A simple approach for improving the hybrid MMVB force field: application to the photoisomerization of s-cis butadiene

MMVB is a QM/MM hybrid method, consisting of a molecular mechanics force field coupled to a valence bond Heisenberg Hamiltonian parametrized from ab initio CASSCF calculations on several prototype molecules. The Heisenberg Hamiltonian matrix elements Q(ij) and K(ij), whose expressions are partitioned here into a primary contribution and second-order correction terms, are calculated analytically in MMVB. When the original MMVB force field fails to produce potential energy surfaces accurate enough for dynamics calculations, we show that significant improvements can be made by refitting the second-order correction terms for the particular molecule(s) being studied. This "local" reparametrization is based on values of K(ij) extracted (using effective Hamiltonian techniques) from CASSCF calculations on the same molecule(s). The method is demonstrated for the photoisomerization of s-cis butadiene, and we explain how the correction terms that enabled a successful MMVB dynamics study [Garavelli, M.; Bernardi, F.; Olivucci, M.; Bearpark, M. J.; Klein, S.; Robb, M. A. J Phys Chem A 2001, 105, 11496] were refitted.     

Evaluation of soybean seed protein extraction focusing on metalloprotein analysis

Two methods of protein extraction for soybean seeds were evaluated in terms of preservation of the metal ions bound to proteins after the extraction and separation procedures. The proteins were firstly separated according to their molar masses by polyacrylamide gel electrophoresis. Then, the protein bands were mapped by synchrotron radiation X-ray fluorescence in order to establish which metal ions were present in each one. Finally, some mapped protein bands were decomposed by microwave-assisted combustion and Ca, Cu, K, Mg, Mn, and Zn were quantified by inductively coupled plasma mass spectrometry or inductively coupled plasma optical emission spectrometry. The extraction methods studied were Method A (based on the treatment of ground soybean seeds with hexane and their extraction with Tris–HCl and β-mercaptoethanol) and Method B (based on the treatment of ground soybean seeds with petroleum ether and their extraction with Tris–HCl, dithiothreitol, phenylmethanesulfonyl fluoride, sodium dodecyl sulfate and potassium chloride). The best method was Method B, in which a 78% higher extraction efficiency was obtained when compared to Method A. Additionally, the metal-protein interactions were more appropriately preserved when Method B was applied, where the most affected ions were those that are bound weakly to proteins, such as Ca, K, and Mg.     

Coupling of an indicator-free electrochemical DNA biosensor with polymerase chain reaction for the detection of DNA sequences related to the apolipoprotein E

This paper describes a disposable indicator-free electrochemical DNA biosensor applied to the detection of apolipoprotein E (apoE) sequences in PCR samples. In the indicator-free assays, the duplex formation was detected by measuring the electrochemical signal of the guanine base of nucleic acids. The biosensor format involved the immobilisation of an inosine-modified (guanine-free) probe onto a screen-printed electrode (SPE) transducer and the detection of the duplex formation in connection with the square-wave voltammetric measurement of the oxidation peak of the guanine of the target sequence.The indicator-free scheme has been characterised using 23-mer oligonucleotides as model: parameters affecting the hybridisation assay such as probe immobilisation conditions, hybridisation time, use of hybridisation accelerators were examined and optimised.The analysis of PCR samples (244 bp DNA fragments, obtained by amplification of DNA extracted from human blood) required a further optimisation of the experimental procedure. In particular, a lower steric hyndrance of the probe modified surface was essential to allow an efficient hybridisation of the target DNA fragment. Negative controls have been performed using the PCR blank and amplicons unrelated to the immobilised probe. A 10 min hybridisation time allowed a full characterisation of each sample.     

A new high-performance liquid chromatographic/electrospray ionization tandem mass spectrometric method for the simultaneous determination of cyclophosphamide, methotrexate and 5-fluorouracil as markers of surface contamination for occupational exposure monitoring

A new high-performance liquid chromatographic/electrospray ionization tandem mass spectrometric (HPLC/ESI-MS/MS) method was developed for the simultaneous quantification of 5-fluorouracil (5FU), methotrexate (MTX) and cyclophosphamide (CP) in environmental samples. These compounds, commonly used in the treatment of cancer, are recognized as genotoxic. In order to estimate the occupational exposure of hospital personnel handling these drugs, wipe samples were taken from the working surfaces and directly analyzed (with trophosphamide as internal standard) using a reversed-phase capillary column and MS/MS detection. This is the first HPLC/MS/MS method for the simultaneous determination of 5FU, MTX and CP. The present method offers high sensitivity, with detection limits of 1.1 microg l(-1) for MTX and CP and 33.3 microg l(-1) for 5FU, avoiding any sample preconcentration procedure. Rapidity, specificity, high accuracy (mean values between 92.4 and 99.9%) and precision (mean RSD values between 3.4 and 12.1%) make the method suitable for the routine determination of these three antineoplastic drugs.     

α-Hydroxyalkylation of heteroaromatic bases by alcohols and hydroxylamine-O-sulphonic acid

The homolytic decomposition of hydroxylamine-O-sulphonic acid in alcoholic solvents was investigated in the presence or absence of protonated heteroaromatic bases and Fe(II) salt. The addition of the α-hydroxyalkyl radicals to the base and their oxidation by Fe(III) salt to the corresponding alkyl cyanide were competitive processes. A redox chain process involving the amino radical cation, NH₃^t., is suggested and the factors affecting the yields of the homolytic substitution are discussed.     

Axially Dissymmetric Bis(triaryl)phosphines in the Biphenyl series: Synthesis of (6,6′-dimethylbiphenyl-2,2′-diyl)bis(diphenylphosphine) (‘BIPHEMP’) and analogues,and their use in Rh(I)-catalyzed asymmetric isomerizations of N,N-diethylnerylamine

The axially dissymmetric diphosphines (?)-(R)- and (+)-(S)-(6-6′-dimethylbiphenyl-2,2′-diyl)bis(diphenyl-phosphine) ((?)-(R)- 10 and (+)-(S)- 10 ; ‘BIPHEMP’) have been synthesized, starting from (R)- and (S)-6,6′-dimethylbiphenyl-2,2′-diamine ((R)- and(S)- 16 ), respectively, via Sandmeyer reaction, liathiation, and phosphinylation. Moreover, racemic 4,4′- dimethyl- and 4,4′-bis(dimethylamino)-substituted analogues 11 and 12 respectively, and the 6,6′-bridged analogues 1,11-bis(diphenylphosphino)-5,7-dihydrodibenz[c,e]oxepin (13) were synthesized and resolved into optically pure (R)- and(S)-enantiomers via complexation with di-μ-chlorob is {(R)-2-[1-(dimethylamino)ethyl]pheny-C? N}dipalladium(II) ((R)- 18 ). The molecular structures of the diphosphines (S)- 10 and (R)- 13 and of two derived cationic Rh(I) complexes,[Rh((S)- 10 )(nbd)]BF₄ and [Rh((R)- 13 )(nbd)]BF 4 were determined by x-ray analyses. Absolute configurations were established for (+)-(S)- 10 by X-ray analyses of both the free diphosphine and of the derived Rh(I) complex, and for (?)-(R)- 13 by X-ray analysis of the derived Rh(I) complex. Configurational assignments for the substituted BIPHEMP analogues 11 12 were achieved by means of ¹H-NMR comparisons. The BIPHEMP ligand 10 and analogues 11 , 12 and 13 are the first examples of optically active bis(triaylphosphines) containing the axially dissymmetric biphenyl moiety. All these new diphosphines proved to be excellent asymmetry-inducing ligands in Rh(I)-catalyzed isomerizations of N,N-diethylnerylamine affording citronellat enamine of 98-99% ee.     

Optimizing control of simulated moving beds--linear isotherm

A new optimization based adaptive control strategy for simulated moving beds (SMBs) is proposed. A linearized reduced order model, which accounts for the periodic nature of the SMB process, is used for online optimization and control. The manipulated variables are the four inlet flow rates, the outputs are the raffinate and extract concentrations. Concentration measurements at the raffinate and extract outlets are used as the feedback information. The state estimate from the periodic Kalman filter is used for the prediction of the outlet concentrations over a chosen horizon. Predicted outlet concentrations are the basis for the calculation of the optimal input adjustments, which maximize the productivity and minimize the desorbent consumption subject to constraints on product purities. The realization of this concept is discussed and the implementation on a virtual eight column SMB platform is assessed, in the case of binary linear systems. For a whole series of typical plant disturbances it is shown that the proposed approach is effective in minimizing off-spec products and in achieving optimal SMB operation, also in the case where there are significant model uncertainties.     

Synthesis and characterization of cobalt(II) and copper(II) complexes with 5-amino-3,4-dimethylisoxazole

Summary Complexes of cobalt(II) and copper(II) with 5-amino-3,4-dimethylisoxazole (5-ADI) have been prepared and studied by means of magnetic susceptibility measurements, near and far i.r. spectra, electronic spectroscopy and, when possible, conductivity measurements. The 5-ADI generally behaves as bridging (N_ring-, O- or N_ring-, -NH₂) ligand. All the complexes have an octahedral sterochemistry, except Co(5-ADI)₂X₂ (X = Cl, Br), Co₂(5-ADI)₇I₄ which are tetrahedral and Cu(5-ADI)₂ (ClO₄)₂ · 4 H₂O which is square planar.     

Symmetries and asymmetries in classical and relativistic electrodynamics

By a comparison between Maxwell's electrodynamics classically interpreted (MT) and relativistic electrodynamics (RED), this paper discusses whether the asymmetries in MT mentioned by A. Einstein in his 1905 relativity paper are only of a conceptual nature or rather involve specific empirical claims. It is shown that in fact MT predicts strongly asymmetric behaviour for very simple interactions, and an analysis is made of the extent of the symmetry achieved by means of relativistic postulates. A low velocity experiment is suggested which could provide another test of the accuracy of RED with respect to MT.     

X-ray spectroscopic characterization of Cu2+-phenanthroline complexes intercalated in α-zirconium phosphate

X-ray photoelectron spectroscopy provides evidence that when [Cu(phen)₂]²⁺(phen = 1,10-phenanthroline) is diffused between the layers of -zirconium phosphate, the complex species does not remain intact after intercalation, but some Cu-N bonds are broken, replaced with Cu-O bonds and the released nitrogen atoms can now interact with the PO₃-OH groups of the host. XPS also provides evidence for coordination of the Cu²⁺ ions when they are diffused by ion exchange in the phenanthroline--zirconium phosphate intercalation compound. Although Cu²⁺ and phen are in a 1 : 1 molar ratio in the interlayer region of the host, so that a 1 : 1 coordination could be expected between the two species, the characteristic peaks of the uncoordinated phenanthroline, even though at a low intensity, are still present. The differences between the two Cu(II)-intercalation compounds are discussed.