Conformational landscape of (R,R)-pterocarpans with biological activity in vacuo and in aqueous solution (PCM and/or water clusters)

All possible combinations of stable dihedral values have been considered in vacuo at the B3LYP/6-31G level for 3,9-dihydroxy-4,8-diprenylpterocarpan (erybraedin C), whose hydroxy out-out conformation had been examined earlier together with the conformational preferences of 3,9-dimethoxy-4-prenylpterocarpan (bitucarpin A) at the same level (Phys. Chem. Chem. Phys. 2004, 6, 2849). The structure with O5 trans with respect to H6a (O(t)) is about 2 kcal/mol less stable in vacuo than that with one of the H6 trans to it (H(t)); in aqueous solution its energy gap is nearly conserved. The in-in arrangement of the hydroxyl groups of erybraedin turns out to be preferred in vacuo (even considering zero point and thermal effects), where pseudo H-bonds are formed between hydroxy hydrogens and pi electron distributions of prenyl groups. The continuum solvent effect (water) at the IEF-PCM/B3LYP/6-31G level on the relative stability of the various rotamers is very limited both on bitucarpin and erybraedin. Considering the dihydrated derivatives, significant differences in the solvation energy are found between the distinct hydration sites, increasing in the order: methoxy O, ring O, hydroxy O, and hydroxy H. In hydroxy-water interactions, in fact, water prefers to behave as an H-bond acceptor unless nearby bulky groups prevent its approach. Interestingly enough, a bridging water molecule between the hydroxy H of erybraedin and the prenyl group can be found. The inclusion of BSSE corrections in hydroxy-water interactions decidedly favors out-out hydrated arrangements, followed by out-in and in-out ones. Bulk solvent effects with IEF-PCM about the dihydrated systems almost invert the stability order found in vacuo. When a four-water cluster is considered using QM methods, waters gather in H-bonded pairs around the solute OH groups. MD simulations, carried out on a pterocarpan solute (J. Phys. Chem. B 2005, 109, 16918), supply water adducts consistent with a liquid state that have also been embedded in the continuum solvent.     

2 + 4] and [4 + 2] cycloadditions of o-thioquinones with 1,3-dienes: a computational study

Cycloadditions of o-thioquinones (o-TQs) with 1,3-dienes could proceed via either a [2 + 4] or a [4 + 2] mechanism. Under kinetic control and with acyclic dienes the reaction affords the spiro cycloadducts 5deriving from the [2 + 4] path as the main products. Under thermodynamic control, or with cyclic dienes, the o-TQs behave as heterodienes to give the benzoxathiin derivatives 4, in most cases with complete regioselectivity. In the present computational study, DFT calculations were performed in order to achieve a deep understanding of both [2 + 4] and [4 + 2] paths. The reactions of three o-TQs with six 1,3-dienes were thoroughly investigated at the B3LYP/TZVP//B3LYP6-31G level, and the two reaction mechanisms were then compared, evidencing that [2 + 4] cycloadditions are kinetically favored, strongly asynchronous, or even unconcerted, while [4 + 2] reactions are thermodynamically favored, quite asynchronous, but undoubtedly concerted. Moreover, the observed regioselectivity was rationalized by mean of the FMO theory and by comparison of the activation energies for different pathways.     

Bounds for the Entries of Matrix Functions with Applications to Preconditioning

Let A be a symmetric matrix and let f be a smooth function defined on an interval containing the spectrum of A. Generalizing a well-known result of Demko, Moss and Smith on the decay of the inverse we show that when A is banded, the entries of f(A)are bounded in an exponentially decaying manner away from the main diagonal. Bounds obtained by representing the entries of f(A)in terms of Riemann-Stieltjes integrals and by approximating such integrals by Gaussian quadrature rules are also considered. Applications of these bounds to preconditioning are suggested and illustrated by a few numerical examples.     

A study of the conformation of some 3,3′-bithienyl and biselenienyl derivatives by measurements of twisting powers in nematic liquid crystals and of dipole moments

The conformation of chiral 2,2′-dinitro-3,3′-bithienyl-4,4′-dicarboxylic acid (Ia), its dimethylester (Ib), and analogous selenium derivatives Ic and Id was investigated by means of induced cholesteric mesophases. A parallel investigation on the diester (Ib) and on other model 3,3′-bithienyls was carried out with dipole moment measurements. The conclusions reached with the two independent methods for derivative Ib are in excellent agreement and indicate, if a single conformation is assumed, a preferred cisoid conformation with a dihedral angle somewhat smaller than 90°. Alternatively, if the existence of both cisoid and transoid conformations having supplementary dihedral angles is assumed, the data indicate a higher population for the cisoid form.     

Ab initio explorative survey of the mechanism catalyzed by mandelate racemase

There is chemical and kinetic evidence that the mechanism of action of mandelate racemase occurs via two acid/base catalysts, one to abstract a proton from the -carbon and the second to deliver it back to the opposite face of the chiral center. Since the mechanistic details are not known, a few hypotheses have been put forward. Therefore we examine the viability of both concerted and sequential mechanisms on proton abstraction from the -carbon of mandelate, either without taking into account environmental effects or with the addition to the model system of several functional groups of the residues belonging to the active site, in order to restrain the partners to particular positions without actually imposing arbitrary constraints. The importance of the environment in screening the most highly charged groups in the substrate and in facilitating the -carbon-bound proton abstraction is evident. From the perusal of the geometries of the system along the reaction energy profile, it seems that there is no tendency toward a concerted mechanism: the proton delivery from mandelate to Lys occurs and subsequently the extra proton on protonated histidine is in turn delivered to mandelate.     

Regioselectivity on the palladium-catalyzed intramolecular cyclization of indole derivatives

Indole 2-carboxamide derivatives 4 underwent palladium-catalyzed intramolecular cyclization reactions to afford beta-carbolinones or pyrazino[1,2-a]indoles according to different reaction pathways. The complete regioselectivity of the reactions was obtained in different reaction conditions.     

The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): a QM/FE approach

The intramolecular mechanism we earlier proposed [Alagona, G.; Desmeules, P.; Ghio, C.; Kollman, P. A. J Am Chem Soc 1984, 106, 3623] for the second proton transfer of the reaction catalyzed by triosephosphate isomerase (TIM) is examined ab initio at the HF and MP2/6-31+G** levels in vacuo for two conformers of the enediolate phosphate (ENEP), with the ethereal oxygen of the phosphate group either syn (X), as in the crystal structure, or anti (Y) with respect to the enediolate carbonyl O. The barrier height for the intramolecular proton transfer occurring in enediolate is very sensitive to electron correlation corrections. The MP2 internal energy barrier is much lower than the HF one, while the free energy (FE) barrier is even more favorable, indicating that the enzyme presence is not requested to speed up that step. An investigation of the dynamical aspects of the mechanism, along the pathway from ENEP A (with H on O(1)) to TS and from TS to ENEP B (with H on O(2)), was, however, carried out in the presence of the enzyme field while using a neutral His-95 with its proton on Ndelta. To perform the FE simulations, it was necessary to parametrize in the AMBER force-field the ENEP A, TS and B species, whose partial charges have been determined with the RESP procedure, with the X and Y arrangements of the phosphate head. Actually, the FE/QM approach produced a low barrier and a substantial balance between A and B, especially at the MP2 level. The trajectories, analyzed paying a particular attention to the positions assumed by His-95 and by the other active site residues, put forward somewhat different H-bond patterns around the X or Y enediolate phosphate.     

Reductive metalation of 1,2-diaryl-substituted ethenes: synthetic applications

Reduction of 1,2-diaryl-substituted ethenes with Na metal in dry THF allowed easy access to a variety of 1,2-diaryl-1,2-disodiumethanes. These diorganometallic intermediates were elaborated into the corresponding 1,2-diarylethanes (aqueous work up), or cycloalkylated with 1,3-dichloropropanes. The last reaction led to a highly diastereoselective synthesis of trans-1,2-diaryl-substituted cyclopentanes.     

The measurement of atmospheric pollutants by passive sampling at the Uffizi Gallery,Florence

Diffusive sampling can be adopted to analyse in detail the temporal and spatial trends of pollutants concentration in specific historic buildings or in museums. An application of this method is discussed in this paper and the results of a still ongoing monitoring campaign at the Uffizi Gallery in Florence, in the framework of an EU-founded Project (MIMIC), are presented. Distinct trends in the concentration of NO2, NOx, HONO, HNO3, O3 and SO2 have been observed in eight successive sampling periods from March 2001 to February 2002. Considerations are given on possible implications for the conservation of indoor artworks.     

Crystal and Molecular Structure of Bis(η5-methylcyclopentadienyl)titana(IV)-cyclohexasulfane Ti(η5-C5H4CH3)2S5

The crystal and molecular structure of Ti(n⁵-C₅H₄CH₃)₂S₅has been determined by X-ray diffraction studies. The substance crystallizes in the monoclinic crystal system [a = 6.8642(5), b = 16.507(1), c = 13.074(1) Å, β = 82.407(3)°, space group P2₁/n, Z = 4]. The geometry about the titanium atom is a distorted tetrahedron, with a (centroid)-Ti-(centroid) angle of 131.29° and a S? Ti? S angle of 93.38°. The six-membered ring TiS₅ has a cyclohexane-like chair configuration. The structural results are compared to those for similar type titanium complexes.