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.     

Preparation of Protected β2‐ and β3‐Homocysteine, β2‐ and β3‐Homohistidine,and β2‐Homoserine for Solid‐Phase Syntheses

The Ser, Cys, and His side chains play decisive roles in the syntheses, structures, and functions of proteins and enzymes. For our structural and biomedical investigations of β‐peptides consisting of amino acids with proteinogenic side chains, we needed to have reliable preparative access to the title compounds. The two β³‐homoamino acid derivatives were obtained by Arndt–Eistert methodology from Boc‐His(Ts)‐OH and Fmoc‐Cys(PMB)‐OH (Schemes 2–4), with the side‐chain functional groups' reactivities requiring special precautions. The β²‐homoamino acids were prepared with the help of the chiral oxazolidinone auxiliary DIOZ by diastereoselective aldol additions of suitable Ti‐enolates to formaldehyde (generated in situ from trioxane) and subsequent functional‐group manipulations. These include OH→O^tBu etherification (for β²hSer; Schemes 5 and 6), OH→STrt replacement (for β²hCys; Scheme 7), and CH₂OH→CH₂N₃→CH₂NH₂ transformations (for β²hHis; Schemes 9–11). Including protection/deprotection/re‐protection reactions, it takes up to ten steps to obtain the enantiomerically pure target compounds from commercial precursors. Unsuccessful approaches, pitfalls, and optimization procedures are also discussed. The final products and the intermediate compounds are fully characterized by retention times (t_R), melting points, optical rotations, HPLC on chiral columns, IR, ¹H‐ and ¹³C‐NMR spectroscopy, mass spectrometry, elemental analyses, and (in some cases) by X‐ray crystal‐structure analysis.     

Standard pH values for potassium hydrogenphthalate reference buffer solutions in 10, 30 and 50% (w/w) 1,4-dioxane/water mixed solvents at temperatures from 288.15 to 318.15 K

Standard pH(S) values for 0.05 mol kg^?1 potassium hydrogenphthalate (KHpH) reference buffer solutions in 10, 30 and 50% (w/w) 1,4-dioxane/water solvent mixtures within the temperature range 288.15–318.15 K are determined from e.m.f. measurements of the cell without transference Pt|H₂|KHPh + KCl|AgCl|Ag|Pt. The consistency of the results is analysed by a recently described method of multilinear regression of the quantity p(a_Hγ_Cl) as a function of both solution composition and temperature. The standard pH(S) determined can be reproduced to within ±0.01 by the equation pH(S) - 4.004 + 3.309w + 0.408z + 1.037w³ - 14.95zw² + 27.1zw³, where w is the weight fraction of dioxane in the solvent mixture,z = (T –θ)/θ, and θ - 298.15 K. Values of the first ionization constant of phthalic acid (H₂Ph; benzene-1,2-dicarboxylic acid) in the above solvent mixtures are also determined from e.m.f. measurements of the cell without transference Pt|H₂|H₂Ph + KHPh + KCl|AgCl|Ag|Pt.     

Nanoscale organization of a phthalocyanine-fullerene system: remarkable stabilization of charges in photoactive 1-D nanotubules

Induction of self-organization between zinc phthalocyanine (ZnPc) and C60 moieties in a novel amphiphilic ZnPc-C60 salt results in uniformly nanostructured 1-D nanotubules. Their photoreactivity, in terms of ultrafast charge separation (i.e., approximately 1012 s-1) and ultraslow charge recombination (i.e., approximately 103 s-1), is remarkable. In addition, the observed ZnPc*+-C60*- lifetime of 1.4 ms implies, relative to that of the monomeric ZnPc-C60 ( approximately 3 ns), an impressive stabilization of 6 orders of magnitude.     

Reaction of singlet oxygen with some benzylic sulfides

Product distribution, total quenching rate (k_T), and rate of chemical reaction (k_r) with singlet oxygen have been determined for some alkyl, benzyl, α-methylbenzyl, and cumyl sulfides. Their contributions depend on the steric hindering around the sulfur atom. In protic solvents, the sulfoxide is the main product via a hydrogen-bonded persulfoxide. In apolar solvents, intramolecular α-H abstraction leads to oxidative C-S bond cleavage, with varying efficiency. The behavior of sulfides is compared to that of alkenes and amines.     

Optical Nanocomposite Planar Waveguides Doped with Rare-Earth and Noble Metal Elements

The present paper is focused on multilayer Er³⁺-doped silica-titania planar waveguides, co-doped with silver, which were prepared by spin-coating on silica glass, or buffered single crystal silicon substrates. The single layer thickness (0.4 m) and refractive index (1.60–1.63) were measured by spectroscopic ellipsometry at 715 nm. The thickness of the waveguides (measured by mechanical profilometry) was 1 m and their optical propagation losses were measured at different laser wavelengths (488 nm, 514 nm and 633 nm), exhibiting an approximately Rayleigh-like behavior. The thermal precipitation of silver nanocrystallites was achieved, both in air and under a controlled atmosphere (dry nitrogen) and these were characterized by visible absorption spectroscopy, which clearly showed the development of a plasmon absorption band near 415 nm, by X-ray diffraction (XRD) and Transmission Electron Microscopy (TEM). The Er³⁺ metastable level lifetimes for the emission at ca. 1.54 m were found to be ca. 4–6 ms, for Er³⁺ concentrations varying between 0.2–2.0 mol% (or (0.4–4.4) × 10²⁰ ions/cm³), but no significant variation was observed with the Ag concentration added (up to 2.5 mol%).     

Collection and analytical characterisation of the atmospheric particulate in the city of Bari

In this paper an application of new procedures for atmospheric particulate analysis is illustrated. PM10, PAHs (benzo[a]anthracene (BaA), benzo[b]fluoranthene (BbF), benzo[j]fluoranthene (BjF), benzo[k]fluoranthene (BkF), benzo[a]pyrene (BaP), indeno[1, 2, 3-cd]pyrene (Ip), dibenzo[a, h]anthracene (DbA)) and heavy metals (Cu, Ni, Zn, Co, Mn, Cd, Fe and Pb) were investigated. PM10 determination was performed by gravimetric method, PAHs were measured by GC-MS, and heavy metals by HPIC. An air quality monitoring campaign on the territory of Bari municipality has been organised, and its results are shown.     

(±)‐6‐tert‐Butyl‐8‐hydroxymethyl‐2‐­phenyl‐4H‐1,3‐benzodioxin and 2,2,2′,2′,6,6′‐hexamethyl‐8,8′‐methylenebis(4H‐1,3‐benzodioxin)

Two compounds containing 1,3‐benzodioxin groups are reported, namely (±)‐6‐tert‐butyl‐8‐hydroxy­methyl‐2‐phenyl‐4H‐1,3‐benzodioxin, C₁₉H₂₂O₃, (I), and 2,2,2′,2′,6,6′‐hexamethyl‐8,8′‐methyl­enebis(4H‐1,3‐benzodioxin), C₂₃H₂₈O₄, (II).The hydroxy groups of neighbouring mol­ecules in (I) are hydrogen bonded to each other, giving rise to double‐row chains. The mol­ecule in (II) adopts a `butterfly' conformation, with the O atoms in distal positions. In both compounds, the dioxin rings are in distorted half‐chair conformations.     

Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.     

Dual-flame photometric detector (DFPD) for the simultaneous G. C. determination of P-, S-, Cl-containing organic compounds

Summary The construction and set-up of a dual-flame photometric detector (DFPD) which, through three channel operation, allows the simulatneous selective determination of P-, S-, Cl-containing compounds eluted from a G. C. column is described. For P- and S-containing compounds the molecular emission bands HPO and S₂ at 526 and 394 nm respectively are measured; for Cl-containing compounds, after reaction with In, the InCl band at 360 nm is recorded. Detectability, specificity, linearity as well as mutual interferences are discussed and compared with those of classical GC-detectors as thermionic (TID) and electron capture (ECD). Some practical applications concerning the pesticide residue analysis in animal and vegetable extracts are shown.

---

Zwei-Flammen-Photometer-Detektor (DFPD) für die gleichzeitige G. C. Bestimmung von P-, S-und Cl-enthaltenden organischen Verbindungen

Zusammenfassung Der Aufbau und die Justierung eines Zwei-Flammen-Photometer-Detektors, welcher durch 3-Kanal Arbeitsweise eine gleichzeitige selektive Bestimmung von P-, S- und Cl-enthaltenden Verbindungen erlaubt, wird beschrieben. Für P- und S-enthaltende Moleküle werden die Molekül-Linien HPO und S₂ bei 526 bzw. 394 nm gemessen; bei Cl-enthaltenden Verbindungen wird, nach Reaktion mit In, die InCl-Linie bei 360 nm registriert. Nachweisgrenze, Spezifität, Linearität sowie Quereinflüsse wechselseitiger Interferenzen werden diskutiert und mit den entsprechenden Werten klassischer GC-Detektoren wie TID und ECD verglichen. Einige praktische Anwendungen bei der Pestizid-Rückstand-Analyse in Extrakten von Tieren und Pflanzen werden gezeigt.

---

Détecteur photométrique à double flamme (DPDF) pour la détermination simultantée des composés organiques contenant du P, S, Cl en CG

Résumé On décrit la construction et la mise au point d'undétecteur photométrique à double flamme («DFPD»=DPDF); celui-ci permet grâce à système à «3 canaux» de déterminersimultanément et sélectivement les substances organiques contenant du P, du S, du Cl, à la sortie des colonnes de chromatographie en phase gazeuse. Pour les substances contenant du P et du S, on mesure l'émission moléculaire correspondant aux bandes dûes à HPO et S₂ (526 et 394 nm. respectivement); pour les composés chlorés, on mesure l'émission correspondant à la bande due à InCl (360 nm.) après réaction avec l'Indium des gaz brulés. Les problèmes relatifs à la limite de détection, à la specificité et à la linéarité de la réponse en fonction de la quantité de substance injectée, ainsi qu'aux interactions entre substances détectées, sont discutés et les rultats obtenus sont compar avec ceux fournis par les détecteurs classiques: thermo-ionique («TID»=DTI) ou à capture d'électrons («ECD»=DCE). Quelques applications pratiques dans le domaine de l'analyse des résidus de pesticides dans des extraits d'origine animale ou végétale sont données comme exemples.