Raffaella Soave

Physicochemical Properties of Zwitterionic l- and dl-Alanine Crystals from Their Experimental and Theoretical Charge Densities

The total experimental electron density distributions rho(r) of zwitterionic L- and DL-alanine crystals, as derived from extensive sets of X-ray diffracted intensities collected at 23 and 19 K, are compared to gain an insight into the different physical properties of the two related chiral compounds in the solid state and to explore the extent of the rho(r) transferability. Relevant parameters that characterize the two crystal forms are obtained, showing differences and similarities in terms of (i) geometric descriptors, (ii) topological indexes, (iii) molecular electrostatic potential Phi(r) distributions, (iv) atomic volumes and charges, (v) molecular electric moments, and (vi) electrostatic interaction energies. To assess the relative stability of the racemate with respect to the pure enantiomer, the crystal lattice energies, as obtained through DFT fully periodic calculations, are also discussed and compared with the experimental sublimation enthalpies after correction for the proton-transfer energies. In-crystal group charges, evaluated with the quantum theory of atoms in molecules, are found to be transferable between the racemic and the pure enantiomer, at variance with group volumes. Similarly, molecular first and third moments are not strictly transferable and indicate that for the zwitterionic alanine molecule the molecular charge distribution in the DL-crystal is more polarized in the c direction by about 10%. By contrast, quantitative agreement is observed for second and fourth moments. Significant differences arise from (1) the crystal packing of the dipole vectors, which are aligned in an antiparallel fashion in the L-crystal, to be compared with a parallel alignment in the racemate, due the polar space group Pna21 of the latter, (2) the strongly attractive electrostatic energy of a homochiral pair in the L-crystal, which is opposed to the corresponding heterochiral pair in the DL-crystal form. The difference between these Ees values amounts to 135-150 kJ mol(-1). Despite this, the two crystal forms are predicted as equally thermodynamically favored by the theoretical P-B3LYP estimates of the crystal lattice energies. Finally, the necessity of an upgrading of the dispersion and exchange-repulsion terms currently adopted within the experimental charge density approach to intermolecular interactions is recognized and discussed.

New bonding mode of CO on stepped MgO surfaces from density functional cluster model calculations

The bonding properties of CO molecules adsorbed at a stepped MgO surface have been studied by means of cluster models and gradient-corrected DFT calculations. At a step site CO interacts with both a Mg4c and a Mg5c ion forming a relatively strong bond, 0.2 eV, but with very small shift of the C–O stretching frequency, +1 cm−1. The results allow us to assign the feature observed at 2148 cm−1 in the IR spectrum to CO at step sites. The other features of the spectrum at 2200, 2159 and 2152 cm−1 are due to CO adsorbed at corner, edge, and terrace sites, respectively, as found in other studies. The results for the step suggest that for some surface defects the direct relationship between strength of the surface electric field and frequency shift is no longer valid because of inhomogeneities in the field.

Asymmetric modular synthesis of a semirigid dipeptide mimetic by cascade cycloaddition/ring rearrangement and borohydride reduction.

A new semirigid dipeptide mimetic was prepared on multigram scale, in good yield, and in a stereocontrolled way, starting from commercially available and unexpensive reagents, i.e., N-benzylpiperidone, tosyl azide, and proline methyl ester. The optimized multicomponent process consisted of a cascade click cycloaddition and a ring rearrangement reaction, followed by a reductive step. Theoretical calculations were performed to elucidate the reaction mechanism and support the stereochemical outcome of the reduction. Finally, the new scaffold was used for the preparation of model peptidomimetics, whose β turn conformation was confirmed by dynamic NMR experiments.

Isothiazoles. Part VIII. Thermal rearrangement to α,β-unsaturated nitriles of cycloadducts from 3-diethylamino-4-(4-methoxyphenyl)-5-vinyl-isothiazole 1,1-dioxide with nitrile oxides and münchnones

Abstract 3-Diethylamino-4-(4-methoxyphenyl)-5-vinyl-isothiazole 1,1-dioxide was reacted with nitrile oxides and munchnones affording the cycloadducts in good yields. The cycloaddition reaction occurred at the vinyl group exclusively. The cycloadducts undergo pyrolytic transformation into α,β-unsaturated nitriles through the isoxazole-or pyrrole-isothiazoline 1,1-dioxide intermediates.

On the role of data quality in experimental charge-density studies

High-resolution X-ray diffraction data were collected at T = 19 K from two similar spherical crystals of the fungal metabolite citrinin, C(13)H(14)O(5). The two data sets were of markedly different quality, one data set (MQ, medium quality) comprising a single octant of the reciprocal lattice and including reflections with obviously peculiar intensity profiles while the second (HQ, high quality) comprised a hemisphere of reflections and showed no flawed profiles. Parallel multipolar refinements were carried out for both. While most of the resulting geometric parameters, including bond lengths and angles, were in close agreement (the standard uncertainties were approximately twice as large for the MQ data, reflecting the smaller number of observations), the agreement is noticeably worse for electronic properties such as electron densities and their Laplacians at the bond and ring critical points. These latter features are especially sensitive to the quality of the low-angle (and strong) intensities, which was not high for the MQ data. By contrast, the magnitudes of the molecular dipole moment from the two experiments are the same within 1 standard uncertainty, with an angle of about 13 degrees between the two vectors. It is concluded that only true high-quality data allow a fully significant and quantitative analysis of the details of the experimental electron density rho(exp), while high-resolution medium-quality data, measured at very low temperature and adequately processed, can still be used for a qualitative analysis, or for the derivation of overall electronic properties.

Isothiazoles. Part 13: Synthesis of sulfamic esters, [1,2]thiazete S, S-dioxides, benzo[e][1,2]thiazine S, S-dioxides or triazoles by reaction of isothiazole dioxides with sodium azide

Abstract The reaction of NaN3 with 5-substituted 3-diethylamino-4-(4-methoxyphenyl)-isothiazole 1,1-dioxides is presented affording [2-cyano-1-diethylamino-2-(4-methoxyphenyl)-ethylidene]-sulfamic acid derivatives, 3-diethylamino-1,1-dioxo-4-(4-methoxyphenyl)-1,2-dihydro-[1,2]thiazete-4-carbonitrile, 3-diethylamino-7-methoxy-1,1-dioxo-1,4-dihydro-benzo[e][1,2]thiazine-4-carbonitrile or triazole derivatives. The outcome of the reaction strongly depends on the C-5 substituent and the correct choice of the reaction conditions allows direction of the reaction towards the formation of the sulfamic esters or the [1,2]thiazete carbonitrile or the triazoles in satisfactory yield.

Model peptides containing the 3-sulfanyl-norbornene amino acid, a conformationally constrained cysteine analogue effective inducer of 310-helix secondary structures

The properties of the constrained tetrasubstituted 3-sulfanylnorbornene amino acid (NRB), when inserted in Ala-Aib model peptides, were extensively studied. The conformational behaviour of these models was evaluated by theoretical calculations, spectroscopic analyses and by X-ray crystallography. Taken together, our data confirm that both (R,R,R,S)- and (S,S,S,R)-NRB enantiomers possess a strong helicogenic effect when inserted in short Ala-Aib sequences, suggesting that the rigid norbornane core has a positive effect on the ability to stabilize helical secondary structures. This information will be essential for future applications in the rational design of conformationally stable peptides targeted on protein–protein interaction (PPI) surfaces.

Progress in the Understanding of the Key Pharmacophoric Features of the Antimalarial Drug Dihydroartemisinin: An Experimental and Theoretical Charge Density Study

The accurate, experimental charge density distribution, ρ(r), of the potent antimalarial drug dihydroartemisinin (DHA) has been derived for the first time from single-crystal X-ray diffraction data at T=100(2) K. Gas-phase and solid-state DFT simulations have also been performed to provide a firm basis of comparison with experimental results. The quantum theory of atoms in molecules (QTAIM) has been employed to analyse the ρ(r) scalar field, with the aim of classifying and quantifying the key real-space elements responsible for the known pharmacophoric features of DHA. From the conformational perspective, the bicyclo[3.2.2]nonane system fixes the three-dimensional arrangement of the 1,2,4-trioxane bearing the active O-O redox centre. This is the most nucleophilic function in DHA and acts as an important CH⋅⋅⋅O acceptor. On the contrary, the rest of the molecular backbone is almost neutral, in accordance with the lipophilic character of the compound. Another remarkable feature is the C-O bond length alternation along the O-C-O-C polyether chain, due to correlations between pairs of adjacent C-O bonds. These bonding features have been related with possible reactivity routes of the α- and β-DHA epimers, namely 1) the base-catalysed hemiacetal breakdown and 2) the peroxide reduction. As a general conclusion, the base-driven proton transfer has significant non-local effects on the whole polyether chain, whereas DHA reduction is thermodynamically favourable and invariably leads to a significant weakening (or even breaking) of the O-O bond. The influence of the hemiacetal stereochemistry on the electronic properties of the system has also been considered. Such findings are discussed in the context of the known chemical reactivity of this class of important antimalarial drugs.

The fungal metabolite austdiol

The title compound, (7R,8S)-7,8-dihydroxy-3,7-dimethyl-6-oxo-7,8-dihydro-6H-isochromene-5-carbaldehyde, C(12)H(12)O(5), is a trans-vicinal diol. Of the two fused rings, which lie approximately in the same plane, the pyran ring is almost perfectly planar, while the cyclohexenone ring adopts a slightly distorted half-chair conformation. The crystal packing is dictated by two strong intermolecular O-H.O interactions, one involving hydroxy and keto groups, the other involving two hydroxy groups. Molecules are linked together through twofold axes, forming zigzag ribbons extended along the a axis.

Structure and stability of bis(dimethylamino)squaraine and its hydrates: A study using XRD, IR spectroscopy, and thermodynamic measurements

By using thermal and pressure measurements, it was found that in the bis(dimethylamino)squaraine (SQ)–water system near room temperature and pressure two hydrates exist, one containing two and the other four molecules of water per SQ unit. Their equilibrium vapor pressure is the key to their apparently erratic behavior under laboratory conditions. X-ray diffraction at 293±2 K established that the space group of the dihydrate (SQ2) is the monoclinic P21/c, whereas that of the tetrahydrate (SQ4) is the orthorhombic Pbcn. The squaraine molecules in both hydrate crystals form stacks parallel to the shortest crystallographic axes (b for SQ2 and c for SQ4); the water molecules lie between adjacent stacks, and are involved in a thick interplay of intermolecular hydrogen bonds. Such interactions are weak enough to leave virtually unchanged the geometry of the organic moieties with respect to that of the anhydrous compound. These results are fully compliant with those drawn from the infrared spectra and thermal and pressure measurements.