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.     

Photoinduced processes within compact dyads based on triphenylpyridinium-functionalized bipyridyl complexes of ruthenium(II)

As an alternative to conventional charge-separation functional molecular models based on long-range ET within redox cascades, a "compact approach" has been examined. To this end, spacer elements usually inserted between main redox-active units within polyad systems have been removed, allowing extended rigidity but at the expense of enhanced intercomponent electronic communication. The molecular assemblies investigated here are of the P-(theta (1))-A type, where the theta (1) twist angle is related to the degree of conjugation between the photosensitizer (P, of {Ru(bpy)(3)}(2+) type) and the electron-acceptor (A). 4-N- and 4-N-,4'-N-(2,4,6-triphenylpyridinio)-2,2'-bipyridine ligands (A(1)-bpy and A(2)-bpy, respectively) have been synthesized to give complexes with Ru(II), 1-bpy and 2-bpy, respectively. Combined solid-state analysis (X-ray crystallography), solution studies ((1)H NMR, cyclic voltammetry) and computational structural optimization allowed verifying that theta (1) angle approaches 90 degrees within 1-bpy and 2-bpy in solution. Also, anticipated existence of strong intercomponent electronic coupling has been confirmed by investigating electronic absorption properties and electrochemical behavior of the compounds. The capability of 1-bpy and 2-bpy to undergo PET process was evaluated by carrying out their photophysical study (steady state emission and time-resolved spectroscopy at both 293 and 77 K). The conformational dependence of photoinduced processes within P-(theta (1))-A systems has been established by comparing the photophysical properties of 1-bpy (and 2-bpy) with those of an affiliated species reported in the literature, 1-phen. A complementary theoretical analysis (DFT) of the change of spin density distribution within model [1-bpy(theta (1))](-) mono-reduced species as a function of theta (1) has been undertaken and the possibility of conformationally switching emission properties of P was derived.     

Localized Orbitals vs. Pseudopotential-Plane Waves Basis Sets: Performances and Accuracy for Molecular Magnetic Systems

 Density functional theory, in combination with a) a careful choice of the exchange-correlation part of the total energy and b) localized basis sets for the electronic orbitals, has become the method of choice for calculating the exchange-couplings in magnetic molecular complexes. Orbital expansion on plane waves can be seen as an alternative basis set especially suited to allow optimization of newly synthesized materials of unknown geometries. However, little is known on the predictive power of this scheme to yield quantitative values for exchange coupling constants J as small as a few hundredths of eV (50–300 cm⁻¹). We have used density functional theory and a plane waves basis set to calculate the exchange couplings J of three homodinuclear Cu-based molecular complexes with experimental values ranging from +40 cm⁻¹ to −300 cm⁻¹. The plane waves basis set proves as accurate as the localized basis set, thereby suggesting that this approach can be reliably employed to predict and rationalize the magnetic properties of molecular-based materials. Corresponding author. E-mail: Carlo.Massobrio@ipcms.u-strasbg.fr Received August 5, 2002; accepted August 9, 2002     

Study of donepezil binding to serum albumin by capillary electrophoresis and circular dichroism

The interaction between human serum albumin (HSA) and the acetylcholinesterase inhibitor donepezil, has been studied by means of capillary electrophoresis frontal analysis (CE/FA) and circular dichroism. CE/FA enabled rapid and direct estimation of the quantity of free donepezil present at equilibrium with a physiological level of serum albumin (600 mol L^–1). Application of Scatchard analysis enabled estimation of the binding parameters of HSA towards donepezil, such as association constant and number of binding sites on one protein molecule. Furthermore, due to enantioseparation ability shown by HSA on donepezil in CE mode, displacement experiments were carried out using ketoprofen and warfarin as coadditives to the HSA based running buffer. The addition of these compounds reduced the enantioresolution of donepezil by HSA only when used at high concentration. These data were confirmed and corroborated by circular dichroism (CD) experiments. Using CD, bilirubin was also applied as a ligand specific to site III of HSA. The observed behaviour suggested that donepezil could be considered a ligand with independent binding to sites I and II; although site III is not the highest affinity site, indirect interaction (i.e. cooperative binding) can be assumed.     

Electromagnetic field-induced protection of chick embryos against hypoxia exhibits characteristics of temporal sensing

We previously studied the response of mammalian cultured cells to weak, 60 Hz-electromagnetic (EM) fields. Two time constants, similar to those observed in chemotaxis, were found to govern the cellular response to the field. We concluded that a system of temporal sensing, similar to that employed in chemotaxis by motile bacteria, was operative. We termed the shorter time (approximately 0.1 s) the "sensing" time, and the longer time (approximately 10 s) the "memory" time. To investigate the possibility that temporal sensing was a general property of EM field-cell interaction, the temporal properties of another EM field-induced effect was studied. The EM field-induced protection against the effects of extreme hypoxia was examined in chick embryos. Embryos were exposed to 60 Hz-magnetic fields, the amplitudes of which were regularly altered throughout the 20-min exposure. Alteration was accomplished either by turning the field off and on at regular intervals (1-50 s), or by introducing brief (10 or 100 ms), zero amplitude gaps, once each second, throughout exposure. When the field was turned on and off at 0.1 s intervals, the protective effect conferred by a constant field was lost. At progressively longer on/off intervals, protection was progressively restored, maximizing at intervals of 10-30 s. Gapping the magnetic field for 10 ms, each second of exposure conferred the same protection as that observed for an uninterrupted field, but gapping the field at 100 ms each second produced a significant reduction in protection. These data exhibit remarkable consistency with those obtained in similar temporal studies of the magnetic field-induced enhancement of ornithine decarboxylase activity in L929 fibroblasts. It appears that temporal sensing is a general feature of the EM field-cell interaction.     

Reactivity of the tetrahydroborate copper(I) complexes [(PR3)2Cu(η2-BH4)] (R = Ph,Cy) toward CO2, COS,and SCNPh

CO₂, COS, and SCNPh react under very mild conditions with the copper(I)-tetrahydroborate complexes [(PR₃)₂Cu(η²-BH₄)] (R = Ph, Cy); CO₂ and COS give the complexes [(PR₃)₂Cu(η²-O₂CH)] and [(PR₃)₂Cu(η²-OSCH)] respectively, whereas SCNPh gives the η²-dithiocarbamate complexes [(PR₃)₂Cu-(η²-S₂CNHPh)]. Addition of PPh₃ under CO₂ to solutions of [(PPh₃)₂Cu-(η²-BH₄)] gives [(PPh₃)₃Cu(η¹-O₂CH)] while addition of PPh₃ and NBu₄ClO₄ under CO₂ gives [(PPh₃)₃Cu(η-O₂CH)Cu(PPh₃)₃] ClO₄.     

Aggregation effects on evaporation and the air/water interface of dodecyltrimethylammonium hydroxide solutions

 The system dodecyltrimethylammonium hydroxide (DTAOH)–water was studied by surface tension, ion-selective electrodes and evaporation in an electrobalance. Results confirmed earlier conclusions about a stepwise aggregation mechanism in DTAOH solutions. The aggregation process started at a total concentration C _T=(2.51±0.10)×10^-4 mol dm^-3) which probably corresponds to the formation of dimers. At C _T= (1.300±0.041)×10^-3 mol dm^-3 there was a change in the surface and evaporation behavior, corresponding to the formation of small, fully ionized aggregates which grew with increasing concentration. At C _T= (1.108±0.010)×10^-2 mol dm^-3 the formation of true micelles with hydroxide counterions in the Stern layer did not change significantly the evaporation and adsorption behavior. This means that between this concentration and C _T=(3.02±0.28)× M28.8n10^-2 mol dm^-3, the changes in structure were gradual. At the latter concentration there was a sudden change in the monolayer state at the air/water interface, with a strong surfactant desorption, and a major change in evaporation behavior. The changes are compatible with the formation of few, large aggregates reducing the total concentration of kinetically independent solute units, which in turn increased the activity of the solvent. This phenomenon is in agreement with literature information. The reduction in the evaporation rate of water was mainly due to the reduction of the water activity, caused by colligative effects. The reduction of the effective area available for evaporation had only a slight effect in water evaporation. Received: 9 January 1997 Accepted: 19 October 1997     

Configuration-interaction calculations for the ground state of OF2, NO 2 − , CN−: Canonical orbitals and exclusive orbitals

The C.I. method is applied to already published double- SCF wave functions for OF₂, NO ₂ ^– and CN^–. All doubly excited configurations are considered. The second order approximation values presented for those cases are compared with the exact energy values in some minor cases. An attempt has been made to improve the rate of convergency of the process by transforming the canonical SCF occupied orbitals into localized ones and the virtual canonical orbitals into a particular type of localized orbitals. These latter show also an intuitively acceptable spatial conformation.

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Zusammenfassung Die CI Methode wird auf bereits bekannte Doppel-Zeta-SCF-Wellenfuntionen für die Systeme OF₂, NO ₂ ^– und CN^– angewandt. Dabei werden alle doppelt angeregten Konfigurationen berücksichtigt. Um die Konvergenz zu verbessern, werden versuchsweise die kanonischen und besetzten SCF-Orbitale in lokalisierte Orbitale und die virtuellen kanonischen Orbitale in einen besonderen Typ von lokalisierten Orbitalen transformiert. Die letzteren zeigen eine besonders geeignete räumliche Anpassung.

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Résumé Pour un calcul de intéraction de configurations, comprenant toutes le configurations à double excitation, on a employé des fonctions d'onde SCF sur une base doublée. Pour le calcul complet on a essayé des formules d'approximation, qu'on a pu vérifier avec le calcul exact sur des cas réduits.Pour améliorer la vélocité de convergence du procés on a transformé les orbitales canoniques SCF en orbitales localisées et aprés on a construit, selon un procedé particulier, des orbitales virtuelles localisées qui montrent une conformation dans l'espace qui est intuitivement satisfaisante.

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Work supported by the Consiglio Nazionale delie Ricerche.     

A first theoretical study on the origin of the metal-mediated regioselective opening of 2,3-epoxy alcohols

Hybrid density functional theory (B3LYP) method allows the study of the role of metal ions (Li(+)) in the regioselective opening of 2,3-epoxy alcohols with lithium halides (Cl, Br, I) to the corresponding halohydrins. The theoretical results largely confirm the experimental results, especially with regards to the regioselectivity observed in the opening of the oxirane ring. The C3 halogen attack is always preferred to the C2 attack, with a significant difference in the TS structures with the reaction pathway under kinetic control. The central role of the lithium cation, linked to the oxygen atoms of the epoxy alcohol, is well documented in the reaction mechanisms presented. The energy differences between the two structures of the proposed TS appear to be ascribed to the different contribution of the X-H-O hydrogen bond between the hydroxyl groups of the reactant and the incoming halogen nucleophile.