Molecular mechanics calculations on some phosphine oxide metal complexes in aqueous and organic solvents

Molecular mechanics calculations were done on tetrahedral phosphine oxide zinc complexes in simulated water, benzene and hexane phases using the DREIDING II force field in the BIOGRAF molecular modeling program. The SUN workstation computer (SUN_ 4c, with SPARK station 1 processor) was used for the calculations. Experimental structural information used in the parameterization was obtained from the September 1989 version of the Cambridge Structural Database. 2 Steric and solvation energies were calculated for complexes of the type ZnCl2 (RlO)2' The calculations were done with and without inclusion of electrostatic interactions. More reliable simulation results were obtained without inclusion of charges. In the simulated gas phase, the steric energies increase regularly with number of carbons in the alkyl group, whereas they go through a maximum when solvent shells are included in the calculation. Simulated distribution ratios vary with chain length and type of chain branching and the complexes are found to be more favourable for extraction by benzene than by hexane, in accord with experimental data. Also, in line with what would be expected for a favorable extraction, calculations without electrostatics predict that the complexes are better solvated by the organic solvents than by water.

Intramolecular carbenoid insertions : the reactions of [alpha]-diazoketones derived from furanyl, thienyl, benzofuranyl and benzothienyl acetic acids with rhodium (II) acetate /

A number of synthetically useful ring systems can be prepared via the intramolecular insertion of a metal-stabilized carbenoid into a heteroaromatic systems. The chemical outcome of these reactions are dependent not only on the nature of the heteroatom but also on the length of the aliphatic tether linking the carbenoid moiety with the aromatic fragment. Our work with furanyl and thienyl systems containing a single methylene tether have allowed for some rather atypical chemistry. For example, treatment of l-diazo-3-(2-thienyl)-2-propanone (6) with catalytic rhodium (II) acetate yields 5,6- dihydro-4^-cyclopenta[Z>]thiophen-5-one (3) while, the isomeric l-diazo-3-(3-thienyl)-2- propanone(15) gives a spiro-disulphide (20). Novel chemistry was also exhibited in the analogous furanyl systems. While treatment of l-diazo-3-(3-furanyl)-2-propanone (52) with Rh2(OAc)4 resulted in the expected 2-(4-Oxo-2-cyclopentenyliden)acetaldehyde (54), isomeric l-diazo-3-(2- furanyl)-2-propanone (8) undergoes vinylogous Wolff rearrangement to give a mixture of 6a-methyl-2,3,3a,6a-tetrahydrofuro[2,i-^>]furan-2-one (44) and 2-(2-methyl-3-furyl)acetic acid (43). Rhodium acetate catalyzed decomposition of l-diazo-3-(3-benzofuranyl)-2- propanone (84) and l-diazo-3-(2-benzofuranyl)-2-propanone (69)also allows for vinylogous Wolff rearrangement, a chemistry unseen in benzofuranyl systems with longer tethers. A number of interesting products were isolated from the trapping of intermediate ketenes. Decomposition of l-diazo-3-(3-benzothienyl)-2-propanone (100) resulted in the formation of 2,3-dihydro-l//-benzo[^]cyclopenta[^thiophen-2-one (102). However, in addition to (102), a dimer was also generated from the decomposition of l-diazo-3-(2- benzothienyl)-2-propanone (109). The insight into the mechanistic underpinnings of the above reactions are provided by molecular modeling at a PM3 level.

A comparative study of protoheme and heme d catalases : role of the heme and the heme pocket in catalysis and ligand binding

Catalase dismutes H20 2 to O2 and H20. In successive twoelectron reactions H20 2 induces both oxidation and reduction at the heme group. In the first step the protoheme prosthetic group of beef liver catalase forms compound I, in which the heme has been oxidized from Fe3+ to Fe4+=0 and a porphyrin radical has been created. Compound II is formed by the oneelectron reduction of comp I. It retains Fe4+=0 but lacks the porphyrin radical and is catalytically inert. Molecular structures are available for Escherichia coli Hydroperoxidase II, Micrococcus Iysodeiktus, Penicillium vitale and beef liver enzymes, which contain different hemes and heme pockets. In the present work, the pockets and substrate access channels of protoheme (beef liver & Micrococcus) and heme d (HPII of E. coli and Penicillium) catalases have been analysed using Quanta™ and CharmMTM molecular modeling packages on the Silicon Graphics Iris Indigo 2 computer. Experimental studies have been carried out with two catalases, HPII (and its mutants) and beef liver. Fluoride and formate' are inhibitors of both enzymes, and their binding is modulated by the heme and by distal residues N201 & H128. Both HPII and beef liver enzymes form compound I with H202 or peracetate. The reduction of beef liver enzyme compound I to II and the decay of compound II are accelerated by fluoride. The decay of compound II is also accelerated by formate, and this reagent acts as a 2-electron donor towards compound I of both enzymes. It is concluded that heme d enzymes (Penicillium and HPII of E. coli) are formed by autocatalytic transformation of protoheme in a modified pocket which contains a characteristic serine residue as well as a partially occluded heme channel. They are less active than protoheme enzymes but also do not form the inactive compound II species. Binding of peroxide as well as fluoride and formate is prevented by mutation of H128 and modulated by mutation of N201.

Stereoselective synthesis of substituted hexahydro-3a,4a-diazacyclopentaphenanthren-4-ones and aminoferrocenes

This thesis explored the development of several methodologies for the stereoselective construction of ligand frameworks and some of their applications. The first segment concerns the application of an enantioselective lithiation at an Sp3_ hybridized position adjacent to nitrogen by means of the widely used and typically highly effective enantioselective lithiation with ( -)-sparteine. This investigation was intended to develop a method to install chirality into a system that would be converted into a family of diaminoylidenes for use as phosphine mimics in transition metal catalysis or as nucleophilic reagents. Molecular modeling of the system revealed some key interactions between the substrate and (-)-sparteine that provided general insight into the diamine's mode of action and should lend some predictive value to its future applications. The second portion focuses on the development of methods to access 1,2- disubstituted aminoferrocenes, an underexplored class of metallocenes possessing planar chirality. Two routes were examined involving a diastereoselective and an enantioselective pathway, where the latter method made use of the first BF3-mediated lithiation-substitution to install planar chirality. Key derivatives such as 1,2- aminophosphines, made readily accessible by the new route, were evaluated as ligands for Pd(II), Pt(II) and Ir(I). These complexes show activity in a number of transformations with both achiral and prochiral substrates. Optimization experiments were conducted to prepare enantiomerically enriched 2-substituted-I-aminoferrocenes by direct asymmetric lithiation of BF3-coordinated tertiary aminoferrocenes. A predictive computational model describing the transition state of this reaction was developed in collaboration with Professor Travis Dudding's group (Department of Chemistry, Brock University). The predicted stereochemistry of the process was confirmed by single-crystal X-ray analysis of a 2-phosphino-l-dimethylaminoferrocene derivative. Enantiomerically pure samples of the aminophosphine ligands derived from this new process have given promising preliminary results in the enantioselective hydrogenation of prochiral alkenes and warrant further stUdy in metal-mediated catalysis.

Molecular mechanics calculations of tin-bis (triphenylphosphine oxide) complexes

The capability of molecular mechanics for modeling the wide distribution of bond angles and bond lengths characteristic of coordination complexes was investigatecl. This was the preliminary step for future modeling of solvent extraction. Several tin-phosphine oxide COrnI)le:){es were selected as the test groUl) for t.he d,esired range of geometry they eX!libi ted as \-vell as the ligands they cOD.tained r Wllich were c\f interest in connection with solvation. A variety of adjustments were made to Allinger's M:M2 force·-field ill order to inl.prove its performance in the treatment of these systems. A set of u,nique force constants was introduced for' those terms representing the metal ligand bond lengths, bond angles, and, torsion angles. These were significantly smaller than trad.itionallY used. with organic compounds. The ~1orse poteIlt.ial energ'Y function was incorporated for the M-X l')ond lE~ngths and the cosine harmonic potential erlerg-y function was invoked for the MOP bond angle. These functions were found to accomodate the wide distribution of observed values better than the traditional harmonic approximations~ Crystal packing influences on the MOP angle were explored thr"ollgh ttle inclusion of the isolated molecule withil1 a shell cc)ntaini11g tl1e nearest neigl1'bors duri.rlg energy rninimization experiments~ This was found to further improve the fit of the MOP angle.

Decoding algorithms using side-effect machines

Bioinformatics applies computers to problems in molecular biology. Previous research has not addressed edit metric decoders. Decoders for quaternary edit metric codes are finding use in bioinformatics problems with applications to DNA. By using side effect machines we hope to be able to provide efficient decoding algorithms for this open problem. Two ideas for decoding algorithms are presented and examined. Both decoders use Side Effect Machines(SEMs) which are generalizations of finite state automata. Single Classifier Machines(SCMs) use a single side effect machine to classify all words within a code. Locking Side Effect Machines(LSEMs) use multiple side effect machines to create a tree structure of subclassification. The goal is to examine these techniques and provide new decoders for existing codes. Presented are ideas for best practices for the creation of these two types of new edit metric decoders.

Modeling Metal Protein Complexes from Experimental Extended X-ray Absorption Fine Structure using Computational Intelligence

Experimental Extended X-ray Absorption Fine Structure (EXAFS) spectra carry information about the chemical structure of metal protein complexes. However, pre- dicting the structure of such complexes from EXAFS spectra is not a simple task. Currently methods such as Monte Carlo optimization or simulated annealing are used in structure refinement of EXAFS. These methods have proven somewhat successful in structure refinement but have not been successful in finding the global minima. Multiple population based algorithms, including a genetic algorithm, a restarting ge- netic algorithm, differential evolution, and particle swarm optimization, are studied for their effectiveness in structure refinement of EXAFS. The oxygen-evolving com- plex in S1 is used as a benchmark for comparing the algorithms. These algorithms were successful in finding new atomic structures that produced improved calculated EXAFS spectra over atomic structures previously found.

Assessing the Reproducibility of Clustering of Molecular Dynamics Conformations on Self-Organizing Maps

The goal of most clustering algorithms is to find the optimal number of clusters (i.e. fewest number of clusters). However, analysis of molecular conformations of biological macromolecules obtained from computer simulations may benefit from a larger array of clusters. The Self-Organizing Map (SOM) clustering method has the advantage of generating large numbers of clusters, but often gives ambiguous results. In this work, SOMs have been shown to be reproducible when the same conformational dataset is independently clustered multiple times (~100), with the help of the Cramérs V-index (C_v). The ability of C_v to determine which SOMs are reproduced is generalizable across different SOM source codes. The conformational ensembles produced from MD (molecular dynamics) and REMD (replica exchange molecular dynamics) simulations of the penta peptide Met-enkephalin (MET) and the 34 amino acid protein human Parathyroid Hormone (hPTH) were used to evaluate SOM reproducibility. The training length for the SOM has a huge impact on the reproducibility. Analysis of MET conformational data definitively determined that toroidal SOMs cluster data better than bordered maps due to the fact that toroidal maps do not have an edge effect. For the source code from MATLAB, it was determined that the learning rate function should be LINEAR with an initial learning rate factor of 0.05 and the SOM should be trained by a sequential algorithm. The trained SOMs can be used as a supervised classification for another dataset. The toroidal 10×10 hexagonal SOMs produced from the MATLAB program for hPTH conformational data produced three sets of reproducible clusters (27%, 15%, and 13% of 100 independent runs) which find similar partitionings to those of smaller 6×6 SOMs. The χ^2 values produced as part of the C_v calculation were used to locate clusters with identical conformational memberships on independently trained SOMs, even those with different dimensions. The χ^2 values could relate the different SOM partitionings to each other.