Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

A protocol is described for the treatment of molecular polarization in force field calculations. The resulting model is consistent in that both inter- and intramolecular polarization are handled within a single scheme. An analytical formula for removing intramolecular polarization from a set of atomic multipoles for an arbitrary static structure or conformation is given. With the help of the intramolecular polarization, these permanent atomic multipoles can then be applied in modeling alternative conformations of a molecule. Equipped with this simple technique, one can derive transferable electrostatic parameters for peptides and proteins using flexible model compounds such as dipeptides. The proposed procedure is tested for its ability to describe the electrostatic potential around various configurations of the N-methylacetamide dimer. The effect of different intramolecular polarization schemes on the accuracy of a force field model of the electrostatic potential of alanine dipeptide is investigated. A group-based scheme for including direct intramolecular polarization is shown to be most successful in accounting for the conformational dependence of electrostatic potentials.     

MO Study of flavin–protein interactions in flavodoxin catalysis

MINDO /3 calculations have been performed on the Clostridium MP flavodoxin active site (a complex of the redox active coenzyme flavin mononucleotide sandwiched between the side chains of methionine and tryptophan) at various redox levels using coordinates derived from x-ray diffraction studies of the holoenzyme. Frontier orbital indices were calculated and indicate that reduction of the flavin is accompanied by induced polar states in the amino acid side chains. This stabilization of charge by the amino acid side chains could account for the reaction rate enhancement of flavin reduction catalyzed by flavodoxin. Frontier orbitals for free flavin, for the flavodoxin bound flavin without the amino acid side chains, and for the oxidized Desulfovibrio vulgaris flavodoxin active site were computed for comparison.     

Determination of ammonia based on the electro-oxidation of hydroquinone in dimethylformamide or in the room temperature ionic liquid, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide

The results detail a novel methodology for the electrochemical determination of ammonia based on its interaction with hydroquinone in DMF. It has been shown that ammonia reversibly removes protons from the hydroquinone molecules, thus facilitating the oxidative process with the emergence of a new wave at less positive potentials. The analytical utility of the proposed methodology has been examined with a linear range from 10 to 95 ppm and corresponding limit-of-detection of 4.2 ppm achievable. Finally, the response of hydroquinone in the presence of ammonia has been examined in the room temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluormethylsulfonyl)imide, [EMIM][N(Tf)₂]. Analogous voltammetric waveshapes to that observed in DMF were obtained, thereby confirming the viability of the method in either DMF or [EMIM][N(Tf)₂] as solvent.     

A three-component coupling process based on vicarious nucleophilic substitution (VNS(AR))-alkylation reactions: an approach to indoprofen and derivatives.

The intermediate anion derived from the vicarious nucleophilic substitution (VNS) of hydrogen reacts with a series of alkyl halides to generate the corresponding alpha-alkylated conventional VNS product in a one-pot process. This one-pot VNS-alkylation reaction offers a convenient route to a range alpha-substituted nitrobenzyl phosphine oxides, sulfones, and esters via a three-component coupling reaction. Reactions of alpha-chloroethyl phenyl sulfone (14) and ethyl 2-chloropropionate (16) with nitrobenzene followed by subsequent addition of an alkylating agent give a series of sulfones and esters bearing an alpha-aryl quaternary center. The VNS-alkylation protocol has been applied to the synthesis of derivatives of Indoprofen from nitrobenzene using readily available inexpensive starting materials. Indoprofen itself was prepared using the conventional VNS reaction in four steps and 24% overall yield from nitrobenzene.     

Characterization of the calcination process of yttria

A complete characterization of the calcination of precipitates obtained from a continuous operation was carried out in this study. The precipitate was obtained by reacting yttrium nitrate and ammonia solutions in a MSMPR reactor. It precipitated out as yttrium hydroxide nitrate hydrate, which has the general form Y₂(OH)_6-x(NO₃)_x·y H₂O. This compound decomposed in consecutive steps with the last reaction occurring at 525°C.The calcination process was characterized by chemical analysis, X-ray diffraction analysis, DTA and TG. In addition, the physical characteristics of calcined powders, such as specific surface area, particle size distribution, pore volume distribution, X-ray crystallite size and conversion were measured as a function of calcination temperature and time. Finally, the kinetics of the reduction of surface area, the growth of crystallite size and conversion were also examined.     

Proton transfers in hydrogen bonded systems. Electron correlation effects in (H3NHOH2)+

The energetics of proton transfer between the N and O atoms of (H₃NHOH₂)⁺ are calculated via ab initio molecular orbital methods. A single-well potential is obtained at the equilibrium intermolecular separation Inclusion of electron correlation via the POL CI technique produces a less steep potential, reducing the energy barrier to proton transfer at greater NO distances.     

Separation and quantitation of components in FD&C Red No. 3 using capillary electrophoresis

The use of capillary electrophoresis as a technique to separate and quantitate components of FD&C Red No. 3 (erythrosine, color index No. 45430) is described. The fluorescein isomers, 2',4',5'-triiodofluorescein (2,4,5-I3F) and 2',4',7'-triiodofluorescein (2,4,7-I3F), the most abundant by-products formed during the preparation of the dye, were selected for quantitation studies. The separation of other lower halogenated impurities was also demonstrated. Electrophoretic mobility of the compounds was achieved in a 50 mM borate, 25 mM sodium dodecyl sulfate buffer at pH 9.3. The limits of quantitation were found to be 0.15% (w/w) (2,4,5-I3F) and 0.14% (w/w) (2,4,7-I3F) (relative to the mass of FD&C Red No. 3). The method is linear from 0.08 to 20.0% (w/w) for 2,4,5-I3F and between 0.06 and 17.0% (w/w) for 2,4,7-13F. In addition, relative standard deviations of 2.03 and 5.11% were determined from precision studies in the repeat analysis of FD&C Red No. 3 for 2,4,5-I3F and 2,4,7-I3F, respectively. Overall, the CE method produced data in excellent agreement with the reference HPLC method, used considerably less solvent and sample, generated less waste and was found to be considerably more cost efficient.     

Inner-sphere electron-transfer reorganization energies of zinc porphyrins

Inner-sphere electron-transfer reorganization energies of Zn(protoporphyrin IX) and Zn(octaethylporphyrin) are determined from band-shape analyses of the first ionization obtained by gas-phase valence photoelectron spectroscopy. The experimentally determined total inner-sphere reorganization energies for self-exchange (120-140 meV) indicate that structural changes upon oxidation are largely confined to the porphyrin ring, and substituents on the ring or solvent and other environmental factors make smaller contributions. Computational estimates by different models vary over a wide range and are sensitive to numerical precision factors for these low reorganization energies. Of current computational models that are widely available and practical for molecules of this size, functionals that contain a mixture of Hartree-Fock exchange and DFT exchange-correlation appear to be the most applicable.     

Chemistry of constrained dioxocyclam ligands with Co(III): unusual examples of C-H and C-N bond cleavage

The reactions between H(2)dc3 and Co(acac)(3) have been studied in the presence and absence of base. In the presence of base, a complex with an intramolecular Co-C bond, Co(dc3-C-(8))(H(2)O), 1, is formed, presumably through heterolytic C-H bond activation. An X-ray crystallographic study demonstrates the presence of a Co-C bond and shows that the diazacyclooctane (daco) subunit adopts the chair-boat conformation with respect to the metal. The cobalt-carbon bond induces strain in the macrocycle as demonstrated by bond angles significantly deviating from tetrahedral. The (13)C NMR resonance of the carbon atom bound to cobalt (-10.5 ppm) suggests significant ionic character in the cobalt-carbon bond. However, we were unable to cleave this bond in the presence of strong acid. In the absence of base, the reaction of Co(acac)(3) with H(2)dc3 resulted in C-N cleavage of the ligand and the formation of a complex of dioxocyclam, Co(dc)(acac), 2. This complex has subsequently been prepared in high yield by the reaction of Co(acac)(3) with dioxocyclam. An X-ray crystallographic study demonstrates that dioxocyclam adopts the heretofore unreported cis configuration, having folded along a N-Co-N axis that is perpendicular to the Co-acac plane.