YETI: An interactive molecular mechanics program for small-molecule protein complexes

YETI, an interactive molecular mechanics program for drug-design applications on small-molecule protein complexes, is described. To model short-range interactions in better agreement with experimental data, its force-field energy expression includes directional potential functions for H-bonds, salt linkages, and metal ligand interactions. The program works on an internal coordinate concept and uses a conjugate-gradient minimizer. YETI is available for distribution through the author. The program has been used to model details of small-molecule binding to the enzyme human carbonic anhydrase I. The impact of the directional potential functions on the geometry of H-bonds and metal-ligand interactions is discussed.     

N,O-heterocyclics. 13. Isoxazolidinium salts as synthons to N,N, O-trisubstituted hydroxylamines

Substituted isoxazolidinium salts react with lithium aluminium hydride to yield open-ring products which have hydroxylamine structures. The bimolecular reaction-mechanism has been investigated by substituent effect and the structure of the products ascertained by spectroscopic methods with the aid of the MIKE technique. The overall process of the ring-opening substitution is controlled by the polarisation of the C? N bond with steric and conformational factors acting mainly at the C-5 position of the nucleus. The mechanism of isoxazolidinium ion reaction defines the use of these synthons towards the synthesis of N,N,O-trisubstituted hydroxylamines and substituted 1,3-amino-alcohols.     

Copper bronze catalyzed Heck reaction in ionic liquids

Heck reaction of aryl iodides and activated aryl bromides catalyzed by copper bronze in tetrabutylammonium bromide as solvent and tetrabutylammonium acetate as base was developed. The effective catalysts are Cu nanoparticles deriving from the reaction of iodobenzene with copper bronze. These nanoparticles are very stable in tetraalkylammonium salts, are easily recycled, and can be stored for months without a loss of catalytic efficiency. [reaction: see text]     

CIS 1,2-functionalization of cyclohexane using selenium intermediates

The trans 1,2-phenylseleno acetate, acetamide, alcohol and nitrile of cyclohexane may be oxidized at selenium by halogens and the phenylseleno moiety displaced by halide to give high yields of 1,2 halide-containing products with cis geometry.     

Negative ion chemical ionization mass spectra of (η6-arene)Cr(CO)3

The negative ion chemical ionization mass spectra, with ammonia and methane as reagent gases, of the (η⁶-arene)Cr(CO)₃ complexes, where the arene is C₆H₅COCH₃, C₆H₅COC₂H₅, C₆H₅COC₃H₇, C₆H₅COC(CH₃)₃, 2-CH₃C₆H₄COC₃H₇, C₆H₅COOCH₃, C₆H₅CH₃, 1,3,5-(CH₃)₃C₆H₃ and C₆H₅CH₂COC₂H₅, are reported. Similar behaviour is observed with the two reagent gases, but ammonia shows a much higher abundance for the ions produced by reactions of [NH₂]^? with sample molecules. The compounds containing the C₆H₅CO group display an abundant [M]^{? ˙}, whereas the other compounds exhibit [M? H]^? as base peak, produced by ion/molecule reactions. A comparison of the negative ion chemical ionization mass spectra of the (η⁶-arene)Cr(CO)₃ complexes with those of the corresponding ligands shows the strong electron withdrawing power of the Cr(CO)₃ group in the gas phase.     

Designing generalized statistical ensembles for numerical simulations of biopolymers

Conformational properties of polymers, such as average dihedral angles or molecular alpha-helicity, display a rather weak dependence on the detailed arrangement of the elementary constituents (atoms). We propose a computer simulation method to explore the polymer phase space using a variant of the standard multicanonical method, in which the density of states associated to suitably chosen configurational variables is considered in place of the standard energy density of states. This configurational density of states is used in the Metropolis acceptance/rejection test when configurations are generated with the help of a hybrid Monte Carlo algorithm. The resulting configurational probability distribution is then modulated by exponential factors derived from the general principle of the maximal constrained entropy by requiring that certain average configurational quantities take preassigned (possibly temperature dependent) values. Thermal averages of other configurational quantities can be computed by using the probability distributions obtained in this way. Moments of the energy distribution require an extra canonical sampling of the system phase space at the desired temperature, in order to locally thermalize the configurational degrees of freedom. As an application of these ideas we present the study of the structural properties of two simple models: a bead-and-spring model of polyethylene with independent hindered torsions and an all-atom model of alanine and glycine oligomers with 12 amino acids in vacuum.     

On the growth and shape of sodium taurodeoxycholate micellar aggregates: a spin-label and quasielastic light scattering investigation

Electron spin resonance (ESR) and quasielastic laser scattering (QELS) measurements have been carried out on sodium taurodeoxycholate (NaTDC) micellar aqueous solutions. Computer simulation of the ESR line shape has been used to quantitatively analyze the rotational dynamics of the cholestan-spin label (CSL) dissolved by the NaTDC micellar aggregates as a function of temperature and NaCl concentration. The local reorientation of CSL has been accounted for motionally-averaged g- and A-tensors assuming fast oscillation around the spin-probe long molecular axis. The overall Brownian tumbling of CSL-micelle complexes has been modeled by an axially symmetric rotational tensor. Good agreement with experimental spectra is obtained. Best-fit rotational parameters and QELS data suggest that, in the circumstance of large aggregation, NaTDC micelles have cylindrical shape and micellar growth occurs along the cylinder axis.     

Molecular-level control of the photoluminescence from PPV nanostructured films

The fabrication of varied molecular architectures in layer-by-layer (LbL) films is exploited to control the photoluminescence (PL) of poly(p-phenylene vinylene) (PPV) in an unprecedented way. This was achieved by controlling the F?rster energy transfer between PPV layers (donors) and layers of a commercial azodye, Brilliant Yellow (BY) (acceptors). Energy transfer was controlled by inserting spacer layers of inert polymers between PPV and BY layers and by photoaligning the BY molecules via trans-cis-trans isomerization. The PPV/BY LbL films displayed polarized PL whose intensity could be varied almost continuously by changing the time of photoalignment, which was carried out by impinging a linearly polarized laser light simultaneously to the PL experiments. For PPV/BY films with no spacer layers, PL was completely quenched, but its intensity increased with the number of spacing layers. Further increase in PL was obtained by photoaligning the BY molecules perpendicularly to the PPV molecules. This minimizes energy transfer, since F?rster processes are directional, dipole-dependent resonant transfers. Energy transfer is also controlled by imparting a preferential orientation of the PPV chains on PPV/BY LbL films deposited onto flexible Teflon substrates that may be stretched.