A finite-element-based coarse-grained model for global protein vibration

Meccanica - Protein mechanical vibrations play a pivotal role in biological activity. In particular, low-frequency (terahertz) modes are related to protein conformational changes, which represent...     

σ−π Contributions in metal-co bond: A theoretical study of RhCO and PdCO

The electronic structure of linear RhC0 and PdCO molecules has been studied by means of effective core potential calculations including configuration interaction. The study of the ⁴Δ and ²Σ⁺ states of RhCO and the ³Σ⁺ and ¹Σ⁺ states of PdCO has shown that their low-spin states are bound and their high-spin states are repulsive. The binding energies of RhCO and PdCO are 4.0 and 7.2 kcal/mol, for the equilibrium bond lengths of 3.87 and 4.03 au, respectively. The interaction between the diffuse 5s metal orbital and the carbon lone pair produces a repulsion in the α-space, as depicted by the negative region along the metal-carbon axis in the electron density difference contour maps. The bonding in low-spin states of RhCO and PdCO is due to the metal-CO π “backdonation”. The present investigation on RhCO and PdCO, preliminary results on ScCO, as well as published results on FeCO, NiCO, CuCO and PtCO allows us to make a general conjecture that a low occupancy of the outer s atomic orbital of the transition metal atom in the complex favours the bonding interaction with the CO moiety. The analogy with properties of LiCO and NaCO systems is pointed out.     

The lift computation for an oscillating flat plate in incompressible potential flow

The initial aim of this work was the estimation of the lift acting on a flat plate performing small oscillations in a plane uniform stream by means of a simplified model based on one or at the most two lumped vortices, and the assessment of its results by comparison to those that were exact. The model was found to work well up to a reduced frequency of about 1 or 2, above which the results diverged from those that were correct. In order to improve the model, its behaviour at very high frequencies was then investigated, discovering: (i) that if the number of lumped vortices is greater than one the possibility to impose all boundary conditions is subject to certain geometrical constraints; (ii) that the asymptotical behaviour is not the right one. A straightforward extension of this conclusion to the exact case of a continuous, vorticity distribution simulating the motion of the plate and to the classical equation describing it leads apparently to an incorrect result. The reason for the discrepancy is found in the singularity displayed by the integral equation which cannot be reproduced by the discrete model. It this therefore concluded that the latter can be trusted at low and middle frequencies but its extension to higher ones is fundamentally uncorrect.

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Sommario Lo scopo iniziale di questo lavoro era il calcolo approssimato della portanza agente su una lamina piana soggetta a piccole oscillazioni in una corrente bidimensionale uniforme per mezzo di un modello semplificato basato su uno o al più due vortici concentrati, e il confronto dei risultati con quelli esatti. Il modello risulta funzionare bene per frequenze ridotte inferiori ad 1 o 2, sopra le quali, tuttavia, i risultati si allontanano da quelli corretti. Per migliorarlo si è allora studiato il suo comportamento alle frequenze molto alte, scoprendo che: (i) la possibilità di imporre tutte le condizioni al contorno quando il numero dei vortici concentrati è superiore a uno è soggetta a certe limitazioni sulla configurazione geometrica; (ii) che il comportamento asindotico non è quello corretto. Un'estensione automatica di questa conclusione al caso esatto in cui il moto della lamina è simulato da una distribuzione continua di vorticità e alla classica equazione che lo descrive sembra condurre ad un risultato errato. La ragione di questa discrepanza viene individuata nella singolarità contenuta nell'equazione integrale, che non può essere riprodotta dal modello discreto. Se ne conclude perciò che esso è utilizzabile alle basse e medie frequenze ma che una sua estensione alle alte è fondamentalmente errata.

     

Assessment of cooperativity in self-assembly

A method has been proposed to assess cooperativity in self-assembly processes. The method is based on a clear distinction between intermolecular and intramolecular processes which are compared with the corresponding reference reactions. It has been applied to two classical cases, namely the self-assembly of helicates and of porphyrin ladders, by using data previously published by the groups of Lehn and Anderson, respectively. Contrarily to the conclusions of the authors, pointing out self-assembly processes driven by positive cooperativity, the method here presented indicates in both cases the absence of cooperative effects. The methods previously used to assess cooperativity, in particular Scatchard plot and/or Hill plot, are criticized as being inappropriate for self-assembly, because they are pertinent to a specific case only, namely the intermolecular binding of a monovalent ligand L to a multivalent receptor M, a case very different from self-assembly which involves both inter- and intramolecular interactions. The present method underscores the fact that positive cooperativity in artificial self-assembling systems is probably much more rare than it was previously thought.     

Solvation of tetraalkylammonium chlorides in acetonitrile-water mixtures: mass spectrometry and molecular dynamics simulations.

The solvation of tetramethylammonium chloride (Me4NCl) and tetra-n-butylammonium chloride (Bu4NCl) in water-acetonitrile mixtures was investigated by mass spectrometry of clusters isolated from the solution. As far as the positive ions are concerned, clusters composed of alkylammonium ions and acetonitrile molecules only were observed, even for mixtures with high water content. In contrast, for the negative ions, clusters composed of chloride with both water and/or acetonitrile molecules were observed. For the smaller system (Me4NCl) we performed quantum chemical calculations and molecular dynamics simulations. It was found that even though water is present in the solvation shell of Me4N+, only acetonitrile has a strong electrostatic interaction with the cation. Water molecules around Me4N+ form hydrogen bonds with other water molecules, and they interact with Me4N+ mainly via dispersive interactions. These results indicate that Me4N+ behaves like a hydrophobic solute. On the other hand, the interaction of Cl- with water and acetonitrile is of comparable strength and, in both cases, the electrostatic interaction dominates. Herein we demonstrate experimentally and theoretically that positive and negative ions give rise to characteristic solvation structures in mixed solvents: even a relatively small organic cation, such as Me4N+, exhibits a hydrophobic-like solvation shell.     

Influence of interchain interactions on the electronic properties of neutral and charged oligodiacetylenes carrying bulk substituents

We discuss the effect of the interchain interactions on the electronic properties of a "dimer", named (CHD(4))(2), built from two molecules of a fully carbazolyl-substituted oligodiacetylene containing four repeating units. Each carbazolyl moiety is connected to its respective backbone through a methylene spacer, and the excitations of the neutral and doubly positively charged dimer are obtained using the CIS (configuration interaction including singles) and CEO (collective electronic oscillator) models. The separation distance between the backbones is fixed to a value that could possibly imply a very weak, if any, interchain interaction between the oligomers. In the charged dimer, where we have not been able to perform CEO calculations, it can be expected from previous results that the CIS method will behave satisfactorily. Contrary to the neutral case and surprisingly enough, the simulated photoinduced absorption (PA) spectra indicate a substituent-induced strong interaction between the oligomers, due to the very large amount of excess charge on the distorted oligomer which is spread over its carbazolyl moieties. Broadening of the lowest energy band due to the latter interaction improves the agreement between the theoretical and the experimental PA spectrum for the corresponding polymer. The through-space charge transfer directly connecting the charged with the neutral molecule could supply an efficient channel for charge transport in substituted polydiacetylenes.     

Cycloaddition reactions of ketoimines. Part II. Synthesis of substituted phenanthridines and cyclopenta[c]quinolines

Substituted 4-benzoyl-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinolines 3 and 6-benzoyl-5,6,6a,7,8,10a-hexahydrophenanthridines 10 are obtained through Lewis acid catalyzed addition of 1-phenyl-2-arylamino-2-methoxyethanones 2 to cyclopentadienes and 1,3-cyclohexadiene respectively. Compounds 3 can be converted to the aromatized analogues by reaction with 2,3-dichloro-5,6-dicyanobenzoquinone in refluxing benzene. Compounds 10 are oxidized by sulfur either in decalin or in quinoline to substituted 6-benzoylphenanthridines.     

Reactions of the unsaturated anion [Re3H4(CO)10]− with car☐ylic acids and x-ray characterization of the anions [Re3H3(CO)10(μ-O2CR)]− (R = H,CF3)

The novel anions [Re₃H₃(CO)₁₀(μ-O₂CR)]^? (R = H, CH₃, CF₃), obtained by reaction of [Re₃H₄(CO)₁₀]^? with the corresponding car?ylic acids, have been characterized by IR and NMR spectra and by X-ray analysis of the formate and trifluoroacetate derivatives. They contain a triangle of rhenium atoms, with the car?ylate group diaxially bridging on the shorter ReRe edge.     

Direct spectrophotometric determination of thiocyanate in serum and urine with a continuous-flow analyzer

A spectrophotometric method for the rapid measurement of thiocyanate in serum and urine without separation from interfering substances is described. Thiocyanate reacts immediately with chloramine-T in presence of iron(III) chloride catalyst to give cyanogen chloride, which reacts with a mixture of γ-picoline (4-methylpyridine) and barbituric acid to form a soluble violet—blue product, which is measured at 605 nm. Other components of physiological fluids react more slowly and do not interfere if the reaction time of the chlorinating step is kept very short. The proposed procedure is compared with a highly selective method, based on the oxidation of thiocyanate to cyanide, and good agreement was obtained for both serum and urine. The method is readily adapted to a continuous-flow procedure with a Technicon AutoAnalyzer.     

60]Fullerene as a substituent

The substituent effect of the dihydro[60]fullerenyl group and its hydrophobic parameters have been evaluated quantitatively. The substituent constant has been determined from the pK value of a fullerene-based, para-substituted benzoic acid 1 in 80% dioxane/water (v/v) by NMR spectroscopy. The resulting Hammett sigma value of 0.06, consistent with a small electron-withdrawing effect of C(60), is a consequence of the fact that only inductive effects can be transmitted through the two tetracoordinate carbon atoms between the fullerene pi system and the para-position of the benzoic acid moiety in 1. The parameter pi, which describes the hydrophobic character of the substituent C(60), has been evaluated as the difference between that of 1 and model compound 2. The pi value, which is larger than 3, indicates that the fullerene cage imparts high hydrophobicity to the molecule to which it is attached. Finally, we have evaluated how the fullerene spheroid influences the acid-base properties and nucleophilicity of the pyrrolidine nitrogen in a suitably functionalized fulleropyrrolidine. The fulleropyrrolidine 4 (pK(BD)(+)=5.6) is six orders of magnitude less basic and 1000 times less reactive than its model 3 (pK(BD)(+)=11.6). This may be related to through-space interactions of the nitrogen lone pair and the fullerene pi system.