Showing papers in "Journal of the American Chemical Society in 1984"

A new force field for molecular mechanical simulation of nucleic acids and proteins

Abstract: We present the development of a force field for simulation of nucleic acids and proteins. Our approach began by obtaining equilibrium bond lengths and angles from microwave, neutron diffraction, and prior molecular mechanical calculations, torsional constants from microwave, NMR, and molecular mechanical studies, nonbonded parameters from crystal packing calculations, and atomic charges from the fit of a partial charge model to electrostatic potentials calculated by ab initio quantum mechanical theory. The parameters were then refined with molecular mechanical studies on the structures and energies of model compounds. For nucleic acids, we focused on methyl ethyl ether, tetrahydrofuran, deoxyadenosine, dimethyl phosphate, 9-methylguanine-l-methylcytosine hydrogen-bonded complex, 9-methyladenine-l-methylthymine hydrogen-bonded complex, and 1,3-dimethyluracil base-stacked dimer. Bond, angle, torsional, nonbonded, and hydrogen-bond parameters were varied to optimize the agreement between calculated and experimental values for sugar pucker energies and structures, vibrational frequencies of dimethyl phosphate and tetrahydrofuran, and energies for base pairing and base stacking. For proteins, we focused on 4>,'lt maps of glycyl and alanyl dipeptides, hydrogen-bonding interactions involving the various protein polar groups, and energy refinement calculations on insulin. Unlike the models for hydrogen bonding involving nitrogen and oxygen electron donors, an adequate description of sulfur hydrogen bonding required explicit inclusion of lone pairs. There are two fundamental problems in simulating the struc­ tural and energetic properties of molecules: the first is how to choose an analytical been placed E(R) which correctly describes the energy of the system in terms of its 3N degrees of freedom. The second is how the simulation can search or span conforma­ tional space (R) in order to answer questions posed by the scientist interested in the properties of the system. For complex systems, solution to the first problem are an es­ sential first step in attacking the second problem, and thus, considerable effort has been placed in developing analytical functions that are simple enough to allow one to simulate the properties of complex molecules yet accurate enough to obtain meaningful estimates for structures and energies. In the case of the structures and thermodynamic stabilities of saturated hydrocarbons in inert solvents or the gas phase, the first problem has been essentially solved by molecular mechanics ap­ proaches of Allinger, I Ermer and Lifson,2 and their co-workers. However, for polar and ionic molecules in condensed phases, unsolved questions remain as to the best form of the analytical function E(R). In the area of proteins and peptides, seminal work has come from the Scheraga 3 and Lifson 4 schools. The Scheraga group has used both crystal packing (intermolecular) and con­ formational properties of peptides to arrive at force fields ECEPP, UNECEPP, and EPEN for modeling structural and thermodynamic properties of peptides and proteins. Levitt, using the energy refinement software developed in the Lifson group, has proposed a force field for proteins based on calculations on lysozyme,S and Gelin and Karplus have adapted this software along with many parameters from the Scheraga studies to do molecular dynamics

Optimized intermolecular potential functions for liquid hydrocarbons

Abstract: Optimized intermolecular potential functions have been determined for hydrocarbons through Monte Carlo simulations of 15 liquids: methane, ethane, propane, n-butane, isobutane, n-pentane, isopentane, neopentane, cyclopentane, n-hexane, 1-butene, cis- and trans-2-butene, isobutene, and benzene. To achieve high accuracy, 12 unique group types were identified and their associated Lennard-Jones parameters were established. The average deviation from experiment for the computed densities and heats of vaporization is 2% and trends for isomeric series are reproduced. Conformation results were also obtained for five liquids and revealed no condensed-phase effects on the conformer populations. Structural analyses focus on trends as a function of chain length and branching of the monomers.

Silicoaluminophosphate molecular sieves: another new class of microporous crystalline inorganic solids

Abstract: Donnees sur une nouvelle classe de tamis moleculaires, qui peuvent etre utilises comme catalyseurs, supports de catalyseurs, adsorbants ou echangeurs d'ions et qui correspondent a une formule generale 0-0,3R•(Si x Al y P z )O 2 avec R=reste d'ammonium quaternaire ou une amine organique

Mechanisms of stereochemical control in propylene polymerizations with soluble Group 4B metallocene/methylalumoxane catalysts

Abstract: Obtention de polypropene isotactique avec des catalyseurs de Ziegler-Natta solubles, determination de la microstructure stereochimique et information concernant le mecanisme de reaction

Photophysical effects of metal-carbon .sigma. bonds in ortho-metalated complexes of iridium(III) and rhodium(III)

Abstract: Dichloro-bridged dimers of the type (M(L)/sub 2/Cl)/sub 2/, where L is 2-phenylpyridine (ppy) or benzo(h)quinoline (bzq) and M is Rh(III) or Ir(III), have been characterized by /sup 13/C and /sup 1/H NMR spectroscopies and by absorption and emission spectroscopies. The NMR results confirm previous formulations of the complexes as dichloro-bridged ortho-metalated dimers in halocarbon solvents but indicate that they are cleaved to monomeric species of the type M(L)/sub 2/CIS in ligating solvents such as dimethylformamide (S = solvent). The absorption spectra of each of the complexes contain several low-energy bands which are assigned as metal-to-ligand charge-transfer (MLCT) transitions. All four of the dimers emit light following photoexcitation of their glassy solutions at 77 K. Their emission spectra and lifetimes lead to assignments of their emitting states as intraligand for the Rh(III) dimers and MLCT for the Ir(III) dimers. The Ir(III) dimers are also found to emit light following excitation at 295 K in deaerated dichloromethane. No emission is seen from the Rh(III) dimers under these conditions. Comparison of these results with previous results from studies of similar Rh(III) and Ir(III) complexes of 2,2'-bipyridine (bpy) and 1,10-phenanthroline (phen) indicates that the ortho-metalated ligands are considerably higher than bpy and phen inmore » the spectrochemical series. In addition to raising the energy of ligand field excited states in their complexes, relative to similar bpy and phen species, they induce lower energy charge-transfer transitions. These effects are consistent with the synergistic function of the ortho-metalated ligands as both strong sigma donors and ..pi.. acceptors.« less

Intramolecular long-distance electron transfer in radical anions. The effects of free energy and solvent on the reaction rates

Abstract: A homologous series of eight compounds of the general structure A-Sp-B where B is 4-biphenylyl, Sp is a rigid saturated hydrocarbon spacer, the steroidal 5..cap alpha..-androstane skeleton, and A is one of a series of 8 different molecular groups with ..pi.. electron networks was synthesized. A liquid solution of these molecules in either 2-methyltetrahydrofuran or isooctane at room temperature was subjected to a 30-ps pulse of solvated electrons. Data are presented that demonstrate in these systems the dependence of the electron transfer rates on the exothermicity of the reaction and on solvent polarity. It is also noted that the electron transfer reactions are free ion reactions.

Dichloro[1,1'-bis(diphenylphosphino)ferrocene]palladium(II): an effective catalyst for cross-coupling of secondary and primary alkyl Grignard and alkylzinc reagents with organic halides

Abstract: Etude d'une trentaine de reactions, avec des complexes de Ni au Pd pour le couplage des bromo-benzene, -styrene, -anisole, -toluene avec le chlorure de butylmagnesium

Characterization of the first examples of isolable molecular hydrogen complexes, M(CO)3(PR3)2(H2) (M = molybdenum or tungsten; R = Cy or isopropyl). Evidence for a side-on bonded dihydrogen ligand

Abstract: Reported were the first examples of isolable transition-metal complexes containing a coordinated dihydrogen molecule, characterized by a variety of spectroscopic and structural methods to possess n/sup 2/-bonded hydrogen. The dihydrogen ligand is symmetrically coordinated in an n/sup 2/ mode with average tungsten-hydrogen distances of 1.95 (23) angstroms (x-ray) and 1.75 angstroms (neutron, ..delta..F). The H-H separation is 0.75 (16) angstrom (x-ray) and 0.84 angstroms (neutron, ..delta..F), slightly larger than that obtained from free H/sub 2/ (0.74 angstroms). The H/sub 2/ ligand axis is approximately parallel to the trans phosphorous-phosphorus direction. Vibrational spectra of solid samples of the H/sub 2/, D/sub 2/, and HD forms (M = W) are consistent with coordination of molecular H/sub 2/. The H/sub 2/ complexes are significant in that they may represent an arrested form of oxidative addition of H/sub 2/ to metals. 1 table (DP)

Oxidation of alcohols to aldehydes with oxygen and cupric ion, mediated by nitrosonium ion

Abstract: Oxydation a temperature ordinaire des alcools allyliques et benzyliques par l'oxygene en utilisant comme catalyseur un melange de chlorure cuivreux et du tetramethyl-2,2,6,6 piperidinoxyle(I), et oxydations plus generales des alcools primaires en presence de chlorure cuivrique et du nitroxyle I

C-H and H-H Activation in Transition Metal Complexes and on Surfaces.

Abstract: : The breaking of the H-H bond in H2 and a C-H bond in CH4 on both discrete transition metal complexes and on Ni and Ti surfaces is studied, and the essential continuity and similarity of the physical and chemical processes in two cases is demonstrated. We begin with an orbital analysis of oxidative addition, delineating four basic interactions: H-H or C-H sigma M electron transfer the reverse M sigma* transfer (both weakening the sigma bond, forming the M-H bond), a repulsive interaction between sigma and metal filled orbitals, and a rearrangement of electron density at the metal. The molecular cases analyzed in detail are d6 ML5, d8 ML4 and CRhoM'L. Coordinative unsaturation is necessary, and consequently sigma M electron transfer dominates the early stages of the reaction. Steric effects are important for CH4 reaction. Activation in angular ML4 or CpM L is achieved through a destabilized yz MO, and d10 ML3, ML2 candidates for activation are described. For our study of the surface we develop tools such as projections of the density of states and crystal orbital overlap populations - the extended structure analogues of a population analysis. These allow a clear understanding of what happens when an H2 or a CH4 molecule approaches a surface. Because of the higher energy of the occupied metal orbitals on the surface the M sigma* interaction leads the reaction. There are great similarities and some differences between the activation acts in a discrete complex and on a surface. (Author)

An efficient asymmetric oxidation of sulfides to sulfoxides

Abstract: Mise au point d'un nouveau reactif: Ti(O-i-C 3 H 7 ) 4 /tartrate de diethyle/eau/t-C 4 H 9 OOH dans les proportions (1:2:1:1). Ce reactif oxyde les sulfures fonctionnalises prochiraux en sulfoxydes optiquement actifs

Chemical derivatization of an array of three gold microelectrodes with polypyrrole: Fabrication of a molecule-based transistor

Abstract: : This document reports the fabrication of a chemically derivatized microelectrode array that can function as a transistor when immersed in an electrolyte solution. The key finding is that a small signal (charge) needed to turn on the device can be amplified. The device to be described MIMICS the fundamental characteristics of solid state transistor, since the resistance between to contacts can be varied by a signal to be amplified. The chemical transistor is the set of three (drain, gate, and source) Au microelectroces covered by polypyrrole.

Bonded and nonbonded charge concentrations and their relation to molecular geometry and reactivity

Abstract: Etude de ces concentrations de charge a l'aide du laplacien de la densite de charge sans utiliser d'orbitales. Exemples de molecules contenant 3 a 6 concentrations locales de charge electronique dans la couche de valence de l'atome central. Relation avec les positions pour l'attaque electro- ou nucleophile

Electronic structure, magnetic properties, ESR, and optical spectra for 2-iron ferredoxin models by LCAO-X.alpha. valence bond theory

Abstract: Calculs sur Fe 2 S 2 (SH) 4 2−,3− , compose modele des sites actifs de ferredoxine: constantes de couplage magnetique de Heisenberg pour les formes oxydee et reduite, spectres d'excitation optique (bande de transfert de charge), tenseurs g et A de RPE, distributions de charge electronique. Discussion du mecanisme de reduction

Polyphosphazene solid electrolytes

Abstract: : The phosphazene polymer (NP(OC2H40C2H4OCH3)n, MEEP, was synthesized and amorphous solvent-free salt complexes were performed with LiSo3CF3, NaSO3CF3, Sr(SO3CF3)2, and AgSO3CF3. A material with the composition (LiSO3CF3)0.25. MEEP has a conductivity of .00008 ohm/cm at 30 C, which is much higher than corresponding poly (ethylene oxide) complexes. The phosphazene electrolytes are promising materials for ambient-temperature high energy density batteries.

Artificial intelligence approach to structure-activity studies. Computer automated structure evaluation of biological activity of organic molecules

Abstract: Application a l'etude du caractere cancerigene des hydrocarbures aromatiques polycycliques, du caractere cancerigene des N-nitrosamines chez les rats et de l'activite pesticide de carbamates de cetoximes

Effect of free energy on rates of electron transfer between molecules

Abstract: Rates of electron-transfer (ET) reactions D/sup -/ + A ..-->.. D + A/sup -/ between aromatic molecules in a rigid organic solid have been measured from 10/sup -7/ to 10/sup 2/s following creation of radical anions by pulse radiolysis. By avoiding the problems of diffusion control and complexing between the donor and acceptor which occur in liquids, these data provide the first opportunity to interpret measurements of electron-transfer rates vs. exothermicity with ET theories. Reactions having free energy changes from -..delta..G/sup 0/ = 0.01 to 2.75 eV were studied. For each reaction, the ET rate constant k(r) is quantitatively measured as a function of distance using the random distribution of distances between D/sup -/, A pairs. The ET rates are very slow for weakly exothermic reactions, are maximized at an intermediate exothermicity lambda, and decrease at high exothermicity. lambda is observed to increase gradually with time, due apparently to solvent relaxation around D/sup -/ ions suddenly formed in the rigid medium. Because this causes the distance dependence of the rates to vary with exothermicity, quantitative comparison of the data with ET theories is possible only if we assume that the distance dependence of electron exchange interactions does not depend onmore » the acceptor. 97 references, 9 figures, 3 tables.« less

Templated synthesis of interlocked macrocyclic ligands: the catenands

Abstract: Synthese d'un catenane comprenant 2 macrocycles imbriques (ce macrocycle etant un hexaoxa [16] paracyclo [0] phenanthrolino-1,10 [0] paracyclophane) a partir de diiodo-1,14 tetraoxa-3,6,9,12tetradecane, de bis-[hydroxy-4 phenyl]-2,9 phenanthroline-1,10 et de Cu(CH 3 CN) 4 + •BF 4 − suivie de demetallation du cuprocatenane obtenu Proprietes du cuprocatenane

Catalysis of the reduction of molecular oxygen to water at Prussian blue modified electrodes

Abstract: On montre que la forme reduite du bleu de Prusse (BP), le blanc de Prusse, presente une activite catalytique pour les reductions d'O 2 et de H 2 O 2 et que la forme oxydee de BP est active pour l'oxydation de H 2 O 2 . Les mesures sont fondees sur l'utilisation de voltammetrie cyclique et d'une electrode tournante a disque et anneau

Photoactivated stereospecific cleavage of double-helical DNA by cobalt(III) complexes

Abstract: Le complexe Co(phen) 3 3+ a faible concentration provoque une scission de l'ADN par irradiation a 254 nm

Chemical derivatization of microelectrode arrays by oxidation of pyrrole and n-methylpyrrole: fabrication of molecule-based electronic devices.

Abstract: : An array of eight Au microelectrodes, each approximately 0.12 microns thick, 3 microns wide, and 140 microns long separated from each other by a distance of 1.4 micron has been fabricated on a 0.45 micron thick Si02 layer grown on a single crystal Si substrate using standard microfabrication techniques. Each electrode can be individually addressed and characterized electrochemically. The individual electrodes can b functionalized with polypyrrole or with poly-N-methylpyrrole by oxidation of pyrrole or N-methylpyrrole, respectively, using conditions similar to those for macroscopic electrodes. The amount of polymer deposited can be controlled and it is possible to electrically connect adjacent microelectrodes with deposited polymer. Since the reduced forms of these polymers are insulating and the oxidized forms are electronically conducting it is possible to prepare electronic devices that are analogous to diodes and transistors using adjacent microelectrodes connected with polymer.

Stereoisomerism and local chirality

Abstract: Etude des concepts classiques et presentation de concepts nouveaux concernant la stereochimie et la chiralite locale