Synthesis

A series of hydroxyphenylketimines, of which 15 are new, was synthesized in methanol at high temperature (200°C) using a sealed steel reactor. This reaction setup especially enhances the synthesis of 2‐hydroxyphenylketimines, with yields up to six times higher than those obtained with the conventional acid‐catalyzed method under refluxing conditions. In fact, some imines were achievable only by the autoclave method.     

A semiempirical study on inhibition of catechol O-methyltransferase by substituted catechols

Catechol and endogenous catechol derivatives are readily methylated by catechol O-methyltransferase (COMT). In contrast, many catechol derivatives possessing electronegative substituents are potent COMT inhibitors. The X-ray structure of the active site of COMT suggests that the methylation involves a lysine as a general base. The lysine can activate one of the catecholic hydroxyl groups for a nucleophilic attack on the active methyl group of the coenzyme S-adenosyl-l-methionine (AdoMet). We studied the effect of dinitrosubstitution of the catecholic ring at the semiempirical PM3 level on the methylation reaction catalysed by COMT. The electronegative nitro groups make the ionized catechol hydroxyls less nucleophilic than the corresponding hydroxyl groups of the non-substituted catechol. As a consequence, dinitrocatechol is not methylated but is instead a potent COMT inhibitor. The implications of this mechanism to the design of COMT inhibitors are discussed.