Normal mode analysis of oligomeric proteins: Reduction of the memory requirement by consideration of rigid geometry and molecular symmetry

A method is presented to reduce the memory requirement of normal mode analysis applied to systems containing two or more large proteins when these systems exhibit symmetry properties. We use a rigid geometry model (i.e., only the dihedral angles of the polypeptide chain are considered as variables). This model allows a reduction by a factor of 8 on average of the number of variables with a concomitant freezing of the high-frequency modes. The symmetry properties of the system are used to reduce further the number of variables that must be considered in the computation. Application of group theory leads to a factorization of the matrices of interest (the coefficient and the Hessian matrices) into independent blocks along the diagonal. The initial, reducible representation is thus transformed into a number of irreducible representations of smaller dimensions. In the case of the C₂ symmetry group, the method leads to a reduction of the size of the matrices that must be manipulated during the computation (coefficient matrix, Hessian matrix, and eigenvectors matrix) by a factor of 256 compared with the usual normal mode analysis in Cartesian coordinate space. The method is particularly well adapted to the study of the dynamics of oligomeric proteins because these proteins often display symmetry properties (e.g., virus coat proteins, immunoglobulins, hemoglobin, etc.). In favorable cases, in conjunction with X-ray diffuse scattering data, the study of systems showing allosteric properties might be considered. © 1994 by John Wiley & Sons, Inc.     

Supercritical fluid extraction of oxadixyl from food crops

Summary This work describes the study of a degradation curve of Oxadixyl in field-treated potato and tomato samples. The residues were extracted using classical and supercritical fluid (SFE) extraction methods and analyzed by HRGC/ECD. The extraction techniques were compared and the results indicate the advantages of using SFE as an alternative method for pesticide analyses in these samples.     

Some aspects of polyethylene photooxidation

The hydroperoxides produced by thermal oxidation of LDPE films were used to study their photolysis. Product analysis, kinetics of hydroperoxide decomposition and product formation as well as experiments with model compounds point to new mechanisms of hydroperoxide photolysis. Intermolecular as well as intramolecular decomposition mechanisms are proposed. In polyethylene, these reactions are essentially non-initiating. In addition, it is confirmed that ketones such as those formed by oxidation of polyethylene do not have a significant initiating effect. Reactions of excited charge-transfer complexes polyethylene-oxygen are proposed to account for initiation of photo-oxidation. One of these reactions yields trans-vinylene groups and hydrogen peroxide whose direct decomposition or subsequent photolysis will generate hydroxyl radicals. It is found that this reaction is quenched very efficiently by small amounts of HALS (Hindered Amine Light Stabilizers) and by amines in general. It is postulated that quenching is due to energy transfer from the charge-tranfer complex polymer-oxygen to a charge-transfer complex HALS-oxygen or amine-oxygen. The data available so far support such a mechanism.     

Electron Transfer in the Cs⊂{Mn4Fe4} Cubic Switch: A Soluble Molecular Model of the MnFe Prussian-Blue Analogues

A mixed-valence {Mn^II₃Mn^IIIFe^II₂Fe^III₂} cyanide-bridged molecular cube hosting a caesium cation, Cs⊂{Mn₄Fe₄}, was synthesized and structurally characterized by X-ray diffraction. Cyclic-voltammetry measurements show that its electronic state can be switched between five different redox states, which results in a remarkable electrochromic effect. Magnetic measurements on fresh samples point to the occurrence of a spin-state change near room temperature, which could be ascribed to a metal-to-metal electron transfer converting the {Fe^II−CN−Mn^III} pair into a {Fe^III−CN−Mn^II} pair. This feature was only previously observed in the polymeric MnFe Prussian-blue analogues (PBAs). Moreover, this novel switchable molecule proved to be soluble and stable in organic solvents, paving the way for its integration into advanced materials.     

Rare-earth Metal Borosilicides R9Si15–xB3 (R = Tb,Yb): New Ordered Structures Derived from the AlB2 Structure Type

Two novel ternary borosilicides R₉Si_15–xB₃ (R = Tb, x = 1.80, R = Yb, x = 1.17) were synthesized from the initial elements using tin flux method. Their crystal structures were determined by means of X-ray single crystal diffraction. Both refer to space group R32, Z = 1: a = 6.668(2) Å, c = 12.405(4) Å [R₁ = 0.027, wR₂ = 0.031 for 1832 reflections with I_o > 2σ (I_o)] for Tb₉Si_15–xB₃, and a = 6.5796(3) Å, c = 12.2599(5) Å [R_F = 0.052, wR = 0.090 for 1369 reflections with I_o > 2σ (I_o)] for Yb₉Si_15–xB₃. The structures represent a new structure type, derived from that of AlB₂, with ordering in the metalloid sublattice resulting in distorted [Si₅B] hexagons. The presence or absence of boron in this ordered structure is discussed on the basis of difference Fourier syntheses, interatomic distances, structural analysis, and theoretical calculations in relation with the parent structures of the binaries AlB₂ and Yb₃Si₅ (Th₃Pd₅ type of structure). Theoretical calculations show substantial covalent interactions between the metal and nonmetal elements. The small percentage of silicon atoms, which are missing in these nonstoichiometric compounds, probably allows strengthening boron-metal and boron-silicon bonding.     

Ion-molecule reactions in the gas phase. part XXII. Reactivity of the cis- and trans-indanediols with dimethyl ether ions

Specific reactivity of cis- and trans-indanediols has been investigated under dimethyl ether (DME) chemical ionization conditions. Several unusual species, such as [M + 29]⁺ and [M + 27]⁺ ions, are produced in high yield. From DME pressure variations and tandem mass spectrometry experiments (low-energy collisions with Ar and NH₃) including some labeled compounds, it appears that [M + 29]⁺ ions are generated by nucleophilic substitution according to a S_Ni pathway from the proton bound[M + DMEH]⁺ adduct ion. On the other hand, [M + 27]⁺ ions are produced from the covalent [M + DME ? H]⁺ adduct ions via a stepwise process inducing a water loss. This latter dehydration occurs from the adducts prepared by [DME ? H]⁺ attachment to the homobenzylic hydroxy site, which allows internal proton transfer from the charged position to the benzylic hydroxy group, promotingthe loss of water. In addition, trans indanediol labeled with ¹⁸O has been used to obtain evidence for the regioselectivity of both water-loss mechanisms from the benzylic site.