Aerobic alcohol oxidation catalyzed by a new, oxygen-bridged heterometallic compound [PPh4][Ru(N)Me2(μ2-O)2Pd((−)-sparteine)]

The reaction between the new hydroxy compound [PPh₄][Ru(N)(OH)₂Me₂] and Pd(OSiMe₃)₂((−)-sparteine) produces (Me₃Si)₂O, H₂O and a new heterobimetallic compound [PPh₄][Ru(N)Me₂(μ₂-O)₂Pd((−)-sparteine)] in good yield. The Ru/Pd bimetallic compound catalyzes the oxidation of aryl and allyl alcohols to the corresponding carbonyl compound in air and the rearrangement of allylic alcohols unsaturated aldehydes. It also oxidizes PPh₃ to O-PPh₃ under O₂.     

Monodisperse chloromethyl-functionalized macroporous polymer particles by seeded polymerization in aqueous media

This study presents a method to produce monodisperse chloromethyl-functionalized macroporous poly(styrene-co-divinylbenzene) polymer particles by seeded polymerization in aqueous media. We observed that the molecular structure of polystyrene seed particles, the composition of the secondary monomer mixtures, and the type of solvents were very important factors that determine the morphology and porosity of the final particles. This study proposes that the molecular chemistry of polystyrene seed polymers, increasing molecular weight or crosslinking, is another factor that can control the porosity of the final particles. Also, the selection of a poor solvent was effective in forming the larger surface area. In this study, it was confirmed that the chloromethyl groups introduced on the surface of porous particles were quantified chemically and their effective incorporation had a close relationship with the surface area.     

Markov processes in single molecule fluorescence

This article examines the current status of Markov processes in single molecule fluorescence. For molecular dynamics to be described by a Markov process, the Markov process must include all states involved in the dynamics and the first-passage time (FPT) distributions out of those states must be describable by a simple exponential law. The observation of non-exponential FPT distributions or other evidence of non-Markovian dynamics is common in single molecule studies and offers an opportunity to expand the Markov model to include new dynamics or states that improve understanding of the system.     

P and H NMR studies of the transesterification polymerization of polyphosphonate oligomers

Polymeric phosphonate esters are an interesting class of organophosphorus polymers because both the polymer backbone and phosphorus substituents can be modified. These polymers have been prepared by ring-opening polymerizations of cyclic phosphites, stoichiometric polycondensations of dimethyl phosphonate with diols in conjunction with diazomethane treatment and by transesterification of polyphosphonate oligomers. Our initial attempts to prepare high molecular weight polymeric phosphonate esters by the transesterification methods were unsuccessful. Results indicate that the reactions of dimethyl phosphonate with diols to form polyphosphonate oligomers with only methyl phosphonate end groups are plagued by a serious side reaction that forms phosphonic acid end groups. These end groups do not participate in the transesterification reaction and limit the molecular weights of the polymers that can be obtained. The phosphonic acid end groups can be converted into reactive methyl phosphonate end groups by treatment with diazomethane, however diazomethane is explosive and the polymerization is slow. An alternative route for the production of high molecular weight polymers is the transesterification of the 1,12-bis(methyl phosphonato)dodecane, formed by the reaction of excess dimethyl phosphonate and 1,12-dodecanediol, with a Na₂CO₃ promoter. This allows polymers with molecular weights of up to 4.5×10⁴ to be prepared, and no phosphonic acid end groups are observed in these polymers. Thermal analyses of the poly(1,12-dodecamethylene phosphonate) have shown that this polymer has reasonable thermal stability (onset of thermal decomposition at 273 °C). This polymer also undergoes a cold crystallization process at 15 °C similar to that which has been observed in some polyesters, polyamides and elastomers.     

Solvent-free Mukaiyama aldol reaction of O-silyl dienolates catalyzed by benzoic acid

The vinylogous aldol reaction of O-silyl dienolates deriving from 2,2-dimethyl-[1,3]-dioxin-4-ones proceeds in moderate to excellent yields in the presence of catalytic amounts of PhCOOH under solvent-free conditions. Modest to good yields can be obtained by using silica gel or 3 Å molecular sieves as heterogeneous catalysts.     

Computational study on the ring distortions of 1,4-dicyanobenzene in the gas phase and in the crystal

A molecular mechanics software enhanced to perform empirical energy calculations on crystals (KESSHOU) was further developed to handle intermolecular electrostatic interactions as well. The packing of the molecules of 1,4-dicyanobenzene and 1,4-diisocyanobenzene in the crystal was studied. The role of the van der Waals and the electrostatic interactions in the balance of nonbonded atom-atom interactions is analyzed. The packing forces are dominated by van der Waals forces. The electrostatic interactions have higher stabilizing contribution for the dicyano isomer than for the diisocyano form. The dependence of the results on the size of the crystal, the molecular mechanics force field (MM2 vs MM3), and the dielectric constant are also assessed. Ab initio MP2/6–311G** geometries of the isolated molecules are in accordance with the observed benzene ring distortions determined by electron diffraction.     

MENTHOR,a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural,biologic, physical,or geometric properties

Summary MENTHOR is a database system for the storage and retrieval of three-dimensional coordinate and charge information on molecules as well as of traditional biological and physical properties. Our molecular graphics system retrieves from MENTHOR structural information in individual molecules and receptor map/macromolecular binding site hypotheses. Substructural searches of MENTHOR are used to find starting coordinates for molecular modeling and traditional database searches of MENTHOR identify compounds for which modeling is needed. It also forms the data to be searched with ALLADDIN, our substructure/geometric search program. MENTHOR expedites molecular modeling by organizing previous work and facilitating transmission of information between individuals. Examples from modeling of D-2 receptor agonists are shown.     

Complete-active-space self-consistent-field/Amber parameterization of the Lys296–retinal–Glu113 rhodopsin chromophore-counterion system

A special hybrid quantum mechanics/molecular mechanics forcefield is defined, parameterized and validated for studying the photoisomerization path of the retinal chromophore in the rhodopsin protein. It couples a multireference ab initio Hamiltonian (CASSCF and second-order multireference many-body perturbation theory using a CASSCF reference) to describe the chromophore while the rest of the protein is approximated with the Amber forcefield. The frontier has been carefully parameterized in order to reproduce full quantum mechanics torsional energy profiles, for both the ground state and the first excited state. It is also shown that replacing the chromophore counterion with point charges is a valid approximation. This result is interpreted in terms of a cancellation effect for which a possible explanation is given.     

Molecular modeling of intercalation complexes of antitumor active 9-aminoacridine and a [d,e]-anellated isoquinoline derivative with base paired deoxytetranucleotides

Summary Intercalators are molecules capable of sliding between DNA base pairs without breaking up the hydrogen bonds between the DNA bases. On the basis of molecular mechanics calculations structural, models of B-DNA tetranucleotide intercalation complexes of some cytostatic active 9-aminoacridines and of a [d, e]-anellated isoquinoline derivative are presented. The drug complexes are stabilized by energetically favouredvan der Waals interactions and by selective hydrogen bonds between the side chains of the drugs and the DNA bases. Semiempirical quantum chemistry calculations revealed that the chromophoric system of the intercalators is able to form ,-charge-transfer interactions with the purine bases of the base paired deoxytetranucleotides. The theoretical findings are of interest for a more specific drug design of cytostatically active agents.

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Molecular Modeling von Interkalationskomplexen antitumoraktiver 9-Aminoacridine sowie eines [d, e]-anellierten Isochinolinderivates mit basengepaarten Desoxytetranukleotiden

Zusammenfassung Interkalatoren sind Moleküle, die in der Lage sind, sich zwischen DNA-Basenpaare einzulagern, ohne die Wasserstoffbrücken zwischen den DNA-Basen aufzubrechen. Auf der Basis von molekülmechanischen Rechnungen werden Tetranukleotid-Interkalationskomplexe von verschiedenen zytostatisch aktiven 9-Aminoacridinen und von einem [d, e]-anellierten Isochinolinderivat präsentiert. Die Komplexe werden durch energetisch günstigevan der Waals-Interaktionen sowie durch selektive Wasserstoffbrückenbindungen zwischen den Seitenketten der Wirkstoffe und den DNA-Basen stabilisiert. Semiempirische quantenchemische Rechnungen ergaben, daß der Chromophor der Interkalatoren in der Lage ist, ,-charge-transfer Wechselwirkungen mit den Purinbasen der basengepaarten Desoxytetranukleotide auszubilden. Die theoretischen Ergebnisse sind für ein spezifischeres Wirkstoffdesign zytostatisch aktiver Verbindungen von Interesse.